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Rolling circle replication

Rolling circle replication (RCR) is a unidirectional replication mechanism utilized by certain circular DNA and RNA genomes, such as those in plasmids, viruses, and viroids, in which a site-specific nick in one strand of the nucleic acid initiates continuous synthesis of a new leading strand by a polymerase, displacing the original nontemplate strand to produce single-stranded linear concatemers that can be further processed into double-stranded forms.^[1] First observed in the single-stranded DNA bacteriophage ΦX174, RCR was described in 1968 as a process generating multimeric tail-like structures during replication.^[2] The mechanism begins when a multifunctional initiator protein—typically a HUH endonuclease with a conserved catalytic tyrosine residue—binds to the double-strand origin (dso) and cleaves one strand via a reversible transesterification reaction, covalently attaching itself to the 5' phosphate end and exposing a 3'-OH primer for leading-strand elongation. This displacement synthesis continues around the circular template, extruding single-stranded nucleic acid that may form secondary structures or be packaged directly in some viruses, while lagging-strand synthesis occurs later at single-strand origins (sso) using host-encoded polymerases and primases.^[3] RCR is prevalent in bacterial plasmids (e.g., pT181 and pMV158 families), single-stranded DNA phages (e.g., M13 and ΦX174), archaeal plasmids, eukaryotic viruses like parvoviruses and adeno-associated virus (AAV), RNA pathogens such as viroids and hepatitis delta virus, and mobile elements such as integrative conjugative elements, enabling high-copy-number maintenance and facilitating horizontal gene transfer.^[1] Unlike bidirectional theta replication, RCR is asymmetric, generates single-stranded intermediates without requiring ATP hydrolysis for unwinding, and relies on the initiator's helicase-like activity for strand separation.^[3] The initiator proteins, often encoded by the replicating element (e.g., Rep proteins), are remarkably versatile, performing not only replication initiation but also roles in conjugation (as Mob proteins) or transposition (as Tnp proteins), which underscores RCR's evolutionary significance in genetic mobility and diversity.

Mechanism

DNA Rolling Circle Replication

Rolling circle replication is a mode of DNA replication in which a circular template, either double-stranded (dsDNA) or single-stranded (ssDNA), is nicked at a specific origin site, enabling continuous synthesis of a complementary strand from the exposed 3'-OH end while displacing the non-template strand as a linear tail. This process contrasts with bidirectional theta replication by producing long, linear concatemeric products rather than discrete circles, and it is prevalent in certain bacteriophages and plasmids. The mechanism relies on strand displacement to unwind the template without the need for extensive primer synthesis on the displaced arm, allowing processive replication over multiple genome lengths. The process initiates with site-specific nicking of the circular template by an endonuclease or initiator protein, such as the A protein in bacteriophage phiX174, which cleaves one strand at the double-stranded origin (dso) and forms a covalent bond between its active site tyrosine residue and the 5'-phosphate end. This generates a 3'-OH primer for DNA polymerase while leaving the 5' end attached to the protein. Elongation follows as the DNA polymerase, often the host's DNA polymerase III holoenzyme, extends the 3'-OH end processively, synthesizing a new strand complementary to the template and displacing the original non-template strand ahead of the replication fork. A helicase, such as the E. coli Rep helicase in phiX174 replication, facilitates strand separation by unwinding the duplex ahead of the polymerase, while single-stranded DNA-binding proteins (SSBs) coat the displaced strand to prevent reannealing. Topoisomerases, including DNA gyrase, relieve the positive supercoils generated during elongation to maintain fork progression.^[2]^[4] Termination occurs when the replication fork completes one or more genome rounds and returns to the origin, where the initiator protein catalyzes a second cleavage to regenerate the original nick site and release the displaced linear strand as a circular monomer via ligation or further processing. In dsDNA contexts, the displaced single strand can then undergo complementary strand synthesis to form a new dsDNA circle, completing the cycle. For ssDNA templates like those in phiX174, the process often produces multimeric tails that are resolved into unit-length circles. DNA ligase seals nicks in the regenerated template or newly formed circles to ensure covalently closed products. This resolution step may involve additional phage-encoded factors to regulate product length and prevent over-replication.^[5] Structurally, rolling circle replication features a characteristic sigma-shaped replication fork, resembling the Greek letter σ, where the circular template remains intact with an extending linear tail of the displaced strand, distinguishing it from the theta (θ) structure of bidirectional replication. In dsDNA circles, the mechanism transitions from an initial theta mode to rolling circle upon nicking, amplifying one strand asymmetrically. This sigma fork allows for high processivity, with the displaced arm serving as a scaffold for potential secondary synthesis.^[2]^[5] A canonical example is the replication of bacteriophage phiX174, an ssDNA phage with a 5.4 kb genome. Upon infection, the incoming +ssDNA circularizes and is converted to the dsDNA replicative form (RF I) through host-mediated complementary (-) strand synthesis primed at a single-strand origin (sso) by RNA polymerase or primase. The closed circular RF II then undergoes stage II replication via rolling circle mode: the phage-encoded A protein nicks the (+) strand at the dso, initiating displacement synthesis of a new (+) strand by host DNA polymerase III and Rep helicase, producing a long ssDNA (+) tail displaced from the RF template. The A protein terminates by cleaving at the origin after each genome length, regenerating the RF template and releasing ssDNA circles coated by SSBs; these ssDNA products are packaged into virions, while the persistent RF supports ongoing replication. This asymmetric process yields hundreds of ssDNA genomes per RF without net RF increase after initial rounds.^[4] The progression rate of the replication fork in rolling circle replication can be modeled using enzyme kinetics, where the strand displacement speed v is given by v = k \cdot [\text{polymerase}], with k as the catalytic constant (turnover number) of the polymerase under saturating dNTP conditions. This derives from the Michaelis-Menten equation for enzymatic velocity, v = \frac{V_{\max} \cdot [S]}{K_m + [S]}, where at high substrate concentration [S] \gg K_m, v \approx V_{\max} = k_{\text{cat}} \cdot [E]; here, k = k_{\text{cat}} represents nucleotides incorporated per polymerase molecule per second, and the fork speed scales linearly with enzyme concentration due to processive elongation without dissociation. For E. coli DNA polymerase III, typical k_{\text{cat}} values range from 500–1000 nt/s, enabling rapid tail extension in vivo.^[6] Illustrations of the mechanism typically depict: (1) the nicked circular dsDNA template with the initiator protein bound at the dso, showing the 3'-OH primer and attached 5' end; (2) the elongating structure with a sigma-shaped fork, polymerase and helicase advancing along the circle while generating a linear ssDNA tail; and (3) termination products as multimeric linear ssDNA or resolved monomeric circles, highlighting the regenerated template for iterative cycles.

RNA Rolling Circle Replication

RNA rolling circle replication is a specialized mechanism employed by certain subviral pathogens, such as viroids, to amplify their circular RNA genomes using host-derived RNA-dependent RNA polymerases (RdRp) without involving DNA intermediates.^[7] This process generates long, multimeric RNA transcripts that are subsequently processed into unit-length monomeric circles, enabling efficient propagation of small, non-protein-coding RNA molecules.^[7] Unlike the more prevalent DNA-based rolling circle replication, which relies on nicking endonucleases and DNA polymerases, the RNA variant utilizes self-cleaving ribozymes and host polymerases redirected to template RNA strands, highlighting its adaptation for RNA-only systems.^[7] The mechanism unfolds in three principal steps. Initiation begins with the circular RNA serving as a template, where a host polymerase—typically RNA polymerase II in the nucleus for Pospiviroidae family viroids—binds and creates a 3' end for priming, often facilitated by specific structural motifs like the left terminal loop in potato spindle tuber viroid (PSTVd).^[7] Elongation proceeds via continuous, reiterative transcription by the RdRp, displacing the newly synthesized strand and producing linear, concatenated multimers of the complementary polarity; this yields exponential amplification, with the number of genomic units scaling with replication rounds and initial template size.^[7] Processing of these multimers involves site-specific cleavage to generate unit-length RNAs, followed by ligation to reform circles; cleavage is mediated by viroid-encoded ribozymes, such as hammerhead ribozymes in avocado sunblotch viroid (ASBVd), or host enzymes like RNase III-like activities in PSTVd.^[7] Ligation may occur via host RNA ligases or autocatalytic means, completing the cycle.^[7] Key enzymes and factors underscore the reliance on host machinery. Host RdRp, such as nuclear-encoded chloroplastic RNA polymerase (NEP) in Avsunviroidae, drives elongation after being hijacked to recognize RNA templates.^[7] Ribozymes provide autonomous processing: the hammerhead ribozyme in ASBVd enables self-cleavage of multimeric transcripts in the chloroplast under symmetric replication. In contrast, Pospiviroidae like PSTVd employ asymmetric replication in the nucleus, where host polymerase II initiates minus-strand synthesis via rolling circle, but plus strands form through distinct, non-rolling mechanisms.^[8] These factors ensure precise control without viral proteins. Structurally, single-stranded circular RNAs maintain stability without supercoiling, adopting rod-like (PSTVd) or quasi-rod-like (ASBVd) conformations that expose functional domains for polymerase binding and ribozyme activity.^[7] The resulting concatenated transcripts form extended linear chains, which are resolved into monomers, preserving the circular form essential for infectivity.^[7] A representative example is the replication of PSTVd, a 359-nucleotide viroid causing potato spindle tuber disease, which localizes to the host cell nucleus and hijacks RNA polymerase II for transcription.^[8] Here, the circular plus strand templates minus-strand multimers via rolling circle, which are cleaved and circularized; plus strands are amplified separately, supporting overall exponential propagation.^[8] This mechanism exemplifies how rolling circle replication amplifies compact, non-coding RNA genomes autonomously in eukaryotic hosts.^[7]

Natural Biological Contexts

In Bacteriophages and Plasmids

Rolling circle replication plays a crucial role in the propagation of single-stranded DNA (ssDNA) bacteriophages, such as φX174 and M13, by enabling asymmetric synthesis of progeny viral genomes during the late stages of infection. In these phages, the process was first elucidated in the 1960s through studies on φX174, where David T. Denhardt and colleagues identified rolling circle intermediates as key structures in ssDNA production. Upon infection, the incoming ssDNA genome is converted to a double-stranded replicative form (RF) by host polymerases, followed by initial RF amplification via bidirectional theta replication. Late in the lytic cycle, replication shifts to the rolling circle mode to generate up to 100-200 ssDNA copies per cell, matching the typical burst size of φX174 infections. For φX174, the viral gene A protein acts as a site-specific endonuclease, covalently binding to the 5' phosphate at the origin of replication (ori) on supercoiled RF DNA to create a nick that initiates strand displacement. This protein remains attached during elongation, where host DNA polymerase III extends the 3' end processively, displacing the non-template strand as a single-stranded tail that is coated by SSB proteins to prevent reannealing. Termination occurs when a full genome-length ssDNA is produced, with gene A cleaving the regenerated ori and ligating the new circle, allowing reinitiation. In parallel, viral coat proteins, particularly gene F product, inhibit further RF synthesis by binding the displaced ssDNA and promoting packaging into procapsids, thus favoring asymmetric ssDNA output over symmetric dsDNA replication. The filamentous phage M13 employs a similar strategy, with its gene II protein performing the ori-specific nicking on RF DNA to launch rolling circle replication for ssDNA progeny synthesis. Unlike lytic phages like φX174, M13 extrusion does not lyse the host, and coat protein assembly on the displaced ssDNA at the membrane inhibits dsDNA synthesis, ensuring continuous virion release without cell death. This mechanism integrates with the phage life cycle by producing ssDNA genomes that are packaged sequentially, supporting high-titer production in infected Escherichia coli cells. In bacterial plasmids, rolling circle replication maintains stable, high-copy-number propagation of small extrachromosomal elements, typically under 10 kb in size, such as the Staphylococcus aureus plasmid pT181. These plasmids feature replication origins with iterons—short repeated sequences that facilitate binding of the plasmid-encoded initiator protein. For pT181, the RepC protein dimer binds the double-stranded origin (dso), nicking the top strand at a specific tyrosine residue to initiate leading-strand synthesis via host polymerases, displacing the non-template strand as ssDNA. After one replication round, producing a monomeric circle and a displaced linear ssDNA that circularizes via the single-strand origin (sso), the modified RepC* form resolves any dimers by nicking the bottom strand, ensuring copy number control through initiator inactivation. This mode allows some plasmids to transition from initial theta replication to rolling circle for maintenance, enhancing efficiency in diverse bacterial hosts. Biologically, rolling circle replication offers advantages for small circular genomes by enabling highly processive, high-fidelity synthesis using host machinery, which minimizes errors and supports rapid amplification without multiple initiation events. Additionally, the transient ssDNA intermediates reduce recombination risks compared to linear forms, as they are quickly converted to dsDNA or coated, promoting genetic stability in compact replicons.

In Eukaryotic Viruses and Viroids

Rolling circle replication is essential for the replication of certain single-stranded DNA (ssDNA) eukaryotic viruses, particularly parvoviruses and adeno-associated virus (AAV). Parvoviruses, such as adeno-associated virus (AAV), depend on a helper virus or cellular factors for replication. The process begins with the conversion of the incoming ssDNA genome to a double-stranded replicative form (RF) in the nucleus. The viral Rep protein, a HUH endonuclease, binds to the terminal resolution site (trs) or inverted terminal repeats (ITRs) and nicks the RF to initiate strand displacement synthesis, producing single-stranded concatemers that are processed into progeny genomes. This mechanism allows for the production of high numbers of viral particles, up to 10^5 per cell in some infections, and is crucial for the virus's dependence on host replication machinery during S phase.^[3] Similar rolling circle dynamics are observed in other animal circoviruses, such as porcine circovirus type 2 (PCV2), small ssDNA viruses that replicate via a double-stranded intermediate in the nucleus, using host polymerases to produce rolling circle concatemers for packaging into virions.^[9] In contrast, viroids—small, non-protein-coding circular RNAs that infect plants—exemplify RNA-based rolling circle replication, primarily in members of the family Avsunviroidae. These viroids, discovered in 1971 by Theodor O. Diener as the causative agents of potato spindle tuber disease, consist of 250–400 nucleotide monomers and replicate entirely using host enzymes without encoding any proteins.^[10] Avsunviroidae members, such as avocado sunblotch viroid (ASBVd), employ a symmetric rolling circle mechanism in chloroplasts, where a host nuclear-encoded RNA-dependent RNA polymerase (RdRp), potentially redirected from the nucleus, transcribes the circular RNA template into multimeric complementary strands.^[11] These oligomers are then self-cleaved by hammerhead or twin hammerhead (sawhorse) ribozymes embedded in the RNA sequences, yielding unit-length monomers that are ligated by host or chloroplastic ligases to form new circular progeny.^[12] This compartmentalization in chloroplasts shields replication from nuclear surveillance and supports efficient amplification, leading to systemic infections that cause economic losses in crops like avocado and peach.^[13] The biological significance of rolling circle replication in viroids lies in its ability to sustain latent, persistent infections in plants, where the circular RNA's stability evades degradation and exploits host RNA turnover pathways for dissemination via plasmodesmata and the phloem.^[14]

Rolling Circle Amplification

Principles and Implementation

Rolling circle amplification (RCA) is an isothermal nucleic acid amplification technique that mimics aspects of natural rolling circle replication, utilizing circularized DNA or RNA templates to generate long, single-stranded products consisting of tandem repeats of the template sequence.^[15] Developed as an extension of biological processes, RCA enables the synthesis of multiple copies from a single circular template without the need for thermal cycling, making it suitable for sensitive detection and analysis.^[16] The core principles of RCA involve the continuous displacement synthesis driven by a strand-displacing polymerase, which extends a primer annealed to the circular template, producing a concatemeric product while displacing the newly synthesized strand. This process results in linear amplification kinetics in its basic form, where the product length grows proportionally with time, or geometric amplification if additional primers initiate branching. Unlike PCR, RCA operates isothermally at constant temperature, avoiding denaturation steps and reducing artifacts such as primer dimers. The technique typically achieves amplification yields exceeding 10^9 copies per template molecule after several hours of reaction.^[15]^[16] Implementation of RCA begins with the preparation of a circular template, often through ligation of linear oligonucleotide probes (such as padlock probes) that hybridize to a target sequence, followed by enzymatic circularization using a thermostable ligase like Ampligase. Next, a target-specific primer anneals to the circular template, and amplification proceeds via addition of a strand-displacing polymerase in a buffer containing deoxynucleotide triphosphates (dNTPs), typically at 30–37°C for 1–16 hours. The reaction can be monitored in real-time using fluorescent intercalating dyes that bind to the accumulating product or via post-amplification hybridization with labeled probes for endpoint detection. For RNA-based RCA, alternatives such as Bst DNA polymerase can be employed to accommodate RNA templates, though phi29 remains the gold standard for DNA due to its high processivity (>70 kb per event) and fidelity.^[15]^[16] The amplification yield in RCA can be modeled using an exponential growth equation derived from the polymerase's replication rate: N = N_0 (1 + r)^t, where N is the final number of product molecules, N_0 is the initial template count, r is the replication rate per unit time (dependent on polymerase processivity and enzyme concentration), and t is the reaction time; this assumes geometric kinetics under optimal conditions, though linear models apply for unbranched synthesis.^[16] RCA was invented in the 1990s by Lizardi et al., who demonstrated its utility for mutation detection and single-molecule counting through isothermal replication of circularized probes, offering advantages over PCR such as simplicity, reduced equipment needs, and minimal amplification bias.^[15] The key enzyme, phi29 DNA polymerase from bacteriophage φ29, provides exceptional strand displacement and processivity, enabling the production of products up to 100 kb long without dissociation.

Variations and Enhancements

Padlock probes represent a key variation in rolling circle amplification (RCA), consisting of circularizable oligonucleotides that hybridize to target DNA sequences flanking a single nucleotide polymorphism (SNP), enabling specific detection through splint-mediated ligation of the probe ends to form a closed circle suitable for subsequent RCA. This mechanism leverages the high fidelity of DNA ligase to discriminate SNPs, with the resulting circular template amplifying only perfectly matched probes, achieving detection sensitivities down to single-molecule levels in applications like in situ genotyping.^[17] Originally developed for multiplexed mutation analysis, padlock probes enhance specificity by minimizing non-specific amplification, as demonstrated in early studies detecting low-abundance hotspot mutations in genomic DNA.^[18] Multiplex RCA extends standard protocols by employing multiple primers or color-coded probes to simultaneously target and amplify distinct sequences, facilitating high-throughput genotyping on arrays.^[19] For instance, padlock probe-based RCA (PLP-RCA) integrates with microarrays, where different primers generate localized, fluorescently labeled rolling circle products (RCPs) for parallel analysis of numerous SNPs or pathogens, improving throughput while maintaining single-molecule resolution.^[20] This approach has been pivotal in genotyping arrays, allowing discrimination of variants across hundreds of loci with error rates below 10^{-5} per base, attributed to the proofreading activity of φ29 DNA polymerase.^[21] To achieve exponential rather than linear amplification, hyperbranched RCA (HRCA) incorporates secondary primers that bind to the initial RCP, initiating additional rounds of rolling circle synthesis and yielding branched, tree-like structures with dramatically increased product yield.^[22] This ramified process, often using a pair of primers under isothermal conditions, boosts signal intensity by orders of magnitude, enabling detection limits as low as 1-10 target molecules, particularly useful in resource-limited settings.^[23] Further enhancements integrate nanoparticles with HRCA, where gold or magnetic nanoparticles conjugated to probes amplify fluorescence or enable magnetic separation, enhancing signal-to-noise ratios in low-abundance analyte detection.^[24] For RNA targets, reverse transcription-RCA (RT-RCA) combines reverse transcription with RCA, using enzymes like avian myeloblastosis virus reverse transcriptase (AMV RT) to generate cDNA from RNA, followed by circularization and amplification of the cDNA template.^[25] This variation addresses RNA's instability, enabling sensitive quantification of RNA molecules with detection limits reaching single copies per cell, as applied in single-cell transcriptomics post-2010.^[26] Similarly, rolling circle transcription (RCT) produces RNA from circular DNA templates using T7 RNA polymerase, generating long, repetitive RNA concatemers for applications in RNA nanotechnology and vaccine development, with yields exceeding 10^9 RNA molecules per template.^[27] Recent advances in the 2020s include CRISPR-RCA hybrids, where CRISPR-Cas systems like Cas12a guide padlock probe ligation for enhanced target specificity, reducing off-target amplification in complex samples such as SNP detection in situ.^[28] Digital RCA further refines single-molecule counting by partitioning RCA reactions into microdroplets or nanowells, enabling absolute quantification without standards and achieving error rates under 10^{-5} through Poisson statistics, with applications in single-cell and extracellular vesicle analysis.^[29] These innovations, including HRCA in single-cell contexts, have expanded RCA's utility beyond traditional diagnostics, addressing limitations in sensitivity and multiplexing observed in earlier protocols.^[30]

Applications

In Diagnostics and Detection

Rolling circle amplification (RCA) has emerged as a powerful tool in diagnostics for detecting pathogens, particularly viral genomes, through the use of padlock probes that enable high specificity and isothermal amplification. For instance, RCA combined with padlock probes achieves detection limits below 30 femtomolar for HIV-1 DNA in microfluidic formats suitable for resource-limited settings as an alternative to PCR. Similarly, RCA-based in situ hybridization assays detect HPV E6/E7 mRNA expression in cervical cancer cells with single-molecule resolution, facilitating early viral oncogene identification. These methods leverage RCA's isothermal nature to simplify equipment needs, making them ideal for point-of-care applications in infectious disease diagnostics. In biomarker assays, RCA supports precise genotyping of single nucleotide polymorphisms (SNPs) and detection of microRNAs (miRNAs) relevant to cancer diagnostics. Ligation-mediated RCA (L-RCA) enables allele-specific amplification directly from genomic DNA, achieving over 99% accuracy in SNP genotyping for pharmacogenomics and disease susceptibility studies. For miRNA detection, multiple primer RCA coupled with CRISPR enhances sensitivity for lung cancer-associated miR-21, detecting as few as 1 fM in clinical samples without reverse transcription steps. These applications highlight RCA's role in identifying low-abundance nucleic acid biomarkers for personalized medicine. Immuno-RCA integrates antibodies with RCA to amplify signals from protein targets, such as cytokines, enabling multiplexed detection in microarrays with femtomolar sensitivity. In this approach, DNA-tagged antibodies initiate RCA upon binding, producing detectable fluorescent products for profiling up to 75 cytokines from immune cells. Aptamer-based RCA extends this to small molecules, using nucleic acid aptamers as recognition elements for targets like heavy metals or metabolites, with enhanced stability over antibodies in point-of-care formats. Aptamer immuno-RCA further improves portability by replacing antibodies with aptamers, reducing degradation in field conditions while maintaining high specificity for analytes like toxins. RCA offers advantages including high specificity from padlock probe ligation, minimal background noise due to isothermal conditions, and compatibility with portable lateral flow assays for visual readouts. These features support rapid, on-site testing without thermal cycling. During the COVID-19 pandemic, RCA-LAMP hybrids detected SARS-CoV-2 RNA with >95% sensitivity for low-copy targets (down to 10 copies/reaction) in under 30 minutes, as demonstrated in colorimetric assays for clinical validation. Recent integrations of RCA with next-generation sequencing (NGS) enhance diagnostics by amplifying rare variants for deep sequencing, improving detection of circulating tumor DNA in liquid biopsies with signal-to-noise ratios exceeding 100:1.

In Biotechnology and Synthesis

Rolling circle amplification (RCA) has emerged as a key tool in DNA nanotechnology for synthesizing long, repetitive single-stranded DNA (ssDNA) scaffolds that serve as building blocks in synthetic biology. By generating periodic nanostructures such as nanorings and nanowires, RCA enables the creation of custom-length scaffolds with defined sequences, overcoming limitations of traditional viral-derived templates. For instance, RCA amplicons from plasmid and viral genome templates have been folded into DNA origami nanorings and linear wire-like structures, facilitating programmable assembly for applications in molecular machines and sensors.^[31] These scaffolds, often exceeding 100 kb in length, support the construction of higher-order DNA architectures like hydrogels and nanoflowers, enhancing structural stability and functionality in synthetic systems.^[32] Yields from such RCA reactions can reach up to 17 µg of amplified DNA per reaction, enabling scalable production for nanotechnology prototypes.^[33] In gene synthesis, RCA facilitates the assembly of large DNA constructs by amplifying synthetic minicircles into high-fidelity templates suitable for genome editing. Linear DNA fragments are circularized and subjected to RCA using φ29 DNA polymerase, producing multimeric ssDNA that can be processed into double-stranded forms for downstream applications like CRISPR-Cas9 template design. This approach accelerates biocatalytic workflows, reducing preparation time by approximately 50% compared to plasmid-based methods while maintaining enzyme activity levels comparable to cellular systems.^[34] RCA products have been integrated into 2010s-era advances in DNA origami, where repetitive scaffolds hybridize with staple strands to form extended nanostructures, such as block macromolecules for large-scale folding.^[35] Additionally, RCA supports the production of CRISPR guide RNAs by amplifying circular templates into long ssRNA precursors, which are then transcribed or directly incorporated into editing complexes, streamlining in vitro assembly of gene-editing tools.^[36] RCA contributes to protein engineering through display technologies that leverage amplified DNA libraries for directed evolution. In RCA-phage display systems, circular DNA templates encoding antibody fragments are amplified into tandem repeats, enabling the construction of large scFv libraries with up to 10^9 variants for high-throughput screening.^[37] This method enhances library diversity and transformation efficiency, supporting iterative evolution of binding proteins like aptamers in vitro. For aptamer evolution, RCA generates ultralong ssDNA backbones functionalized with aptamer motifs, such as Apt19S for cell-specific capture, allowing selection of high-affinity binders against targets like tumor cells.^[32] RCA has also been explored for creating artificial chromosomes by producing extended repetitive DNA arrays that mimic centromeric sequences, though yields remain in the microgram range for constructs over 100 kb.^[38] Emerging applications in 2025 include the engineering of synthetic viroids via rolling circle mechanisms for gene therapy delivery. These circular RNAs, produced through RCA-inspired replication of viroid-like templates, form low-immunogenic carriers that encapsulate therapeutic payloads, such as mRNA for sustained expression in target cells. Platforms leveraging RCA for circRNA synthesis offer scalable production with minimal off-target effects, positioning them as vectors for stem cell engineering and viral mimicry in therapy.^[39]

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Sep 21, 2025 · In this review, recent advances in RCA-based single molecule counting assay are overviewed and their applications in single cells and single EVs ...
[36]
DNA Origami Nanostructures with Scaffolds Obtained from Rolling Circle Amplification
### Summary of RCA in DNA Origami Scaffolds
[37]
Advances in Rolling Circle Amplification (RCA)‐Based DNA ...
Dec 21, 2023 · Rolling circle amplification (RCA) is an efficient isothermal enzymatic process for synthesis of ultralong ssDNA depending on a circular DNA ...2 Rca Process And Rca-Based... · 3.1 Dna Hydrogel · 4.3 Tumor Therapy
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RCA and MDA-WGA | Thermo Fisher Scientific - US
Padlock probe- and rolling circle amplification-based RNA in situ hybridization assay for detecting HPV E6/E7 mRNA expression. Rao, X., Zheng, L., Wei, K ...
[39]
Rolling circle amplification of synthetic DNA accelerates biocatalytic ...
Jun 24, 2020 · A cell-free workflow using synthetic DNA minicircles and rolling circle amplification enables comparable biocatalytic activity to cell-based workflows in ...
[40]
DNA Block Macromolecules Based on Rolling Circle Amplification ...
Thousands of nucleotide(nt)-long single strand DNAs, generated from rolling-circle-amplification (RCA), were used as scaffolds to create DNA nanoscale wires and ...
[41]
Rolling Circle Transcription-Amplified Hierarchically Structured ...
Jun 19, 2019 · Here we describe the construction of organic–inorganic hybrid RNA flowers (hRNFs) via rolling circle transcription (RCT), an enzyme-catalyzed nucleic acid ...
[42]
Exploitation of rolling circle amplification for the construction of large ...
Aug 10, 2025 · We have exploited rolling circle amplification (RCA) to produce a long strand of DNA with tandem repeats of scFv sequences, which is found to be ...
[43]
Amplification of over 100 kbp DNA from Single Template Molecules ...
Aug 18, 2021 · The success rate of RCR amplification from a single copy of template DNA was confirmed to be around 82% for 16 kbp DNA, and 23% for 208 kbp DNA.Missing: post- | Show results with:post-
[44]
Circular RNA: From non-coding regulators to functional protein ...
This study establishes an efficient, low-immunogenicity platform for circRNAs' production, offering a novel tool for gene therapy, stem cell engineering, and ...