# DNA Replication Termination: From Terminal Fork Geometry to Complete and Separable DNA Products

## Abstract

DNA replication must end without leaving unreplicated DNA, an active replisome on the product, or physical links that prevent daughter molecules from separating. These requirements create a distinct mechanical problem at the end of replication: the remaining parental duplex shrinks while torsional stress must be redistributed, replisomes enter one another's path, the final leading- and lagging-strand junctions must be converted into continuous DNA, and fork rotation can transfer intertwining into the replicated products. The solution is not one universal reaction. Programmed fork traps position terminal encounters in some bacterial chromosomes and episomes, origin firing and fork velocity generate broad encounter zones in many eukaryotic chromosomes, and rolling-circle or end-replicating systems terminate by strand transfer or processing of a physical DNA end. Nevertheless, these architectures can be compared as transformations of a terminal DNA substrate. Forks first reach a geometry that permits or requires remodeling; residual DNA synthesis and end processing then complete the nascent strands; in characterized yeast and metazoan systems, separate structural, biochemical, and extract studies support a model in which loss of fork DNA permits CMG ubiquitylation followed by Cdc48- or p97-dependent extraction; and topoisomerases or site-specific recombination remove direct links between products. Circular-template experiments directly expose covalent and topological product states; locus-resolved chromosomal assays can reveal incomplete or delayed synthesis. Failure therefore produces different pathologies depending on the interrupted transition, including renewed replication after bacterial fork fusion, persistent terminal gaps or replisomes, catenated products, and under-replicated DNA carried into mitosis. The central unresolved questions are the native structure of an unperturbed bacterial fork fusion, how final torsional stress is partitioned between the parental interval and daughter precatenanes, the minimal DNA change that licenses CMG removal, and the order of nascent-strand closure, replisome extraction, and product unlinking after the last parental interval disappears.

## 1. Termination converts two moving forks into finished DNA products

The last interval of a replicon cannot be completed by treating elongation as though it simply continues to zero. During theta replication in vitro, torsional stress can appear as positive supercoils ahead of the fork or right-handed precatenanes behind it [1]. In Tus-arrested plasmids, the unreplicated region is supercoiled and the replicated region contains precatenanes [2, 3]. Precatenanes also form before termination in stalled bacterial plasmids [4], while fork rotation and precatenation are favored at termination regions and protein-DNA barriers in budding yeast [5]. In *Xenopus* egg extracts, topoisomerase II prevents topological stress from stalling converging forks [6] and, in separate plasmid assays, removes precatenanes behind replication forks [7]. The terminal topological problem can therefore occupy both the shrinking parental interval and the replicated products.

Chemical and physical completion are likewise separable. In SV40, most mapped forks arrest when replication is about 91% complete [8], and a late intermediate of about 91% completion accumulates in vivo and in vitro [9]. Termination-region gaps then persist in both nascent strands [10] and, depending on the preparation, in separated circular daughters [11] or nicked and gapped catenated dimers [12]. ColE1 products can be completely replicated yet remain open at the termination point [13]; polymerase III can copy a primed single-stranded circle to an interrupted duplex [14]; and unit-length M13 RFII molecules can retain a single viral-strand discontinuity [15]. A mutational footprint assigns polymerase I a specific role in terminating ColE1 lagging-strand synthesis [16]; chromosome profiling implicates RNase HI and Ligase A in *Escherichia coli* completion [17]; and purified SV40 reactions require a 5-prime-to-3-prime exonuclease and ligase for covalently closed products [18, 19]. Catenated oligomers can appear while one linked circle is still replicating [20], and multiply intertwined daughter dimers can persist after synthesis [21]. Failure at any of these transitions leaves an incompletely synthesized, protein-bound, or physically inseparable product. The biological problem is therefore to convert a terminal fork geometry into DNA molecules that are covalently complete, cleared of replication machinery, and able to separate.

For broader background, readers are referred to the review *Mechanisms of DNA Replication Termination* [22] and, for bacterial chromosome architecture, to the review *Interplay between Chromosomal Architecture and Termination of DNA Replication in Bacteria* [23]. Here, termination is organized as a substrate trajectory rather than a list of factors: encounter position creates the terminal geometry; topological relaxation and accessory helicases permit convergence; polymerases, nucleases, and ligases close the remaining nascent-strand junctions; helicase-centered replisomes are dismantled; and direct links between replicated products are removed. Fork pausing, repair, mitotic synthesis, chromosome movement, and segregation enter the argument only when they reveal one of those substrate transitions or the consequence of its failure.

A synchronized plasmid-replication system in *Xenopus* egg extracts provides the continuous worked example used here, without implying a universal pathway. Topoisomerase II prevents topological stress from stalling converging forks [6], while RTEL1 and MCM10 become crucial for convergence when that stress rises [24]. The leading strands then pass one another and ligate to downstream lagging strands before CMG leaves the DNA [25]. Loss of fork-shaped DNA permits CMG ubiquitylation and unloading in the same extract system [26]. A separate study places CRL2-LRR1-dependent Mcm7 ubiquitylation upstream of p97-dependent extraction [27], while another identifies Mcm7 polyubiquitylation followed by p97/VCP/Cdc48-dependent helicase disassembly [28]. Together, these separate assays support a preparation-level working sequence in which topological relief sustains convergence, leading strands pass and ligate, and CMG is then marked and extracted; no single assay times every transition. Plasmid-topology assays independently show that topoisomerase II can remove precatenanes behind replication forks [7].

Structural and purified systems explain why the unloading switch can be sharp without turning those measurements into parts of the *Xenopus* experiment. Budding-yeast and human replisome structures show that the excluded DNA strand occludes a shared E3-binding surface on elongating CMG [29]. Purified budding-yeast reactions further show that fork-shaped DNA represses Mcm7 polyubiquitylation and that Cdc48 unfolds ubiquitylated Mcm7 [30]; CMG ubiquitylation followed by Cdc48-Ufd1-Npl4 activity is sufficient for disassembly in a minimal system [31]. These structural and biochemical results explain the DNA-sensitive switch within the working sequence without extending the *Xenopus* observations to yeast or human cells. Precatenane removal occurs during replication, but its timing relative to helicase passage and unloading is not resolved by these experiments. Whether the same licensing logic exists outside eukaryotic CMG is also unknown.

The comparisons that follow therefore retain four variables that determine what a termination assay can reveal: template geometry, the route by which the terminal position is chosen, the molecular substrate measured, and the time at which it is observed. These variables explain why a polar barrier, a broad termination zone, a catenated plasmid, and a mitotic under-replicated locus can all illuminate termination without representing interchangeable stages of one sequence.

## 2. Where forks meet: emergent zones and programmed traps

The terminal substrate is set by replication architecture. Origin use and fork movement generate encounter zones, whereas polar barriers constrain which fork arrives and where. A zone is therefore a probability distribution over fork encounters, while a trap is an oriented boundary condition on that distribution. Neither mode, however, completes nascent DNA simply by positioning an encounter: the last stretches of synthesis, replisome removal, and product separation remain downstream problems. Rolling-circle and end-replicating systems present still different substrates because synthesis ends through strand transfer or physical-end processing rather than collision of two conventional forks. Keeping these substrates separate is essential because the same word, termination, otherwise conflates encounter geography with chemically different endpoint reactions.

### 2.1 Emergent zones arise from origin use, fork movement, and local barriers

Fork encounters move when a replication program changes. In living *Escherichia coli*, sister replisomes separate after initiation and return toward midcell as completion approaches [32]. A two-origin chromosome undergoes distinct termination events [33], and in an oriX strain the rightward oriX fork first meets the leftward oriC fork [34]. Across bacteria, no trap was detected in the assayed *Vibrio cholerae* system [35], *Pseudomonas aeruginosa* terminates opposite oriC rather than at *dif* [36], and mutational bias places likely *E. coli* and *Bacillus subtilis* termination near *dif* [37]. Simulations nevertheless reproduce GC-skew transitions better with fork-meeting and Tus-Ter models than with one fixed *dif* site [38]. In a *Pseudoalteromonas* lineage, the chromid ter2 region even moved from near ori2 to approximately the opposite position [39]. The causal order is origin placement, fork direction and speed, then encounter position; a terminus-associated marker may correlate with the endpoint without specifying it. Encounter geography can therefore evolve independently of a fixed chromosomal landmark.

Viral episomes show how a local barrier can bias this emergent landscape. In a transfected oriP plasmid, initiation maps near the dyad-symmetry element and the direct repeats contain a barrier and termination site [40]; cell-cycle-dependent EBNA1 recombinase-like activity is required for termination in the reported episomal system [41]. Human B-cell assays also place a barrier and termination site in the oriP tandem repeats [42], with EBNA1 contributing to barrier formation [43]. Yet single-molecule maps show variable EBV initiation and fork progression without one fixed genomic terminus [44]. Thus, oriP biases some encounters without dictating every endpoint. SV40 termination has been localized to the nuclear matrix [45], while HPV-16 theta replication terminates in a mapped interval and epithelial differentiation shifts HPV-16 and HPV-31 toward rolling-circle replication [46]. Each endpoint remains specific to its viral replication mode and preparation.

Locus maps likewise resolve positioned subsets within eukaryotic chromosomes. Pea-root rDNA contains two sequence-determined regions where joining is delayed to the S-G2 boundary [47]; a human replicon junction maps to intron 44 near a recombination hotspot [48]; the chicken alpha-globin terminus lies just downstream of alphaA [49]; and two Physarum genes between synchronized flanking origins coincide with termination sites [50]. Replication mapping excluded a Chinese-hamster hotspot from its proposed identity as a replicon junction [51], illustrating that proximity is not proof of encounter. Early *Xenopus* rDNA initiates and terminates without detectable sequence specificity [52]. In a related embryonic rDNA study, these events recurred at 9-to-12-kb intervals, again without detectable sequence dependence [53]. During development, pausing becomes site regulated while termination remains distributed [54], although absolute polar barriers define fusion sites in some *X. laevis* and *X. borealis* repeats [55]. Human rDNA terminates mainly by convergence across the repeat, with a positioned event in some molecules [56]. At the 3′ end of mammalian rDNA, a barrier blocks bidirectional progression and aligns replication with transcription [57, 58], and TTF-I has polar contrahelicase activity [59]. Local barriers thus constrain a broader encounter distribution rather than replacing it.

Budding-yeast chromosome III directly links that distribution to origin use. Converging forks occupy a zone of at least 4.3 kb [60], while changing initiation sites on a ring chromosome creates a new 3-to-10-kb termination region [61]. Genome-wide Okazaki-fragment directionality attributes most budding-yeast termination to passive encounters set by origin-firing kinetics rather than cis elements or pausing [62]. A fitted model supports stochastic origin-activation times [63], while asynchronous fork departure and speed differences provide another proposed route to dispersed termination [64]. In human and mouse genomes, interactions among forks, including forks from distinct origins, can also predetermine encounter positions [65]. FORK-seq maps individual initiation and termination events on pulse-chased yeast nanopore reads [66]. D-NAscent identifies active origins, fork direction, and termination sites on individual ultra-long reads [67], while DNAscent v2 supports aggregated whole-genome maps of origin and termination locations with less data [68]. Combing reconstructs initiation zones around a termination zone [69], and HydEn-seq maps yeast zones through strand-specific ribonucleotides [70]. FORK-seq detects more dispersed events than population maps [71], while a two-dimensional neutral-alkaline method separately establishes fork direction and termini in SV40 [72]. Population directionality reports the average transition between fork orientations, whereas a single molecule can expose an individual encounter drawn from that distribution. The method therefore changes the scale of the observable, not the physical requirement that two fork trajectories intersect.

Mammalian genome maps similarly distinguish a zone from the reaction within it. Okazaki-fragment sequencing delineates human initiation and termination zones through fork directionality [73]. Polymerase usage separates transcription-start-site impediments from merging-fork termination [74], and transcription shapes both initiation and termination genome-wide [75]. Repli-Seq distinguishes convergent termination sites from broad constant-timing regions [76]. TrAEL-seq maps zones of initiation and termination in mammalian cells [77], whereas BrdU nanopore sequencing identifies initiation and termination on individual human molecules across S phase and genome-wide [78]. Drosophila nanopore maps reveal broad termination without a consistent sequence or chromatin motif [79]. An earlier strand-asymmetry model proposed random termination between adjacent mammalian origins, but did not directly image fusion [80]. These results define encounter probabilities and positions; they do not yet establish that every zone uses the same molecular fusion pathway.

Protein barriers create mechanistically distinct zones in yeast rDNA. In fission yeast, Reb1-mediated contacts between Ter sites strengthen polar arrest [81]. Swi1-Swi3 acts at three rDNA barriers but not a fourth plasmid-inactive site [82], and also functions at the imprinting site and RTS1 [83]. Ter1 mutations that prevent Sap1 binding in vitro are defective for arrest in vivo [84]. Sap1 also causes polar arrest at Ter1 while regulating *mat1* at SAS1 without fork pausing [85]. Reb1 and its two sites are required at RFB2 and RFB3 [86], although Reb1 dimerization is dispensable at Ter3 [87]. RTS1 and its trans factors form a polar barrier [88]; Rtf1 interactions set its polarity and efficiency [89]; Rtf2 stabilizes the arrested fork, blocks Srs2-dependent restart, and permits completion by an incoming fork [90]; and Lsd1-Lsd2 controls rDNA terminators [91]. Budding-yeast rDNA instead uses a Fob1-dependent barrier [92, 93] whose arrest function is separable from silencing [94] and whose strongest site forms a checkpoint-activating structure at termination [95]. These pathways locally determine which fork pauses and which fork must complete the interval.

Other maps extend the range without defining a common fusion chemistry. *Entamoeba* rDNA episomes terminate in a defined spacer [96], *Trypanosoma brucei* chromosome 1 shows variable central encounters approached from both sides [97], and Arabidopsis chromosome 4 contains reproducible zones with chromatin marks distinct from early initiation zones [98]. Peripheral labeling in regenerating rat liver suggests that very early initiation and very late termination occur near the nuclear periphery [99]. Vertebrate strand asymmetry supports replicons of roughly 50 to 100 kb and terminal regions ranging from sites to broad zones [100], while a positioned-origin, random-termination model explains serrated human skew profiles [101]. Archaeal evidence is also mixed: *Methanosarcina* termini remain computational predictions from Z-curve analysis [102], whereas two-dimensional gels show stochastic collision within *Sulfolobus* inter-origin fusion zones [103]. In each case, mapping establishes where the end game begins, not how the final duplex is dissolved.

### 2.2 Programmed polar traps position bacterial fork encounters

The *E. coli* trap was resolved from geography to mechanism. Okazaki-fragment polarity placed the regional terminus between *rac* and *man* [104], and restriction mapping tied cloned DNA to that terminus region [105]. A P2-induced *dnaA* chromosome showed fork retardation between *aroD* and *rac* [106], whereas an integratively suppressed *dnaA* chromosome showed fork cessation near *aroD* [107]. T1 and T2 first established two oppositely acting sites [108]; further mapping found additional polar pauses on both sides of the region [109]. Plasmid complementation placed a required trans factor near T2 [110]. In a chromosomal assay, T1 inhibition was lost without *tus*, and the assayed sites were used during termination in wild-type cells [111]. In ColE1-derived plasmids, T1 and T2 retained polarity and *tus* dependence, as did inhibition in the R6K terminus region [112]. TerE blocks only counterclockwise replication [113], TerF functions in chromosome and plasmid contexts with site-specific complex stability [114], and arrest maps to the first base of the 22-bp TerB sequence [115]. T1, T2, and Tus define the core system [116, 117], while Tus blocks forks when bound to terminator sites [118]. Sequence homology links the chromosomal sites to R6K terR [119]; a 216-bp R6K fragment blocks forks [120]; *E. coli* extracts bind chromosomal and R6K *ter* sequences [121]; and purified Ter protein footprints them [122]. The evidence therefore progresses from a broad region, to oriented sites, to a site-bound trans factor. That hierarchy establishes a polar positioning device rather than a generic completion enzyme.

Tus-Ter biochemistry explains how the device becomes directional. Tus-Ter complexes mediate arrest at 23-bp sites [123], and Tus binds such sites tightly and specifically [124], with major- and minor-groove contacts [125] and single-base determinants that affect binding and arrest together [126]. Mass spectrometry detects a one-to-one complex but did not resolve mutant affinities [127]; Ter sites also differ in Tus affinity [128]. Affinity cleavage [129] and the crystal structure [130] supplied structural constraints. At an oriented site, purified Tus stops leading-strand synthesis while the last lagging primers lie 50 to 70 nucleotides upstream [131]. Tus arrests DnaB polarly through Tus-DnaB and Tus-Ter contacts without requiring melting or base flipping [132], and the L1 loop contributes to that interaction [133]; RTP uses a distinct contrahelicase mechanism in *Bacillus* [134]. At TerB, opening the nonpermissive face traps cytosine 6 [135]. Substitution at GC6 strongly compromises arrest in vivo despite only a slight effect on Tus affinity, supporting lock-dependent permanent blockade [136]. Fork speed sets the competition between Tus displacement and arresting conformations [137], while asymmetric Tus-Ter sites block plasmid replisomes in the nonpermissive orientation [138]. Directionality therefore arises from an encounter-dependent state, not affinity alone.

Mutations and heterologous motors test that distinction. Tus mutants alter DNA binding and arrest to different degrees [139, 140], and a general ability to impede proteins on single-stranded DNA is insufficient to block a bona fide helicase [141]. Tus and RTP inhibit helicases used in symmetric replication but not conjugative or rolling-circle motors [142]. Tus-Ter can impede SV40 T-antigen helicase and forks in vitro [143, 144], yet host assays show strong Tus-TerB and RTP-Ter specificity [145], and *Dickeya* Tus differs from *E. coli* Tus by forming an exceptionally stable lock from a moderate initial complex [146]. The barrier is also conditional: a bacterial modulator permits helicase passage in vitro [147]. Passage of an RNA transcript through the assayed *E. coli* and *B. subtilis* termini dissociates terminator protein and abolishes replication-fork arrest [148]. A separate analysis found that RNA-chain invasion can functionally inactivate an arrest site even though Tus and RTP themselves impede transcription polarly [149]. Negative supercoiling also promotes DnaB bypass [150]. These perturbations are not ancillary exceptions. They identify the variables that determine whether the bound complex becomes a functional barrier: the approaching motor, competing traffic, DNA topology, and encounter kinetics.

Perturbations reveal how trap geometry changes the terminal substrate. Activating inverted Ter sites with induced Tus arrests replication, delays completion of the engineered *E. coli* chromosome, and causes filamentation [151]. In an *E. coli* chromosome replicated unidirectionally under integrated R1 control, *tus* inactivation reduces elongated cells, an effect attributed to eliminating polar arrests and shortening completion time [152]. TerB also creates an orientation-dependent deletion hotspot [153]. Plasmid mapping found 15 to 24 under-replicated bases after fusion at Tus-Ter [154]; one fork can arrest before the opposing fork stops at the same site [155]; and the earliest intermediate after Tus complementation was consistent with a D-loop bearing the stopped leading strand [156]. The chromosomal trap is nested: sites admit forks but oppose their exit [157], comparative analyses identify conserved enteric architectures [158], and substantial Tus occupancy is restricted to six inner *E. coli* sites within an inferred ancestral trap [159]. In reconstitution, traps flanking oriC reduce concatemers, whereas traps opposite oriC impede propagation unless UvrD is supplied [160]. Plasmids add bounded variants: termination can occur away from the origin [161], pKD1 uses a cis-acting barrier [162], loss of *tus* or a pOU47 Ter site yields multimers and rolling-circle tails [163], a bipolar *Bacillus* site arrests in either orientation [164], and R6K terminators set product endpoints [165]. R6K terminus activity is membrane independent, and the terminus sequence does not encode a trans-acting factor necessary for termination [166]. The R6K termini were later examined by chemical probing [167]; the region binds an approximately 40-kDa *E. coli* protein at inverted repeats [168], not through DNA folding [169]. Exonuclease-defective *polA* alleles produce over-replication, especially without Tus, revealing a polymerase I completion function beyond confinement [170]. The trap positions the collision, but downstream enzymes process what that collision leaves.

The *B. subtilis* trap follows the same logic with a different assembly. Early cloning missed DNA spanning terC while recovering both flanks [171]. A later 10.9-kb clone contained terC [172], while overlapping cosmids covered four of five fragments replicated last [173]. Genetic evidence supports a preferred arrest site [174], and sequencing localized the clockwise fork arrest that defines terC to approximately 30 nucleotides [175]. Its activity depends on orientation relative to the clockwise fork [176]. Deleting the wild-type terminator can reveal an alternative route [177]; strains 168 and W23 retain a conserved terC intermediate [178]; loss of binding redirects convergence opposite oriC, including on artificial chromosomes [179]; and displaced traps recruit TerIII while forks can fuse with one still arrested at TerI [180]. RTP expression is required for terC arrest [181] and RTP binds a 209-bp terC fragment [182]. Footprinting identifies two protected regions [183], arrest is polar [184], and dimeric RTP acts at the site [185]. Two RTP dimers bound at the terminus produce polar fork arrest [186, 187], consistent with cooperative, unequal site affinities in the RTP-DNA structure [188] and progressive DNA bending and unwinding [189]. The terminator has a bipartite architecture of overlapping RTP sites [190, 191], further defined by missing-nucleoside interference [192] and mutagenesis [193]. Mapping narrows the locus, occupancy identifies the complex, and polarity tests show what that complex does. Together they converge on an oriented two-dimer barrier.

Structural and relocation tests separate assembly from arrest. Terminator DNA changes RTP conformation [194], and a C110S structure resolves the high-affinity TerI B-site complex [195], following preliminary crystallization [196]. One assay supports a critical RTP-DnaB interaction [197], whereas another argues against highly specific replisome recognition [198]; the evidence here does not establish that the assays are commensurable. Analysis of RTP mutants indicates that complex stability is not the overriding determinant of arrest and that an approaching fork must actively disrupt the complex or remove RTP [199]. Across mutant terminators, proximal half-site affinity does not consistently predict arrest efficiency [200]. Sequence-specific binding and polar replisome inhibition nevertheless remain directly demonstrable [201]. Variant sites extend the barrier to psiL1 [202], a theta-plasmid terminator [203], and a newly identified chromosomal terminator that excludes candidate stringent-response sites [204]; homologs occur in four close *Bacillus* relatives [205]. Relocated terminators retain arrest activity [206], and RTP-dependent Tn917 enrichment near terI and terII does not require dimer resolution or chromosome translocation [207]. The decisive functional variable is therefore the response of the assembled complex to an approaching replisome, not occupancy measured in isolation. Tus and RTP use different molecular assemblies to confine an encounter while leaving product completion to later reactions.

### 2.3 Termination without conventional fork convergence

Rolling-circle replicons terminate by recognizing a site and transferring or closing a strand. In phiX174, sequence requirements for termination and reinitiation were tested within its 30-bp origin region [208]. In f1, the plus-strand origin also serves as the termination signal [209], yet its initiation and termination domains overlap without being identical [210]. PhiX174 A-protein biochemistry supports a role in the terminal step [211]. The protein has site-specific nicking-closing activity within the origin sequence [212], and termination circularizes the displaced strand [213]. Small plasmids reuse origins in different ways. The pT181 and pC221 origins can cross-react as termination signals [214]; pT181 sequence requirements overlap, but RepC binding is dispensable for termination [215]; and a 22-bp pKYM origin segment is sufficient [216]. In a pT181 construct carrying two directly oriented origins, synthesis initiates at one and terminates at the other in vitro [217]. Rolling-circle initiators have origin-specific nicking-closing activities [218], although Tyr191 is needed for initiation but not termination in one system [219], and a pUB110 Rep mutation may alter origin affinity or recognition of a terminal conformation [220]. A 36-bp haloarchaeal sequence is sufficient for termination while part of its hairpin is initiation specific [221]; a genomic-DNA screen can recover such sequences [222]; and CTXphi synthesis begins and ends at a mapped 22-bp origin in plasmid and prophage forms [223]. Here the worked mechanism is site recognition, strand cleavage, displacement, and strand closure, not the merger of two replisomes. Origin reuse therefore does not imply identical initiation and termination chemistry.

Mobile elements and small viruses present other terminal determinants. ISCR28 favors a 5′-GXXT-3′ sequence at terIS [224]; comparative Helitron analysis found little support for a functional 3′ hairpin [225]; and a sequence-independent stem-loop is essential for porcine-circovirus termination but not initiation [226]. Sixteen of 26 recovered porcine circoviruses showed template switching during origin biosynthesis [227]. Adenovirus studies place termination at both physical ends [228, 229]; SPO1 cistron 32 mutations specifically affect termination [230]; and parvovirus H-1 contains a terminal turn-around structure [231]. These substrates end synthesis through cleavage, transfer, or end processing rather than dissolution of a duplex between opposing forks.

Chromosome ends pose a related strand-completion problem. TEN1 is essential for telomeric C-strand synthesis in the assayed colon-cancer cells [232]. Individual human telomeres have chromosome-specific origin use, fork rates, directions, and termination positions [233], while Ssu72-dependent lagging-strand synthesis terminates the fission-yeast telomere cycle [234]. Incomplete duplication of the C-rich telomeric strand by lagging-strand synthesis creates a second telomere end-replication problem [235]. In *Saccharomyces cerevisiae*, incongruent telomere ends likewise implicate the incompletely replicated lagging-strand telomere as the primary source of the end-replication problem [236]. A *Borrelia* telomere sequence is sufficient to resolve a circular replicon into a linear form [237], whereas N15 lytic replication produces a circle with unresolved hairpin telomeres, consistent with a dimer intermediate [238]. Mitochondrial data remain less unified: perturbing selected factors accumulates late intermediates or impairs completion [239], regulation of the balance between abortive D-loops and complete replication has been proposed [240], and fish D-loop sequences correlate with termination [241]. These observations define candidate terminal states, not one common mitochondrial pathway.

Encounter maps should therefore be read from the substrate backward. Origin timing produces zones; Tus, RTP, and local eukaryotic barriers constrain fork approach; rolling-circle and end-replicating systems terminate on different structures. A mapped endpoint answers where a terminal reaction begins, not whether nascent DNA is covalently complete, the replisome has been removed, or replicated products are physically separable.

## 3. Dissolving the last parental duplex

As two forks approach, the shrinking parental interval must absorb or export the torsional stress created by continued unwinding. Fork rotation and precatenation preferentially occur at budding-yeast termination regions and protein-DNA barriers [5]. Precatenanes also form before termination in stalled bacterial plasmids [4]. A torsional-gradient model proposes that supercoiling ahead of the fork and precatenation behind it interconvert through such swiveling [242]. The important qualification is spatial: budding-yeast sister intertwines occur at termination sites but are not enriched there relative to the rest of the genome [243]. Termination therefore intensifies a general topological problem rather than creating an entirely new linkage. The terminal task is to keep the last parental segment traversable while preserving a route for subsequent daughter separation. This model predicts that restricting fork rotation should retain more stress ahead of the replisome, whereas permissive rotation should transfer more of the burden to daughter unlinking. Measuring precursor supercoiling and daughter interlinks in the same perturbation would distinguish redistribution from a general failure of topological control.

A protein barrier can fix where this topological problem is encountered without specifying how it is solved. Bacillus subtilis RTP is a dimer whose monomers are approximately 14.5 kilodaltons [244]. Its symmetry and secondary structure have been examined biophysically [245], and its crystal structure was determined at 2.6 angstrom resolution [246]. Among the tested C110 variants, C110S most closely preserves wild-type secondary structure, stability, self-association, and DNA binding [247]. Those measurements constrain barrier architecture, but the mechanistically discriminating evidence comes from the DNA states and enzyme requirements downstream of arrest.

Topoisomerase perturbations show that torsional relaxation remains necessary before synthesis and segregation are complete. Topoisomerase II activity supports late SV40 replication [248, 249]. In vivo inhibition slows replication of the last 5% while producing catenated dimers, linking defective approach to persistent daughter interlinks without equating the two endpoints [249]. Type II topoisomerases likewise support fork convergence or fusion [6, 250, 251]. The readouts resolve different consequences of the same physical constraint: forks stall in Xenopus extracts [6], breaks and rearrangements rise at yeast termination regions when Top2 function is compromised [250], and the bacterial meeting interval is lost when Topo IV is inactivated [251]. Other late circular-genome substrates recruit different activities. African-trypanosome mitochondrial topoisomerase IA is essential for resolving late theta structures [252], whereas Thermus thermophilus requires the AddA-AddB helicase-nuclease complex for completion [253]. Across the assayed systems, linked or obstructed late DNA substrates recur, whereas the implicated enzyme differs.

Accessory helicases become limiting when the final duplex is difficult to traverse. They can sustain terminal fork convergence when topology is limiting [24, 254]. Rrm3 and RTEL1 docking positions accessory helicases through analogous contacts with CMG and polymerase epsilon beside the lagging-strand template [255]. Pif1-family helicases promote protein-barrier traversal and final fork merger [256, 257], while Tof1-Csm3 opposes Rrm3 at arrested yeast forks [258]. These results suggest that recruitment supports bypass while fork-protection factors modulate helicase access.

Not every obstructed terminus is simply overwound duplex DNA. Genetic, genomic, and structural analyses recover noncanonical DNA structures at yeast termination or pause regions [259, 260]. Rrm3 and Sen1 restrain the supercoils, hybrids, and reversed converging forks that accumulate at termination regions and telomeres [259], whereas Smc5-Smc6 retains the Sgs1-Top3-Rmi1 complex where crossed-strand intermediates must be processed [260]. Consistent with a locus-specific substrate burden, Sgs1 loss delays rDNA completion even though genome-wide forks move faster [261]. Taken together, these substrate-specific phenotypes imply that local DNA and protein architecture determines whether swiveling, helicase bypass, or joint-molecule processing becomes the rate-limiting transition.

### Conditional intermediates at bacterial fork fusion

Physical intermediates argue against an instantaneous merger of two bacterial replisomes. Defined bacterial termination regions retain replication-fork intermediates [262, 263, 264]. In Bacillus, the first clockwise fork is blocked or severely impeded by a sequence-based site [263]; in E. coli, two-dimensional gels detect late convergence pauses at Ter but not at dif [264]. These observations establish a persistent terminal geometry. They do not, by themselves, identify the chemical branch or strand that must be removed.

Processing experiments narrow that transition. Purified RecQ and topoisomerase III can resolve converging forks [265]. RecBCD is required to process DNA produced when forks converge [266, 267]. SbcC-SbcD also acts on convergence-associated DNA [268, 269], including a palindrome-like intermediate processed with ExoI [269]. The order of these observations matters: physical persistence predicts a processing substrate, biochemical resolution establishes capability, and genetic requirements connect that capability to completion. Two further studies place controlled degradation of excess DNA after fusion as a brake on terminus over-replication [270, 271]. One directly assigns 3-prime flaps to fusion when 3-prime exonucleases are absent [270]; the other proposes transient passage beyond the doubling point followed by incision, resection, and joining by RecBCD, ExoI, SbcDC, and RecG [271]. The 3-prime flap is therefore a supported conditional product, but the other assays do not establish it as the obligatory intermediate at every unperturbed fork encounter.

### Encounter can precede chemical completion

SV40 makes the distinction between encounter and closure visible. A late replication state accumulates at about 91% completion [8, 9]. The remaining approximately 470 base pairs lie near the expected termination center in mapped chromosomes [8], and mature form-I DNA appears only after the late intermediate in the extract reaction [9]. Gaps occur in both newly synthesized strands within this region [10]. Their persistence explains why physical completion need not yield a covalently continuous product: isolated nuclei require cytosolic functions for Okazaki-fragment joining and terminal-gap filling [11], whereas permeabilized CV-1 cells complete without added cytosol but recover nicked, gapped catenated dimers [12]. The preparation changes the soluble requirement, not the common observation that nearly completed, linked daughters can retain nascent-strand discontinuities.

In Xenopus egg extracts, leading-strand passage and ligation precede CMG unloading [25]. In this system, eliminating the last parental duplex creates the substrate for nascent-strand joining before replisome release. That experimentally resolved order supplies the bridge from topological dissolution to the chemical finishing reactions below.

## 4. Finishing nascent DNA

### 4.1 Template traversal can end before covalent completion

Replication can finish as monomeric circular products in reconstituted systems [272, 273, 274], showing that initiation, elongation, terminal synthesis, and closure are jointly achievable. The route to that endpoint nevertheless includes a distinct late synthesis phase. Ribonucleotide mapping places a switch from polymerase epsilon to polymerase delta on nascent leading strands during budding- and fission-yeast termination [275], but increasing polymerase-delta abundance twofold to fourfold in fission yeast does not alter polymerase usage across termination zones or origin efficiency [276]. Polymerase identity therefore changes without evidence that polymerase abundance sets the transition. At a larger scale, aphidicolin-treated rat fibroblasts merge accumulated replicon-sized intermediates by synthesizing across the gaps between them [277]. Both observations place residual synthesis after ordinary fork progression, although they concern different substrate scales.

The strongest discrimination comes from reactions that copy all or nearly all available template yet retain an interruption [13, 14, 278]. Exhaustion of template therefore does not itself generate a ligatable or sealed junction. In one SV40 chromosome preparation, replication completes and progeny co-sediment with mature 50-55S chromosomes [279]. Fractionation separates total synthesis and Okazaki-fragment joining from efficient conversion to covalently closed mature DNA [280]. In human cell extracts, cytoplasmic activity produces resolved relaxed closed circles, while nuclear extract promotes negative supercoiling [281]. A nearly complete intermediate also accumulates when ddTTP inhibits the late SV40 reaction, implicating polymerase activity in the final synthesis step [282]. Fractionation then supplies the causal test: complete monomer formation depends on restoring missing soluble replication activities [283, 284, 285]. RF-C is required in the more resolved systems [284, 285], and omission of PCNA also prevents completion in one of them [285]. These experiments move the explanation from a missing product to a missing transition between an interrupted circle and a closed monomer.

Other genomes deliver different structures to the same conceptual boundary. Adenovirus end regions receive preferential, strand-specific label during completion in a soluble complex [286]; Toxoplasma plastid DNA forms linear oligomers with a common endpoint consistent with rolling-circle tail processing [287]; and pulse-labeled herpes-simplex-virus intermediates lack detectable termini before slowly maturing into terminal virion DNA [288]. Separated initiation and termination domains are sufficient for rescue of minimized f1/M13 phagemids, although that assay does not resolve the terminal chemistry [289]. These observations locate or delimit completion, but they do not imply a shared end reaction.

Retroviral plus-strand products make the residual substrate strand-specific. Antisense inhibition yields full-length avian-retroviral DNA with complementary single-stranded LTRs, consistent with arrest before displacement finishes the ends [290]. Foamy-virus DNA instead carries a variable central plus-strand gap with neither a fixed boundary nor a detectable flap [291], whereas a lentiviral central termination sequence forms a nonproductive reverse-transcriptase complex after several adenosines [292]. At HIV strong-stop DNA, the modified A58 residue of the tRNA-Lys3 primer is required for correct plus-strand termination [293, 294]. The variable is therefore the structure that defines the last polymerase position: an incompletely displaced LTR, a distributed gap, a sequence-stalled complex, or a modified primer boundary. That structure determines what must next be removed or filled.

### 4.2 Primer and flap processing creates a ligatable nick

For primer-bearing or flap-containing nascent junctions, closure requires processing that leaves compatible 3-prime-hydroxyl and 5-prime-phosphate ends. Terminal processing can depend on polymerase I [16, 15]; loss of its 5-prime exonuclease in M13 leaves a unit-length but unjoined product [15], directly separating product length from sealability. E. coli chromosome-completion assays also implicate RNase HI and Ligase A [17]. In purified SV40 systems, a 5-prime-to-3-prime exonuclease and DNA ligase are required for covalently closed daughter circles [18, 19]. Pyrococcus abyssi RNase HII cleaves fully annealed RNA-DNA junctions and single embedded ribonucleotides [295], a biochemical capability compatible with primer removal but not, by itself, proof that it carries the terminal reaction in vivo. Together, the results define the substrate transition: an RNA-containing or mismatched junction must become a ligatable nick before closure can occur.

Mitochondrial reactions resolve that transition at nucleotide-scale geometry. Mitochondrial 5-prime-flap intermediates can be converted toward ligatable ends [296, 297]. Without polymerase-gamma exonuclease, synthesis continues into duplex DNA and creates an unligatable flap [296]; MGME1 cleavage instead leaves short flaps, gaps, or nicks that polymerase gamma can extend or excise to a ligatable nick [297]. Non-flap RNA junctions take another route: EXOG processes residual RNA before nascent circular strands are joined [298, 299], and one to three ribonucleotides left by RNase H1 impair ligation [300]. These products explain why primer removal is not a binary event. The decisive output is the exact end chemistry handed to ligase.

Genetics tests whether this end chemistry matters to genome maintenance. Loss of mitochondrial end-processing functions compromises completion and accumulates abnormal linear, deleted, or fragmented molecules [301, 302, 303]. Structural and biochemical studies show that mitochondrial nucleases can access and process 5-prime flaps [304, 305]. During copy-number restoration in human cells, ligase-III depletion increases nicks and impairs recovery, whereas RNase-H1 depletion prevents recovery and produces nicked intermediates [306]. The assays do not rank all mitochondrial nucleases under one matched condition, but they converge on a sequential requirement for end preparation followed by sealing. Plastids reach an analogous chemical state through a different enzyme: maize PEN1 removes RNA primers in vitro, and pen1 mutation produces plastid-DNA breaks [307].

Kinetoplast minicircles reveal why timing matters as much as catalytic capability. Antipodal protein complexes contain activities capable of complete primer removal followed by gap filling on newly synthesized L strands [308]. Yet newly copied minicircles reattach to the network while still nicked or gapped, and their repair and covalent closure continue later in the network cycle [309, 310, 311, 312]. Trypanosome endonuclease I removes the residual 5-prime ribonucleotide; its depletion blocks minicircle reattachment and delays kinetoplast segregation [313]. The opposite perturbation is equally informative: TbPIF5 overexpression prematurely removes primers and joins Okazaki fragments on theta-form minicircles, arrests further lagging-strand elongation, and yields truncated products [314]. Delayed closure thus preserves a substrate needed for continued synthesis and network assembly, rather than merely reflecting slow repair.

Telomeres impose the same chemical problem on asymmetric chromosome ends. Human end mapping finds that up to approximately 80% of replicated C strands end at CCAATC-5-prime, revealing constrained processing without identifying the enzyme [315]. Telomere end processing extends beyond duplex synthesis, with late intermediates persisting after fork passage [316, 317]. Replicated telomeres also retain strand-specific end structures [318, 319]. Dedicated factors support C-strand fill-in at this boundary [320, 321]. The shared problem is strand-specific end completion, not a common end geometry or enzyme.

Retroviral sequence modules show why identical structural perturbations need not produce identical biological endpoints. Deleting sequence adjacent to the Moloney murine leukemia virus polypurine tract leaves aberrant plus-strand ends consistent with failed primer removal or upstream mispriming [322]. Mutating the HIV central polypurine tract and termination sequence disrupts central-flap formation in three studies [323, 324, 325], but the measured consequences differ: replication falls 10-fold to 100-fold in one assay [323], single-cycle infection remains intact while APOBEC-sensitive defects emerge in another [324], and spreading infection fails in a third [325]. The structural result is reproducible, whereas functional necessity depends on the endpoint and context. Hepatitis B virus presents a different repair substrate. Its relaxed circle loses the RNA primer and covalently linked polymerase during conversion toward cccDNA [326]; FEN1 can then cleave a flap, after which FEN1, polymerase, and ligase generate covalently closed circular DNA [327]. In this system, end removal, fill-in, and sealing form a directly reconstructed progression.

### 4.3 Covalent closure and physical separation are ordered but separable

Ligation converts a correctly processed nick into continuous DNA, but product maturation may continue afterward. SV40 systems expose incomplete nascent-fragment joining [328, 329]. Ligase-I-defective extract directly accumulates unstable unligated intermediates [328], whereas TTP-dependent strand-size redistribution was interpreted as Okazaki-like fragment joining [329]. Product maturation can also be delayed beyond local DNA synthesis [330, 331, 332, 333]. Mature DNA can form after aphidicolin has stopped fork movement, while ultraviolet-A lesions block that conversion [331]; in tsFT20 cells, within-replicon elongation continues while merger into larger DNA is delayed [332]; and pea replicon-sized fragments are not joined until G2 despite earlier Okazaki-fragment ligation [333]. These discriminations show that a late merger reaction can be delayed independently of ordinary chain elongation, although the molecular junction in the plant and older cell assays remains unresolved.

Circular bacterial products expose how covalent closure is coordinated with topology. A 14-enzyme oriC cycle couples Okazaki-fragment maturation and decatenation to reusable covalently closed monomers [334]. In an earlier purified oriC system, primer removal, gap filling, and ligation are required to produce closed circular daughters [335]. E. coli minichromosomes pass through dimeric intermediates before becoming closed monomers [336, 337]. A ligase-inhibited oriC reaction resolves the order more sharply: nicked dimers are decatenated to open circles before ligation produces closed supercoiled molecules [338]. Likewise, nonsegregated pBR322 daughters can be converted in vitro into separate mature circles [339, 340], with high topoisomerase-I concentration sufficient to resolve the final Cairns intermediate and catenated dimers [340]. A ligatable nick can therefore persist through unlinking; sealing and separation are coupled outputs, not obligatorily simultaneous reactions.

Circular yeast plasmids terminate as multiply interlocked catenanes that are resolved during S phase [341]. In budding yeast, Top2 depletion prevents decatenation after replication, whereas catalytically inactive Top2 yields hypercatenated, gapped daughter DNA [342]. Human topoisomerase II contributes both to replication completion and to postreplicative chromosome processing [343, 344]. A fractionated SV40 system similarly requires topoisomerases I and II for complete daughter synthesis and segregation [345]. Protein removal adds another output: at budding-yeast fork convergence, replisomes are removed while cohesin remains, and CMG disassembly is required for proper sister cohesion [346]. These systems show that covalent continuity, daughter topology, and replisome disposition can remain separable late states, and their order is system specific.

### 4.4 Specialized strand-transfer, hairpin, and end reactions

Rolling-circle systems replace the converging-fork junction with a protein-linked strand end. Conjugative relaxases cleave and rejoin oriT DNA in reactions assigned to transfer termination [347, 348]; in R388, two TrwC tyrosines act sequentially and Tyr26 performs the terminal strand transfer [347], while RP4 assays suggest that the second cleavage requires a TraI dimer [349]. IS rolling-circle transposition is likewise constrained by defined element ends [350, 351]: IS1294 begins at oriIS and ends at the opposite terIS [350], whereas IS91 catalytic tyrosines are required for exact-end circular single strands [351]. Site recognition and strand transfer thus replace gap filling as the defining terminal chemistry.

Small rolling-circle plasmids show that the fate of the protein-DNA intermediate decides whether another round can begin. Purified pC194 RepA performs a termination-like strand transfer in which E210 and Y214 contribute differently to hydrolysis and transesterification [352]. Replacing the catalytic glutamate with tyrosine converts that sequence into two transesterifications coupled to reinitiation [353], directly showing that a change in bond-transfer chemistry changes reuse. RepK can terminate at a truncated pKYM origin and reuse that region for reinitiation [354]. By contrast, pT181 RepC leaves termination with an oligonucleotide attached to its active tyrosine, preventing productive recycling [355, 356]. RepC* still binds and religates DNA but loses nicking-closing and replication activity [356]. Acidic pH suppresses cleavage and hydrolysis of the covalent pMV158 RepB-DNA intermediate, although replication remains largely maintained except at pH 4.5 [357]. These comparisons identify intermediate disposition, rather than cleavage alone, as the branch between closure, reinitiation, and initiator inactivation.

Single-stranded phages split terminal cleavage from daughter circularization. In phiX, displaced-strand circularization is a discrete terminal reaction [358, 359]. In fd, replicated viral strands are cleaved and circularized after rolling-circle synthesis [360]. A purified system times cleavage to completion of a full round and assigns cleavage and circularization to gene 2 protein [361]. Replacing the normal replication system with T4 enzymes preserves gene-2-protein cleavage to unit length but makes circularization inefficient [362]. That uncoupling identifies two chemical transitions that normally appear as one product-forming event.

Hairpin-ended genomes instead convert a replicated inverted-repeat junction into new termini. Poxvirus concatemer or inverted-repeat substrates resolve into linear hairpin-ended products in infected-cell and extract assays [363, 364, 365, 366]. Temperature-sensitive mutants that fail this reaction retain concatemeric telomere-fusion intermediates [365], whereas resolution still occurs when novobiocin blocks virion assembly [367], separating the end reaction from packaging in that experiment. MVM NS1 nicks the right-end telomere, and cleavage of the hairpin is followed by strand-displacement synthesis [368]. In a separate assay, NS1-containing extracts resolve the junction palindrome asymmetrically, producing distinct termini and nicked intermediates associated with newly synthesized DNA [369]. Rudivirus Rep both nicks the initiating hairpin and later reseals it to terminate replication [370]. Porcine-circovirus Rep proteins can cleave and reseal origin DNA in reactions proposed to terminate rolling-circle synthesis [371, 372], and deletion experiments indicate that the origin-flanking palindrome is required for termination but not initiation [373]. AAV end resolution adds a polymerase-dependent variant in which Rep68 becomes covalently attached and the reaction requires polymerase delta, ATP, and deoxynucleotides [374]. The shared endpoint is a mature terminus, but the tested substrates distinguish direct resealing, nick-and-synthesis resolution, and palindrome-dependent closure.

Bacterial protelomerases solve an analogous end problem through two transesterifications. They resolve replicated telomere junctions into hairpin-ended linear products [375, 376]. ResT resolution uses separable features: a hairpin-binding region promotes prehairpin formation [377], Tyr335 is the active-site nucleophile [378], and the C-terminal domain supports DNA binding and both transesterification steps [379]. Depleting ResT accumulates replicated telomere intermediates and depletes linear plasmid forms [380], connecting the purified chemistry to product maintenance in cells. TelA separates core resolution from reaction control. Its N-terminal domain regulates auxiliary activities without being required for telomere resolution [381, 382], and catalytic-site substitutions can redirect replicated junctions toward Holliday and Cre-like recombinant products instead of hairpins [383, 384]. Substrate binding therefore sets up resolution, while reaction-direction control determines whether cleavage is returned as a telomere or diverted into recombination.

Finally, herpes simplex virus matures replicated concatemers through packaging-coupled cleavage. Concatemeric DNA is cut into genome-length molecules in linkage with capsid packaging [385, 386]. This reaction occurs after production of the replication concatemer, so it lies beyond fork encounter and nick ligation but within the broader endpoint of producing a transmissible completed genome.

## 5. Replisome disassembly as a DNA-geometry switch

Replisome removal is coupled to the end of synthesis through a change in the DNA presented by CMG. Structural comparison in budding yeast and humans places Dia2 and LRR1 on a common face of CMG that is occluded by the excluded DNA strand during elongation and exposed after termination [29]. In Xenopus egg extracts, converging CMGs pass one another and unload independently, while fork-shaped DNA suppresses CMG ubiquitylation until convergence removes that protection [26]. An open CRL2-Lrr1 structure provides a compatible recognition mechanism: a flexible Lrr1 pleckstrin-homology domain can target the ligase to terminated CMG [387]. These observations support a DNA-sensitive recognition model across the named systems, but they do not constitute one experiment that follows the same molecular surface from yeast structure to Xenopus unloading.

The switch occurs after a defined synthesis transition in the reconstituted Xenopus system. There, leading strands pass one another and ligate to downstream lagging strands before CMG unloads [25]. Loss of a fork substrate can therefore be placed after strand passage and ligation in that preparation, whereas product unlinking has not been timed within the same sequence. The next steps can be resolved into three biochemical decisions: recognition of the altered CMG-DNA geometry, construction of an Mcm7 ubiquitin signal, and extraction of the marked helicase.

### 5.1 Yeast couples exposed CMG geometry to Cdc48 extraction

In budding yeast, cellular and purified systems place SCF-Dia2-dependent Mcm7 ubiquitylation upstream of CMG disassembly [388, 30, 31]. Reconstitution explains how this modification can remain termination selective. Fork DNA represses SCF-Dia2 activity during elongation; after termination, K48-linked chains extend beyond a five-ubiquitin Cdc48 threshold, and Mcm7 is unfolded [30]. A separate purified system establishes that Cdc48-Ufd1-Npl4 is sufficient to disassemble SCF-Dia2-modified CMG [31]. Thus, the yeast evidence connects a protected elongating state to an exposed, ubiquitylated, and extractable helicase without requiring disappearance of CMG by degradation. A review of the yeast pathway likewise describes MCM7 ubiquitylation, CDC48 recruitment, CMG unfolding, and replisome disassembly after termination [389].

### 5.2 Metazoan S-phase unloading separates recognition, marking, and extraction

Metazoan systems use a related geometry-sensitive route, but the supported roles remain species specific. Two Xenopus studies place CRL2/CUL2-LRR1-dependent CMG ubiquitylation upstream of replisome disassembly [27, 390]. One follows release of CMG together with associated replisome proteins from chromatin [27]; the other also establishes CUL2-LRR1 cooperation with UFD1-NPL4-CDC48 in *Caenorhabditis elegans* embryos [390]. Purified human CUL2-LRR1 then resolves the chain-building step: sequential E2 enzymes construct a specific K48 chain on MCM7 that converts CMG into a p97 substrate [391]. In the reported human system, RNF168 and BRCA1 also promote MCM7 polyubiquitylation during replication termination [392]. These results establish more than one contribution to MCM7 marking, but they do not by themselves place all of the ligases in one linear pathway.

Extraction requires both the ubiquitin signal and productive engagement by the unfoldase machinery. In Xenopus extracts, termination-specific Mcm7 polyubiquitylation permits p97-dependent disassembly of active CMG at converging forks [28]. Two studies place UBXN7 at the coupling of ubiquitylated CMG to p97 [393, 394]. It bridges CUL2-LRR1 and p97 during unperturbed S phase in one system [393], while cooperative recruitment links UBXN7 to p97-UFD1-NPL4 in the other [394]. Reconstitution with human proteins further shows that UBXN7, FAF1, and FAF2 lower the ubiquitin threshold at which p97-UFD1-NPL4 unfolds CMG, in reactions relevant to both S phase and mitosis [395]. Recruitment can also be controlled before chain recognition: TIMELESS-TIPIN is required for efficient CUL2-LRR1 recruitment and CMG ubiquitylation in *C. elegans* embryos [396]. Together, these experiments assign distinct jobs to an E3-recruitment factor, the MCM7 chain, p97 adaptors, and the p97-UFD1-NPL4 unfoldase.

Cellular phenotypes show why timely extraction matters without changing the biochemical order. Human somatic cells require CUL2-LRR1, p97, and UBXN7 to unload terminated replisomes, and the same experiments support the existence of a mitotic route when S-phase unloading fails [397]. Human LRR1 loss prevents CMG unloading, sequesters limiting replisome components, progressively slows S phase, and activates an ATR-Chk1-Wee1 G2/M checkpoint [398]. In mouse embryonic stem cells, CUL2-LRR1 targets CMG-MCM7 for p97 extraction during S phase, whereas TRAIP acts through a separate mitotic route [399]. The physiological consequence is therefore not merely persistence of a chromatin signal: failure to recycle replisome components can compromise later replication.

### 5.3 Lesion-associated and mitotic routes respond to different terminal states

Convergence at an interstrand crosslink does not reproduce unperturbed termination. In replication-coupled crosslink repair, CMG removal after fork collision enables subsequent processing [400, 401]. In Xenopus extracts with a cisplatin crosslink, unloading permits reversal of one fork before incision of the other [400]; BRCA1-dependent removal allows a leading strand to approach the lesion [401]. Ubiquitin output can then select between repair routes. Short TRAIP-built CMG chains recruit NEIL3, whereas longer chains drive p97-dependent unloading and permit the Fanconi pathway to act [402]. In the tested vertebrate system, BRCA1 also promotes MCM7 K48 ubiquitylation and p97-dependent extraction at an interstrand crosslink through a reaction analogous to, but regulated differently from, termination-coupled unloading [403]. Lesion-associated unloading therefore shares components with the S-phase termination route while responding to a distinct DNA substrate and repair decision.

Mitotic clearance is also stage restricted. In Xenopus extracts and *C. elegans*, mitotic TRAIP-dependent MCM7 ubiquitylation converges on p97/VCP-mediated CMG extraction [404, 405]. The chain architecture differs from the S-phase route: TRAIP builds K6- and K63-linked chains on Mcm7 [405]. TRAIP can bind terminated replisomes during S phase without ubiquitylating them; CDK phosphorylation activates TRAIP-dependent unloading in mitosis [406]. Binding is thus not equivalent to pathway execution, and the mitotic reaction should not be narrated as uncontrolled continuation of S-phase unloading.

Deubiquitylases and delayed-clearance routes further delimit when extraction is allowed. Mammalian USP37 binds CDC45 and counteracts CUL2-LRR1-dependent CMG ubiquitylation [407]. In human cells and Xenopus extracts, USP37 has been proposed to prevent TRAIP-dependent unloading when converging forks stall at DNA-protein crosslinks or under topological stress [408]. In *dia2*-deficient budding yeast, old CMGs that persist into the next S phase are removed through an Rrm3-dependent route with likely Pif1 backup, whereas newly assembled CMGs remain when their ubiquitylation is defective [409]. In human cells, USP7 loss increases chromatin-bound MCM and impairs its dissociation in mid-to-late S phase; USP7 and MCM-BP were proposed to promote unloading near the end of S phase [410]. These routes may clear persistent CMG, but they have not been shown to execute the normal Dia2 or CUL2-LRR1 reaction.

The resulting architecture is stage and substrate dependent. A review of eukaryotic replisome disassembly distinguishes the S-phase termination pathway from additional mitotic and repair-associated routes in higher eukaryotes [411]. The excluded DNA strand occludes the Dia2/LRR1 E3-binding face on elongating CMG [29], whereas in Xenopus extracts DNA removal or digestion triggers CMG ubiquitylation [26]. Crosslink geometry changes the processing enabled by CMG removal [400], TRAIP chain length selects repair-associated outputs [402], and mitotic CDK activates a TRAIP route for replisomes that persist [404, 406]. Different DNA contexts are associated with distinct ubiquitin outputs that converge on Cdc48- or p97-dependent extraction in the named yeast and metazoan systems.

## 6. Unlinking replicated products

Completion of nucleotide incorporation does not guarantee physical separation. Pulse-labeled SV40 DNA passes through multiply intertwined catenated dimers before mature monomers appear [21]. Electron microscopy of ColE1 preparations likewise identifies catenated oligomers alongside active replication intermediates, including a catenane in which one linked circle is still replicating [20]. During hypertonic treatment of SV40-infected cells, completed daughter circles accumulate as highly intertwined catenated dimers that still require topological separation [412]. A free *Trypanosoma* kinetoplast minicircle intermediate was instead assigned as a trefoil knot using electrophoretic and sedimentation behavior, restriction and topoisomerase responses, and electron microscopy [413]. Catenanes and knots are therefore physical product states, not synonyms for failed chromosome movement.

### 6.1 Geometry determines where links form and which links are visible

Partly replicated bacterial circles can carry torsional stress as positive supercoils ahead of a fork or as right-handed precatenanes behind it in an in vitro theta system [1]. Two Tus-arrested plasmid preparations directly partition supercoils into the unreplicated region and precatenanes into the replicated region [2, 3]. In Xenopus plasmid replication, Topo II can unlink DNA by removing precatenanes behind the forks and is required for product unlinking but not for complete template replication [7]. The shrinking parental duplex and the replicated region can thus carry different topological burdens at the same time.

Replication can also produce knotted sisters, and two bacterial plasmid studies place Topo IV on that substrate [414, 415]. Knot number and complexity increase as the replicated bubble grows [414], while separate genetic and physical analysis assigns Topo IV both knot-forming and later unknotting activities, with inadvertent knot formation proposed when fork progression is impaired [415]. These results make substrate identity consequential: a reaction that simplifies a catenane need not have the same effect on a knotted replication bubble.

Models propose how type IIA topoisomerases might discriminate among these geometries, but they do not establish a cellular route. Two simulation studies make geometry, rather than catenation alone, the source of selective strand passage [416, 417]. One reproduces an unlinking advantage only after features of type IIA catalysis are included [416]; the other proposes that Topo IV recognizes crossings that permit decatenation and unknotting without indiscriminate supercoil relaxation [417]. A free-energy model instead predicts that supercoiling can increase the cost of catenation and thereby favor link removal [418]. Geometric analysis of anomalous electrophoretic migration supports the more limited proposal that freshly replicated circles may contain hemicatenanes as well as ordinary catenanes [419]. Each model identifies a possible selectivity principle; none establishes which structure predominates in an unperturbed chromosome.

### 6.2 Biochemical capacity does not by itself establish physiological rank

Purified bacterial reactions reveal several routes to monomer products. A two-stage model assigns Topo IV a critical role in the second stage of unlinking in its bacterial replicon system [420]. In purified *E. coli* theta systems, Topo III can decatenate daughter molecules to monomers without gyrase [421, 422]. One preparation shows complete decatenation under oriC and pBR322 conditions in which gyrase is inefficient [421]. In oriC and pBR322 reactions with a matched comparison, Topo IV stimulates monomer formation sevenfold to tenfold while gyrase is ineffective under the tested conditions [423]. Purified gyrase can nevertheless decatenate multiply linked pBR322 daughter dimers distributively in another preparation, with activity depending on supercoiling, salt, and HU [424]. These results establish capacity and an assay-bounded comparison. They do not support a universal rank order across substrates or conditions.

Cellular evidence adds access, localization, and genetic compensation. In *Escherichia coli*, Topo III can restore timely decatenation in Topo-IV-defective cells and remove precatenanes in vitro [425]. It normally assists Topo IV at or near replication forks, where it acts on catenated and precatenated rings [426]. Topo IV has a distinct cellular case: localization places it behind replication forks [427], while selective quinolone inhibition accumulates replication catenanes that resistant Topo IV prevents [428]. Together, these observations support removal of inter-DNA links behind *E. coli* forks [427, 428]. As plasmid catenanes are progressively unlinked, their negative supercoiling increases [429]. Physiological rank must therefore name the organism, substrate, comparator, and endpoint.

### 6.3 Circular products expose late topological states

Circular bacterial and phage templates make residual links countable. At high salt, late ColE1 intermediates retain parental strands intertwined once near the origin; at lower salt, they convert to daughter monomers or singly linked catenanes [430]. Two purified lambda replication systems complete a round with intertwined or catenated daughter circles [431, 432]. These products show that complete replication and complete unlinking can be separated experimentally, but they do not specify the corresponding order on a linear chromosome.

SV40 provides a more resolved set of late states. Under conditions that expose a topological block, termination-region sequence influences whether catenated replicated dimers accumulate [433, 434]. One study contrasts those dimers with gapped monomers [433]; the other reports sequence dependence only when Top2 activity is reduced by hypertonic treatment, not during normal growth [434]. In cell-free SV40 replication, Topo II is uniquely required for daughter decatenation even though either Topo I or Topo II can support fork propagation [435]. ICRF-193 accumulates catenated dimers and late Cairns intermediates while also impairing final-duplex unwinding [436]. The latter drug therefore affects more than one late reaction and cannot alone establish an unperturbed temporal sequence.

Topoisomerase inhibition across SV40 systems accumulates late or catenated daughter products rather than monomeric minichromosomes [437, 438, 439]. Recovery experiments then distinguish a reversible linked state from irreversible failure. The arrest is reversible in one inhibitor series [438], and C-family catenated dimers produced by ICRF-193 separate into monomers after drug removal [439]; VM26 establishes the blocked conversion without the same recovery assignment [437]. Combined topoisomerase inhibition in SV40 and yeast plasmids instead generates nearly complete molecules with shifted or dispersed apparent termination positions [440]. The first set tracks linked replicated products, whereas the last also shows that topological perturbation can change where late intermediates are recovered.

Structural endpoint assignments impose further boundaries. Fully replicated SV40 circles can remain joined at a single-strand bridge in the termination region, but that structure does not distinguish a hemicatenane from a Holliday junction [441]. Latent EBV genomes progress from theta circles early in S phase to catenated dimers late in S phase [442]. Newly completed, already segregated SV40 monomers are initially one or two linking numbers more relaxed than mature viral DNA [443]. That last change concerns monomer supercoiling after segregation, not a residual link between daughters.

### 6.4 Genome architecture changes the physiological unlinking problem

Yeast minichromosomes tie enzyme requirement to circular geometry. Top2 impairment produces catenated circular minichromosome dimers in yeast [444, 445]. In the fission-yeast mutant, the catenated ARS-plasmid accompanies chromosome-separation failure [444]; synchronized budding-yeast mutants accumulate multiply intertwined 2-micron dimers [445]. Positive supercoiling of catenated yeast plasmids directs Top2 toward decatenation before relaxation [446], and Cdc5 and Cdc14 promote timely catenane resolution through Top2 regulation [447]. Yet most sister minichromosomes examined after S phase and before anaphase were not topologically interlocked [448]. More decisively, Top2 loss causes catenated final products on circular minichromosomes, whereas comparably small linear YACs can complete replication and segregate without Top2 [449]. Interphase catalytic inhibition also traps inactive Top2 near heterochromatin and produces unresolved catenates, although the experiment does not show that every linkage joins newly replicated sisters [450]. Circularity therefore changes both the trapped substrate and the apparent requirement.

Kinetoplast studies recover catenated minicircle dimers [451, 452, 453]. In free *Trypanosoma cruzi* minicircle DNA, physical properties only suggest late formation [451]. TbPIF1 depletion in *T. brucei* reduces other intermediates while accumulating multiply interlocked, covalently closed dimers also seen after mitochondrial Topo II depletion [452]. In *T. equiperdum*, etoposide produces radiolabeled, multiply interlocked daughter-minicircle catenanes as late replication intermediates [453]. All three systems expose links between circular daughter products, but they differ in whether late formation is inferred or recovered after perturbation.

Mitochondrial DNA adds evidence for hemicatenane resolution but not one universal product sequence. Three studies connect mammalian TOP3A to mtDNA termination-intermediate resolution or decatenation [454, 455, 456]. Depletion stalls forks, increases catenation, and impairs intermediate resolution in one system [454], while a separate analysis finds broader replication roles for both TOP3A and TOP1MT [455]. Human mitochondrial TOP3A resolves a replication-termination hemicatenane at the heavy-strand origin, enabling mtDNA decatenation and nucleoid separation [456]. Other perturbations change the recovered structures without establishing this sequence. Mirin alters supercoiling and accumulates hemicatenated termination intermediates independently of MRE11 [457], whereas TFAM dosage correlates in opposite directions with termination intermediates and decatenation [458]. In two TOP3A-patient muscle samples, high-molecular-weight species were consistent with hemicatenated products and were removed by T7 endonuclease I, supporting but not proving that assignment [459]. At fission-yeast telomeres lacking Taz1, a different impeded geometry produces entanglements whose removal is promoted by long-lived Top2 reaction intermediates rather than the usual completed catalytic cycle [460].

### 6.5 Covalent chromosome dimers require a different unlinking reaction

Not every direct DNA linkage is a topoisomerase substrate. XerCD-*dif* resolves recombination-generated *E. coli* chromosome dimers [461, 462], and FtsK activates that resolution reaction while also facilitating decatenation [462]. In vivo, XerCD-*dif* or Cre-*loxP*, combined with FtsK translocation, can unlink bacterial chromosomes, although the experiment does not establish one universal replication-stage geometry for those links [463].

Topology constrains the route taken by this recombination machinery. Mathematical analyses favor progressive simplification of linked substrates [464, 465]. In the absence of Topo IV, XerCD-*dif*-FtsK can remove replication-generated links through local reconnection, with minimal routes most probable [464]; the model identifies a stepwise route that strictly reduces complexity at each step [465]. XerCD plus FtsK directionally decatenates DNA circles in vitro, but a role in removing the final replication catenation links in vivo remains proposed rather than directly timed [466]. These reactions demonstrate that unlinking capacity depends on both molecular geometry and the permitted strand-transfer chemistry.

## 7. Failure reveals which handoff broke

A failed endpoint is informative only when it can be connected to the substrate that persisted. Recurrent synthesis after fork fusion points to a failure to extinguish replication competence. Breakage after convergence with a damaged fork points to a failure of substrate protection or processing. DNA synthesis in mitosis or daughter cells points to a completion delay, but not necessarily to the same molecular lesion in every locus. These branches should remain separate because their shared downstream consequences do not establish a shared upstream mechanism.

### 7.1 Fork fusion can fail to extinguish replication competence

Fork fusion can trigger new replication in *E. coli* [467, 468]. One study detects local re-replication of DNA that has already been copied [467], while the RecG-deficient system places pathological replisome assembly and new initiation at collisions between opposing forks [468]. RecG also processes fork-fusion intermediates, and origin-independent forks can reach the normal termination region [469]. These results establish collision-linked restart under defined failure conditions, not a requirement for recurrent initiation during normal termination.

The amount and location of extra replication depend on the number of forks and on the perturbation. RecG loss increases regional amplification in *E. coli* [470, 471]. The termination signal is especially strong when cells carry an additional origin [470], whereas amplification near both origin and terminus does not by itself identify a fork-fusion mechanism [471]. RecG-deficient cells also accumulate extra forks and branched DNA, but the proposed sequence from collision to a 3′ flap and then PriA-dependent re-replication was not directly visualized [472]. The consequential uncertainty is therefore structural: a 3′ flap could be a routine transient normally removed by RecG-dependent processing, or an abnormal branch enriched only after that processing fails.

Repair and topoisomerase mutants produce related copy-number phenotypes through additional routes. Topo III has been proposed to cooperate with RecG on RecA-generated D-loops during double-strand-end repair, thereby preventing terminus amplification and promoting completion [473]. In specified *topA topB* mutants, R-loop-dependent replication is proposed to increase the number of forks trapped at Ter/Tus barriers and drive RecA-dependent amplification [474]. After UV irradiation, delayed forks that converge in the terminus appear to impair completion and transiently over-replicate the region [475]. Three spontaneous fragile sites in the *E. coli* termination region accumulate recurrent Holliday junctions and breaks, with barrier-associated collapse and mechanical shearing of unsegregated sisters offered as break mechanisms [476]. These mutant, repair, and damage settings reveal several routes to a similar regional signal, so copy-number gain cannot identify the broken handoff by itself.

### 7.2 Damaged-fork convergence creates repair substrates

Convergence can rescue or destabilize a perturbed fork, depending on its state. Homologous-recombination factors preserve blocked yeast forks so that an incoming fork can converge [477, 478]. In fission yeast, Rad52 and Rad51 protect terminally arrested forks so that convergence can occur [477]. In the budding-yeast camptothecin system, protected blocked forks merge and the fused structures then require Mus81-dependent resolution [478]. A collapsed barrier fork creates a different branch in fission yeast. Rad52-, Exo1-, and Mus81-dependent inter-fork strand annealing can delete repetitive DNA [479], whereas Fml1-MHF suppresses that route in part through a fork-restoration activity demonstrated on regressed substrates in vitro [480]. In the same fission-yeast system, merging a canonical fork with a reversed, barrier-stalled fork can instead generate excess DNA that is excised and ectopically integrated [481]. These outcomes identify processing after perturbed convergence, not the chemistry of an ordinary fork encounter.

Lesion structure further changes the rescue route. In Xenopus extracts, a leading-strand abasic lesion can be bypassed before convergence or when an incoming fork triggers termination [482]. ATR activity reduces breakage when a functional SV40 fork converges with a stalled fork [483]. The former identifies two routes around one lesion in an extract; the latter assigns checkpoint protection during stressed convergence. Neither can be generalized to a lesion-free fusion event.

Viral and locus-specific systems expose failures at later handoffs. Human Topo I increases the yield of finished circular products in an SV40 T-antigen in vitro system [484]. In a human-cell-derived synthesome assay, doxorubicin inhibits an operationally defined termination stage, whereas ara-CTP and camptothecin predominantly affect earlier stages [485]. The HPV11 E1-UAF1-USP1 interaction is required to complete bidirectional theta replication, while a Fanconi-pathway role in daughter separation is suggested rather than demonstrated [486]. In the PhiX174 in vitro pathway, C protein reduces multimeric and sigma products generated when coupled termination and reinitiation are skipped; slowing at the origin is the proposed explanation [487]. At budding-yeast rDNA, SLX1-SLX4 is required for completion when SGS1-TOP3 is absent, while terminal decatenation by Sgs1-Top3 and cleavage of stalled forks by Slx1-Slx4 remain proposed substrate assignments [488]. Each assay isolates a late failure, but their terminal substrates and causal strengths differ.

### 7.3 Delayed completion follows several cell-cycle routes

Persistence of synthesis beyond S phase occurs in several human settings [489, 490, 491]. Transcription start sites can remain under-replicated until G2/M and finish after RNA polymerase II is removed [489]. Under mild replication stress, RAD51- and RAD52-dependent synthesis continues through G2 and the G2/M transition [490]. Double-fork stalls can persist as unreplicated DNA through mitosis, followed by complementary-strand synthesis and resolution in daughter cells [491]. The first route is tied to transcriptional obstruction, the second to stress-responsive late synthesis, and the third to inheritance of an unresolved double stall.

Fragile-locus experiments explain why some regions reach those late states. FRA3B can remain incomplete when forks are slowed [492, 493]. In lymphoblastoid cells, its initiation-poor 700-kb core requires long fork travel, whereas fibroblasts use a different initiation program [492]; FISH timing indicates that some aphidicolin-treated cells enter G2 before the tested FRA3B sequences complete replication [493]. At 1p31.1 and 3q13.3, FISH/BrdU profiling indicates incomplete replication of fragile alleles in the tested fetal-lung fibroblasts even without exogenous stress, unlike lymphocytes [494]. Polymerase eta provides a direct synthesis safeguard at common fragile sites by copying non-B DNA during S phase and preventing under-replicated DNA from persisting into mitosis [495]. Initiation density, cell type, fork speed, sequence structure, and polymerase capacity can therefore determine whether completion is deferred.

Mitotic DNA synthesis also has substrate-specific requirements. Two human common-fragile-site studies place MUS81 and POLD3 in the MiDAS reaction [496, 497]. RAD52 is required for MiDAS and for their timely recruitment in one study [496], while entry into mitotic prophase recruits MUS81 and promotes POLD3-dependent synthesis at incompletely duplicated loci in the other [497]. MutS beta facilitates MiDAS in the tested common-fragile-site contexts [498], while TopBP1 recruits the SLX4 nuclease scaffold to under-replicated DNA to promote mitotic synthesis [499]. These factors occupy different positions in substrate recognition, cleavage, and synthesis; their shared effect on MiDAS does not make their biochemical roles interchangeable.

The dependencies change at other loci and under other perturbations. MiDAS is detected beyond common fragile sites [500, 501]. In human cells, folate deprivation induces a RAD51-, SLX1-, and POLD3-dependent route at FRAXA whose failure causes instability and missegregation [500]; human telomeres in the tested cancer-cell systems also undergo MiDAS, without establishing an identical pathway [501]. In human cells under mild stress, RAD51 protects under-replicated mitotic DNA and supports MiDAS before anaphase [502]. Structure-selective nucleases act differently after other perturbations. Both Chk1-depleted cells and common fragile sites place Mus81-family nucleases on mitotic completion intermediates [503, 504]. In Chk1-depleted cells, Mus81-Eme1 cleaves nascent DNA synthesized during MiDAS [503]; at common fragile sites, MUS81-EME1 and ERCC1 process persistent replication intermediates or under-replicated DNA, and their depletion increases anaphase bridges [504].

Late completion is not restricted to experimentally stressed mammalian cells. Budding yeast can enter mitosis before all replication is complete [505, 506]. In *smc5-smc6* mutants, the strongest delays occur at rDNA and other natural impediments [505]. In 20% to 40% of unperturbed cells, final synthesis at subtelomeric and other difficult loci occurs during anaphase after cyclin-Cdk activity falls [506]. Human 53BP1 nuclear bodies provide a later route still, enabling completion of inherited under-replicated DNA in daughter cells through altered replication timing and repair-pathway choice [507]. A late synthesis signal must therefore be assigned to its locus, perturbation, and cell-cycle stage before it can diagnose which completion handoff failed.

## 8. Decisive unresolved mechanisms

The first unresolved mechanism is the structure of an unperturbed bacterial fork-fusion intermediate. RecG-deficient cells support a model in which collision generates a 3′ flap that can seed PriA-dependent replication, but that complete structure-generating sequence was not directly visualized [472]. Opposing-fork collisions do trigger pathological replisome assembly and new replication when RecG is absent [468]. One alternative is that a short flap is a normal transient that RecG and exonucleases usually remove. Another is that the branched substrate is created or stabilized only after normal processing has failed. Direct, time-resolved structural capture immediately before and after a wild-type fusion, followed by the same measurement after acute RecG loss, would discriminate a constitutive intermediate from a mutant product. The answer matters because the first model places branch processing within normal termination chemistry, whereas the second places it in quality control.

A second question is whether the location called a terminus controls completion or merely records where other timing programs bring replication to an end. In *Vibrio cholerae*, similar terminus copy numbers on the two chromosomes and crtS-dependent changes in inferred synchrony connect termination timing to initiation timing [508]. In slowly growing *Helicobacter pylori*, fluorescence places replisome termination or resolution near midcell beside the septum [509]. Human heart mtDNA presents yet another architecture: some initiation occurs away from the heavy-strand origin, while that origin acts as a terminus [510]. These observations admit at least three explanations for positional regularity: inherited origin timing, active spatial coupling to cell organization, or an asymmetric origin-to-terminus program. A matched assay that records the last synthesis event, replisome disappearance, and product state with both spatial and temporal resolution would determine which layer is positioned in each system. Without that distinction, a terminus map cannot reveal whether encounter geography or post-encounter chemistry is regulated.

The third question is what molecular event licenses CMG removal. Structural evidence supports exposure of a Dia2 or LRR1-binding face when the excluded DNA strand no longer masks CMG [29], while Xenopus extracts show that fork-shaped DNA suppresses ubiquitylation until convergence [26]. Yet exposure of the ligase-binding face, loss of fork geometry, E3 recruitment, achievement of a ubiquitin-chain threshold, and engagement by p97 could be separable checkpoints. Defined CMG substrates that vary only the DNA emerging from the helicase should therefore be tested in one preparation for E3 binding, Mcm7 chain architecture, and p97 extraction. Comparing those results with CDK-activated TRAIP unloading in mitosis would reveal whether S-phase and mitotic routes read the same geometry or merely converge on the same unfoldase [404, 406]. This distinction explains how premature unloading is avoided during elongation and how a persistent replisome becomes removable after S phase.

The fourth question concerns reaction order after the last parental interval disappears. Xenopus assays establish that leading strands pass and ligate before CMG unloading [25], and a separate Xenopus plasmid assay shows that Topo II can remove precatenanes while complete replication still occurs when unlinking is blocked [7]. Those results leave three live alternatives for product unlinking: it may precede ligation, follow CMG extraction, or proceed in parallel with both. High-resolution AFM with automated tracing can quantify stalled Xenopus theta structures and late products [511], but topology, strand continuity, and CMG occupancy must be measured in the same time course to order the transitions. The order matters because it defines which DNA geometry is presented to Topo II and whether retained CMG constrains the final link.

Finally, a factor associated with late replication must be separated from indirect effects on fork movement, cell-cycle timing, or repair. In budding yeast, the Nse6-Smc6 neck interaction is important for repair-intermediate resolution but dispensable for the tested replication-termination endpoint [512]. Conversely, Cdh1 depletion in mammalian cells slows forks, reduces the measured frequency of termination events, and changes S-phase timing [513]. The alternatives are a direct termination reaction, an indirect change in how often or when forks meet, and a repair function that becomes visible only after failure. Acute, stage-specific perturbation combined with a physical terminal-substrate assay would distinguish these possibilities more sharply than event counts or downstream segregation phenotypes alone. Resolving this issue is necessary to assign factors to a handoff rather than to the cellular consequences of missing it.

## 9. Conclusions

Replication termination is an ordered change in DNA and replisome state, not merely the coordinate at which two forks meet. A shrinking parental interval must cease to support fork progression, nascent strands must become continuous, the helicase must lose its elongating DNA geometry and be removed, and direct links between products must be resolved. These transitions can be coupled without being simultaneous.

The Xenopus experiments show how such coupling can work. Leading strands pass and ligate before CMG unloads. Across separate studies, loss of fork-shaped DNA permits Mcm7 ubiquitylation and p97-dependent extraction follows; the complete sequence has not been timed in one assay. Product unlinking is a separately measured reaction whose position relative to ligation and CMG removal remains unknown. Yeast and metazoan studies support related recognition and extraction principles, while lesion-associated and mitotic pathways use different triggers and ubiquitin outputs.

Genome geometry explains why the remaining handoff can look different across systems. Circular substrates expose catenanes, knots, and hemicatenanes directly. In linear-chromosome studies, unresolved topology may instead be visible indirectly through segregation phenotypes. Programmed barriers position an encounter but do not finish synthesis, and late synthesis can reflect transcription, sparse initiation, difficult sequence, damage, or inherited under-replication. Failure is therefore mechanistically informative only when the persisting substrate and cell-cycle stage are known.

The decisive unknowns are the native bacterial fork-fusion structure, how final torsional stress is partitioned between the parental interval and daughter precatenanes, the minimal DNA change that licenses helicase removal, and the order of strand closure, replisome extraction, and unlinking. Resolving them will show how genome architecture selects among different routes to the same biological endpoint: DNA that no longer supports a replisome and daughter molecules that can be inherited separately.

## Evidence-label legend

`[F-T]`: complete exact primary-source full text was inspected and used for every claim attributed to the manifestation. `[PAR]`: an exact identifier-matched target-paper passage was inspected, but complete primary full text was not used. `[ABS]`: claims use only the validated exact target abstract. `[SEC]`: a review or other secondary source is used for framing or explicitly attributed one-hop support.

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