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Concatemer

A concatemer is a long, continuous DNA molecule composed of multiple copies of the same genetic sequence linked end to end in a head-to-tail arrangement.^[1] These structures form through the self-ligation of monomeric DNA units, producing oligomers that vary in size depending on the replication context.^[1] Concatemers are a key feature in molecular biology, particularly as replication intermediates in certain viruses and cellular processes.^[2] In viral DNA replication, concatemers serve as precursors to mature genomes, where linear or circular viral DNAs are concatenated during synthesis and later cleaved at specific sites for packaging into virions.^[3] For instance, in bacteriophage T7 replication, concatemers arise from rolling-circle mechanisms, resulting in double-helical molecules with 3'-ended tails that are processed into unit-length genomes.^[4] Similarly, bacteriophage lambda produces concatemers in its late replication stage, comprising tandem repeats that constitute up to 60% of intracellular DNA before resolution.^[5] In herpesviruses, such as herpes simplex virus type 1 (HSV-1), replication generates head-to-tail concatemers from initially circularized genomes, which are essential for subsequent cleavage and packaging by viral enzymes recognizing terminally redundant sequences.^[6] Beyond viruses, concatemers appear in mitochondrial DNA transmission in yeast, where they facilitate homoplasmy by propagating selected mtDNA clones, and in transgenic DNA integration, where injected molecules often form tandem repeats.^[7]^[2] The formation and processing of concatemers highlight recombination-dependent mechanisms in DNA metabolism, influencing genome stability and viral propagation.^[8] Studies of these structures have advanced understanding of replication strategies, with implications for genetic engineering and antiviral therapies targeting concatemer resolution.^[9]

Definition and Characteristics

Definition

A concatemer is a long continuous DNA molecule consisting of multiple copies of the same genetic sequence linked end-to-end in a head-to-tail orientation, resulting in linear or circular multimers of varying lengths. These structures arise from the polymerization of monomeric DNA units, often through processes like self-ligation or replication intermediates, and are characterized by their tandem repetition of a defined genome segment.^[1]^[10] The term "concatemer" derives from the Latin root concatenare, meaning "to link together," reflecting the chained arrangement of repeated sequences. It was introduced in molecular biology during investigations into viral DNA replication in the 1960s and early 1970s, particularly in the context of bacteriophage studies where such multimers were identified as key intermediates. Seminal work on phages like lambda highlighted concatemers as precursors to mature viral genomes, essential for packaging into virions.^[11] Concatemers differ from related DNA structures such as plasmids, which are typically monomeric and form closed circular molecules without tandem repeats, or general multimers/oligomers, which may not imply specific head-to-tail genome duplication. Instead, concatemers emphasize the repetitive, serial linkage of identical units, often exceeding the size of a single genome to facilitate biological processes like viral maturation.^[1]^[12]

Structural Features

Concatemers consist of tandemly repeated unit-length genomes linked in a continuous DNA molecule, typically observed in viral replication intermediates.^[13] Most viral concatemers adopt linear forms, comprising head-to-tail chains of genomic units with terminal redundancy at the ends and junctions.^[14] Circular concatemers, however, arise in certain synthetic biology applications, such as rolling-circle amplification from circular templates, and in mitochondrial DNA contexts where recombination or replication yields closed-loop multimers.^[1] Terminal redundancy features overlapping nucleotide sequences at the termini of each unit genome within the concatemer, typically spanning 2-10% of the genome length in bacteriophages like T4, where it measures about 3-5 kb on a 169 kb genome.^[15]^[16] Concatemer size varies widely, ranging from dimers (two unit genomes) to large oligomers comprising hundreds of units, depending on the replication system; for instance, herpes simplex virus 1 concatemers vary in size, with many intracellular replication intermediates sub-unit length (median ∼34 kb or 0.22 units), though longer forms up to several units occur.^[17] Junction sequences in concatemers maintain head-to-tail orientation without inversions, incorporating specific nucleotide overlaps for structural stability, as seen in herpesvirus type II genomes with single-repeat junctions of about 1 kb.^[14] These structures are visualized through techniques such as pulse-field gel electrophoresis, which reveals high-molecular-weight smears indicative of large linear multimers, and electron microscopy, which displays them as extended linear threads.^[18]^[19]

Biological Role

In Viral Replication

Concatemers play a crucial role in the replication of viruses with linear double-stranded DNA genomes, serving as essential intermediates that facilitate genome amplification and packaging into virions. In these viruses, concatemers are long, head-to-tail multimers of the viral genome formed during replication, allowing for the production of multiple unit-length genomes from a single template. This process is particularly vital for overcoming challenges associated with linear DNA replication, such as incomplete filling of the 5' ends during lagging-strand synthesis.^[20] For viruses like herpesviruses and adenoviruses, concatemers address the end-replication problem by providing excess DNA at the termini, ensuring that full-length genomes can be generated despite the limitations of host or viral polymerases.^[20] In herpesviruses, such as herpes simplex virus (HSV), the linear genome circularizes upon entry into the host cell, initiating recombination-dependent replication that yields concatemeric intermediates consisting of multiple head-to-tail linked units. Similarly, in adenoviruses, wild-type replication avoids excessive concatenation, but E4 region mutants accumulate defective concatemers due to dysregulated DNA end-joining by host factors like DNA-PK and NHEJ proteins, highlighting the necessity of viral proteins in preventing aberrant multimers. These concatemers supply the terminal redundancy required for complete replication of genome ends.^[6]^[20] Concatemers also enable efficient genome amplification by acting as extended templates for multiple rounds of transcription and replication, thereby increasing viral yield within infected cells. In poxviruses, such as vaccinia virus, replication occurs in cytoplasmic factories and involves recombination events that generate concatemers, potentially through rolling-circle mechanisms, which support high levels of DNA synthesis and progeny production. These multimers contain head-to-head and tail-to-tail junctions, allowing sustained replication independent of specific origins. During late stages of the viral life cycle, concatemers serve as precursors for packaging, where unit-length genomes are excised via site-specific cleavage—often at packaging signals—to ensure full-length encapsidation into capsids. For instance, in bacteriophage T7, concatemers form through recombination at terminal redundancies and are typically 1.5 to 5 times the length of a single genome unit, providing substrates for terminase-mediated cutting during head-filling.^[21]^[22]^[23] The formation of concatemers confers an evolutionary advantage to viruses with terminally redundant genomes, such as herpesviruses and T7, by preserving sequence integrity across replication cycles and enabling robust propagation in diverse host environments. This strategy compensates for the inherent instability of linear ends, allowing viruses to maintain essential terminal sequences critical for replication initiation and packaging efficiency. In HSV, for example, concatemers can comprise up to dozens of genome units, supporting high-titer infections, while in adenovirus E4 mutants, the accumulation of defective multimers underscores the selective pressure for precise regulation to avoid replication defects. Overall, concatemers thus optimize the viral life cycle for efficient dissemination.^[24]^[25]^[26]

In Cellular Processes

In eukaryotic cells, concatemeric mitochondrial DNA (mtDNA) plays a crucial role in maintaining genome stability and ensuring proper inheritance during cell division. In the yeast Saccharomyces cerevisiae, the mitochondrial recombinase Mhr1p facilitates the formation of concatemeric mtDNA structures, which are essential for the transmission of mtDNA to daughter cells. These concatemers allow for the selective packaging and segregation of mtDNA clones, promoting homoplasmy—the state where all mtDNA molecules within a cell are identical—and preventing the accumulation of heteroplasmic variants that could disrupt mitochondrial function.^[7] This process is particularly important in budding yeast, where mtDNA is distributed asymmetrically, and Mhr1p-dependent recombination generates linear concatemers that mimic phage-like packaging mechanisms to ensure equitable inheritance.^[27] Concatemeric DNA intermediates also contribute to programmed genome rearrangements in certain protozoan eukaryotes, such as ciliates. During macronuclear development in Paramecium tetraurelia, a ciliate model organism, internally eliminated sequences (IESs)—non-coding DNA segments targeted for removal—are excised and form circular concatemers composed of ultra-short DNA fragments (typically around 27 base pairs). These concatemers serve as templates for the transcription of small regulatory RNAs, including double-stranded RNAs that guide the epigenetic elimination of IESs from the somatic genome, thereby sculpting the expressed macronuclear genome essential for cellular differentiation.^[28] This mechanism highlights concatemers' role in facilitating precise DNA processing and heterochromatin formation, distinct from the linear IES release observed in related ciliates like Tetrahymena thermophila. In bacteria, concatemeric DNA forms infrequently but occurs in specific contexts related to plasmid maintenance and chromosomal recombination. Rolling-circle replication, a common mechanism for small, circular plasmids in species such as Staphylococcus aureus and Escherichia coli, generates linear concatemeric intermediates through unidirectional strand displacement, which are subsequently processed into monomeric circles to sustain plasmid copy number and propagation.^[29] Additionally, homologous recombination events can produce transient multimeric chromosomal forms, leading to concatemer-like structures that must be resolved by site-specific recombinases (e.g., XerCD in E. coli) to avoid segregation defects and maintain genome integrity during cell division.^[30] Concatemeric structures appear as transient intermediates in certain DNA repair pathways, particularly non-homologous end joining (NHEJ), though they are not the central outcome of repair. In NHEJ, which ligates double-strand breaks without a homologous template, multiple DNA fragments can be aberrantly joined to form head-to-tail concatemers, especially during transgene integration or in response to ionizing radiation in eukaryotic cells. For instance, in sea urchin embryos, NHEJ-mediated ligation of exogenous DNA results in concatemeric arrays at integration sites, illustrating how this pathway can concatenate compatible ends inefficiently under high DSB loads.^[31] These intermediates are typically resolved or degraded to prevent genomic disruptions, underscoring NHEJ's error-prone nature in favoring rapid repair over precision. Aberrant concatemer formation in cellular processes is implicated in pathological conditions, particularly those involving mitochondrial dysfunction and genomic instability. In mitochondrial disorders, uncontrolled mtDNA concatemerization—often triggered by oxidative stress or replication defects—can lead to heteroplasmy shifts and impaired energy production, as seen in models of ROS-induced rolling-circle replication that propagate mutant mtDNA clones. Such dysregulation contributes to diseases like mitochondrial encephalomyopathies, where excessive concatemers disrupt nucleoid organization and mtDNA maintenance. In broader eukaryotic contexts, faulty concatemer resolution during recombination or repair can exacerbate chromosomal instability, promoting aneuploidy and oncogenic transformations, as evidenced by mtDNA concatemers facilitating lymphoid cell proliferation in cancer models.^[32] These links emphasize the delicate balance required for concatemer processing to avert disease.

Formation and Processing

Mechanisms of Formation

Concatemeric DNA structures are primarily assembled through rolling-circle replication, a mechanism prevalent in viruses such as bacteriophages and herpesviruses, where a nick in the circular template initiates continuous strand displacement synthesis, yielding linear head-to-tail multimers.^[33] In bacteriophage T7, this process begins with a nick introduced in the double-stranded circular DNA, allowing T7 DNA polymerase (encoded by gene 5) to extend the 3' end while displacing the nontemplate strand, progressively elongating the concatemer with multiple genome units; the host RNA polymerase initially primes replication, but T7 polymerase takes over for high-fidelity elongation.^[33] Similarly, in herpes simplex virus type 1 (HSV-1), after initial theta replication produces circular daughter molecules, a switch to rolling-circle mode—facilitated by the viral helicase-primase complex (UL5, UL8, UL52) and DNA polymerase (UL30)—generates long concatemers essential for packaging, with the single-stranded DNA-binding protein ICP8 stabilizing intermediates and promoting strand annealing during recombination events that may contribute to elongation.^[34] In poxviruses like vaccinia virus, concatemer formation occurs via strand displacement synthesis driven by the viral DNA polymerase (E9L), which catalyzes the conversion of nicked or linear duplex substrates into high-molecular-weight head-to-tail concatemers without requiring a circular template; this process is enhanced by the viral primase-nucleotidyltransferase (D5R), which generates short oligoriboadenylate primers to initiate synthesis at nicks, leading to iterative displacement and annealing of newly synthesized strands.^[35] Although a dedicated viral DNA ligase (A50R) is present, it is nonessential for concatemer assembly, as host ligases can compensate, but the polymerase's intrinsic strand-transfer activity promotes the joining of replicated units through terminal redundancies during infection.^[36] Topoisomerases, including viral and host variants, alleviate torsional stress from supercoiling during these bidirectional replication events from multiple origins, ensuring processive concatemer elongation.^[36] Adenoviruses employ recombination-dependent mechanisms for occasional concatemer formation, where E4 region proteins (such as ORF3 and ORF6) regulate intermolecular recombination to either facilitate controlled viral genome joining or inhibit excessive host-mediated double-strand break repair that would otherwise produce aberrant multimers; mutants defective in the E4 region exhibit increased concatemer accumulation via nonhomologous end joining, highlighting the proteins' role in balancing recombination for efficient replication without pathological concatenation.^[37] In bacterial systems supporting phage replication, host recombinases like RecA can aid concatemer assembly by promoting homologous strand invasion and exchange at replication forks, particularly in recombination-proficient backgrounds.^[38] In vitro studies demonstrate concatemer formation using purified viral enzymes under controlled conditions, such as ATP-dependent reactions where vaccinia DNA polymerase and primase process linear DNA substrates into multimers via nick-initiated strand displacement and annealing, mimicking viral pathways without cellular factors.^[35] These systems underscore the minimal enzymatic requirements—polymerase for elongation, primase for initiation, and occasional ligase for sealing junctions—while topoisomerases prevent entanglement in elongated products.^[35]

Resolution into Monomers

The resolution of concatemers into individual monomeric genome units is a critical step in the maturation of viral and cellular DNA, enabling proper packaging into capsids or segregation into organelles. This process typically involves site-specific enzymatic cleavage at junction sequences, often coupled with packaging to ensure precise genome length selection and end generation for stability. In many systems, resolution is mediated by ATP-dependent molecular motors that recognize specific signals, such as packaging and cleavage (pac) sites, to excise unit-length genomes while avoiding aberrant fragments.^[39] In herpesviruses, site-specific cleavage is performed by the terminase complex, composed of the UL15, UL28, and UL33 proteins in herpes simplex virus type 1 (HSV-1), which recognizes pac signals at concatemer junctions to generate mature unit-length genomes with defined termini. The terminase's endonuclease activity, primarily from the UL15 subunit, initiates cuts at these direct repeat sequences, followed by ATP hydrolysis-driven translocation during packaging into preformed capsids. This process ensures sequential resolution and packaging, with the complex docking to the portal vertex for efficient genome insertion.^[40]^[41] Similarly, in bacteriophages such as lambda, packaging-coupled resolution involves the terminase enzyme (gpA and gpNu1 subunits) and portal protein (gpB), which sequentially cleave concatemers at cos sites while translocating DNA into the prohead. Terminase binds the cosN nick site, performs an initial stagger cut to generate 12-base sticky ends, and uses ATP to power packaging until a second cut at the downstream cos site terminates the process, yielding mature genomes with cohesive termini for circularization upon infection. This headful mechanism selects genomes slightly longer than one unit length, with terminase's ATPase activity coupling cleavage to translocation for high fidelity.^[39]^[42] Enzymatic requirements for resolution generally include ATP-dependent endonucleases within terminase-like complexes and associated ligases to process ends, as seen across diverse systems. For instance, in vaccinia virus (a poxvirus), late-gene products, including the A22R protein, a Holliday junction resolvase, are essential for cleaving concatemer junctions post-replication, requiring ATP for the site-specific recombination-like resolution at inverted terminal repeat sequences to produce monomeric genomes suitable for encapsidation.^[43]^[44] These late proteins act after initial replication, ensuring temporal control to prevent premature processing.^[43]^[44] Defects in resolution machinery can lead to persistent uncleaved concatemers, impairing packaging and reducing viral fitness. In adenovirus, mutations in early region 4 (E4) genes, such as ORF3, disrupt interactions with host DNA-dependent protein kinase (DNA-PK), allowing non-homologous end joining to form aberrant concatemers that are too large for efficient capsidation, thereby decreasing progeny yield and infectivity. This highlights the virus's reliance on modulating host repair pathways to prevent faulty joining and ensure proper monomer resolution.^[45]^[46] In cellular contexts, mitochondrial DNA (mtDNA) concatemers, arising from rolling-circle replication or recombination, are resolved into monomers during organelle segregation, primarily through homologous recombination or exonuclease digestion to maintain genome integrity and homoplasmy. Reactive oxygen species can accelerate this by promoting concatemer formation and subsequent recombination-mediated segregation, with exonucleases like those in the mitochondrial replisome trimming excess to yield standard circular monomers for distribution to daughter mitochondria.^[47]

Applications in Biotechnology

Synthetic Concatemers

Synthetic concatemers are artificially constructed nucleic acid structures generated in laboratory settings to facilitate biotechnological applications, such as gene assembly and nanotechnology. These structures mimic natural concatemeric forms but are engineered for precise control over length, composition, and functionality, enabling the creation of repetitive sequences that are challenging to synthesize chemically.^[48] In vitro synthesis of synthetic concatemers often employs rolling-circle amplification (RCA) or its controllable variant (CRCA) to produce long single-stranded DNA concatemers (lssDNAc). In CRCA, a padlock oligonucleotide is circularized using T4 DNA ligase and extended by strand-displacing polymerases like Bst 2.0, yielding concatemers up to 500–1000 base pairs in length by modulating reaction time and temperature. This method achieves high yields of 3–5 μg per 200 μL reaction and uniform products, with costs as low as ¥2–¥15 per assay, making it scalable for biotechnological construction.^[49] Ligation-based assembly methods further enable the construction of synthetic concatemers from oligonucleotides, particularly for repetitive genes. T4 DNA ligase efficiently joins short oligonucleotides as brief as 8 nucleotides, provided a minimum 5-base pair duplex overlap, allowing hierarchical assembly into genes up to 128 base pairs, such as beta-actin segments. For repetitive elements, enzymatic strategies like Golden Gate assembly split target genes into 70–80 bp synthons with 4 bp overhangs, enabling scarless ligation into full constructs up to 456 base pairs, overcoming limitations in direct chemical synthesis of repetitive DNA. Gibson assembly, a homology-based variant, complements these by seamlessly joining multiple fragments, supporting the creation of artificial repetitive sequences with high fidelity rates of 12.5–87.5% across clones. These approaches provide high uniformity and yield for engineering complex genetic elements.^[50]^[51] Hybrid RNA/DNA concatemers represent advanced synthetic structures formed by pairing oligonucleotides via phosphoramidite synthesis, resulting in A-form double helices confirmed by circular dichroism. Short linkers promote linear concatemer formation, while longer linkers yield self-limited complexes (bimolecular or tetramolecular) with programmable geometries, as analyzed through UV melting and gel shift assays. These hybrids are digestible by RNase H (in 10 ± 7 minutes) or imidazole, offering controlled disassembly, and serve as building blocks for nanotechnology applications like nanomachinery and therapeutic scaffolds due to their cost-effective design and structural versatility.^[52] In gene synthesis, synthetic concatemers are pivotal for assembling large repetitive sequences in vaccine design and protein engineering. Vector-enzymatic methods using Type IIS restriction enzymes like SapI and T4 ligase enable ordered head-to-tail multimerization of DNA fragments into concatemers encoding up to 500 repeats of peptide epitopes, such as TKPTDGNGP or RG1 motifs, enhancing immunogenicity in vaccines against pathogens like human papillomavirus. These concatemeric antigens improve stability and bioactivity, facilitating gradual release in therapeutic contexts and supporting tandem-repeat proteins for biomaterials. Overall, synthetic concatemers offer advantages in high yield, uniformity, and scalability, surpassing traditional synthesis limits for biotechnological innovation.^[48]^[53]

Research and Diagnostic Tools

Concatemers play a significant role in advanced sequencing technologies, particularly nanopore sequencing, where they facilitate the analysis of long-range chromatin structures. In this approach, DNA concatemers are ligated to capture multiple chromatin interactions and concurrent modification patterns in a single read, enabling the detection of higher-order features that are obscured in shorter-read methods. For instance, a 2019 study demonstrated that nanopore sequencing of chromatin concatemers revealed multi-way interactions comprising 41.83% of observed conformations in yeast, providing insights into spatial organization beyond pairwise contacts.^[54] In biosensing applications, DNA concatemers serve as signal amplifiers in fluorescence-based assays for biomolecule detection. These structures are formed through aptamer-mediated hybridization, creating extended chains that enhance fluorescence output upon target binding, thereby improving sensitivity and selectivity. A 2023 fluorescence aptasensor utilizing DNA concatemers achieved detection limits as low as 53 cells/mL for Acinetobacter baumannii, showcasing their utility in rapid pathogen identification without enzymatic amplification.^[55] Lambda phage concatemer DNA is widely employed as a size standard in gel electrophoresis, particularly for pulsed-field gel electrophoresis (PFGE), due to its uniform multimeric lengths ranging from 50 kb to over 1 Mb. This ladder provides precise calibration for resolving large DNA fragments in genomic analyses. Recent innovations, such as 3D-printed devices, have improved concentration and visualization of these concatemers by using polyacrylamide roadblocks to park DNA at interfaces, enhancing resolution in low-abundance samples.^[56]^[57] Synthetic concatemers are valuable models in viral research, mimicking natural replication intermediates to investigate DNA packaging mechanisms and defects. In vitro packaging assays with bacteriophage T4 using synthetic linear DNA concatemers have revealed the motor's promiscuity, allowing packaging of non-native sequences and highlighting conformational plasticity that contributes to packaging errors under stress. These systems also aid in identifying drug targets by simulating terminase-mediated cleavage and translocation defects in herpesviruses and phages.^[58]^[59] In diagnostics, detection of concatemeric mitochondrial DNA (mtDNA) forms via PCR offers insights into replication fidelity in mtDNA disorders. Abnormal concatemers, indicative of replication errors, can be amplified and sequenced to assess heteroplasmy and segregation defects. For example, in AIDS-associated lymphomas, PCR-based identification of mitochondrial genome concatemers has been linked to cellular dysfunction, supporting their role as markers for mitochondrial alterations in disease states.^[60] Recent studies (as of 2024) have also examined concatemers in gene editing applications, revealing frequent concatemeric insertions of adeno-associated virus (AAV) vectors during CRISPR-Cas9-mediated genome engineering. These findings provide insights into integration mechanisms, off-target effects, and strategies to enhance precision in therapeutic vector design.^[61]

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Dec 13, 2024 · In this paper, we analyzed the formation of hybrid RNA/DNA concatemers and self-limited complexes by a pair of oligonucleotides using UV melting, circular ...
[51]
Incorporation of RG1 epitope concatemers into a self-adjuvanting ...
Incorporation of RG1 epitope concatemers into a self-adjuvanting Flagellin-L2 vaccine broaden durable protection against cutaneous challenge with diverse human ...
[52]
A DNA concatemer-based fluorescence aptasensor for selective and ...
A highly sensitive and selective fluorescence aptasensor was constructed for the quantification of A. baumannii based on aptamer-mediated DNA concatemers.
[53]
[PDF] Lambda Ladder - DNA Size Standards - Bio-Rad
The lambda ladder consists of suc- cessively larger concatemers of λ cl857 Sam7. These DNA size standards may be used as size markers for CHEF, FIGE, and other ...Missing: 2023 | Show results with:2023
[54]
Concentration of lambda concatemers using a 3D printed device
Feb 17, 2023 · A bis-acrylamide roadblock was cured in a proof-of-principle 3D printed device to concentrate DNA at the interface between the roadblock and solution.
[55]
A Promiscuous DNA Packaging Machine from Bacteriophage T4
After headful packaging, the motor cuts the concatemeric DNA and dissociates from the DNA-full head (C). ... Streisinger G,Emrich J,Stahl M. M (1967) Chromosome ...
[56]
A coupled in vitro system for the formation and packaging ... - PubMed
Analysis of the DNA products from these in vitro reaction showed that concatemeric DNA is formed very efficiently by g1- g2- extracts but not by g1- g3.5- or g1 ...
[57]
Identification of Mitochondrial Genome Concatemers in AIDS ...
Taken together, our results suggest that formation of mtDNA concatemers is associated with oncogenic transformation in lymphoid cells. Keywords: Mitochondrial ...2.4. Pcr And Sequence... · 3. Results · 3.2. The El Cccdna Is Formed...