ArticleNucleic acids research2018
Rolling circle amplification shows a sinusoidal template length-dependent amplification bias.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Amplification bias in sequencing-based spatial transcriptomics: sources, mechanisms, impacts, and mitigation strategies.Briefings in bioinformatics · 2026Review
- Programmable AND-gate strategy to reduce false positives in rolling circle amplification.Biosensors & bioelectronics · 2026Article
- A TtAgo-Driven Autocatalytic Circuit with Thermal-Enhanced Kinetics for One-Pot Nucleic Acid Detection.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Improving Spatial Transcriptomics with Dual-Color Coding and Cell Painting.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Long-read RNA sequencing of transposable elements from single cells using CELLO-seq.Nature protocols · 2025Review
- Rolling Circle Amplification as a Molecular Tool for Spatially Resolved Signal Amplification in Single Molecule Counting Assay.Biosensors · 2025Review
- Efficient small fragment sequencing of human, cattle, and bison miRNA, small RNA, or csRNA-seq libraries using AVITI.BMC genomics · 2024Article
- Massive multiplexing of spatially resolved single neuron projections with axonal BARseq.Nature communications · 2024Article
- Beyond the base pairs: comparative genome-wide DNA methylation profiling across sequencing technologies.Briefings in bioinformatics · 2024Article
- Efficient small fragment sequencing of human, cow, and bison miRNA, small RNA or csRNA-seq libraries using AVITI.bioRxiv : the preprint server for biology · 2024Article
- Revealing an initiation inhibition of RCA and its application in nucleic acid detection.Acta biochimica et biophysica Sinica · 2023Article
- A novel linear displacement isothermal amplification with strand displacement probes (LDIA-SD) in a pocket-size device for point-of-care testing of infectious diseases.Sensors and actuators. B, Chemical · 2023Article
- Massive Multiplexing of Spatially Resolved Single Neuron Projections with Axonal BARseq.bioRxiv : the preprint server for biology · 2023Article
- Synthesis and cloning of long repeat sequences using single-stranded circular DNA.Frontiers in bioengineering and biotechnology · 2023Article
- Oxime formation coordination-directed detection of genome-wide thymine oxides with nanogram-scale sample input.Chemical science · 2022Article
- Rapid quantification of microRNA-375 through one-pot primer-generating rolling circle amplification.The Analyst · 2022Article
- Programmable High-Speed and Hyper-Efficiency DNA Signal Magnifier.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2022Article
- Nucleic acid amplification strategies for volume-amplified magnetic nanoparticle detection assay.Frontiers in bioengineering and biotechnology · 2022Review
- Padlock Probe-Based Generation of DNAzymes for the Colorimetric Detection of Antibiotic Resistance Genes.International journal of molecular sciences · 2021Article
- Rolling Circle Amplification as a Universal Method for the Analysis of a Wide Range of Biological Targets.Russian journal of bioorganic chemistry · 2021Article
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5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Biophysical properties of DNA such as its longitudinal and torsional persistence length govern many processes and phenomena in biology, DNA nanotechnology and biotechnology. It has, for example, long been known that the circularization efficiency of short DNA fragments shows a periodic pattern where fragments with integer helical turns circularize much more efficiently than those with odd helical half turns due to stronger stacking of duplex ends. Small DNA circles can serve as templates for rolling circle amplification (RCA), which is a common and extremely robust amplification mechanism for nucleic acids. We discovered a strong template length-dependent amplification efficiency bias of RCA with the same periodicity as B-DNA. However, stacking cannot explain the mechanism behind this bias as the presence of the polymerase in the bifurcation fork inhibits base stacking of ends. Instead, coarse-grained molecular dynamics simulations imply that different amplification efficiencies come from a varying fraying probability of the last two downstream base pairs. We conclude that an increased strain-promoted fraying probability can increase the polymerization rate compared to a relaxed template.
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