A Mechanism for Ramified Rolling Circle Amplification

Overview

Journal BMC Mol Biol

Publisher Biomed Central

Specialty Molecular Biology

Date 2010 Dec 9

PMID 21138587

Citations 6

Authors

Thomas P Beals

James H Smith

Raymond M Nietupski

David J Lane

Affiliations

Soon will be listed here.

Abstract

Background: Amplification of single-stranded DNA circles has wide utility for a variety of applications. The two-primer ramified rolling circle amplification (RAM) reaction provides exponential DNA amplification under isothermal conditions, creating a regular laddered series of double-stranded DNA products. However, the molecular mechanism of the RAM reaction remains unexplained.

Results: A RAM reaction model predicts exponential accumulation of a double-stranded DNA product size series, and product-size ratios, that are consistent with observed RAM reaction products. The mechanism involves generation of a series of increasing size intermediate templates; those templates produce RAM products and recursively generate smaller intermediate templates. The model allows prediction of the number of rounds of circular template replication. Real-time RAM reaction data are consistent with the model. Analysis of RAM reaction products shows exponential growth limitation consistent with the model's predictions.

Conclusions: The model provides a rationale for the observed products of the RAM reaction, and the molecular yield among those products. Experimental results are consistent with the model.

Citing Articles

Isothermal nucleic acid amplification and its uses in modern diagnostic technologies.

Srivastava P, Prasad D 3 Biotech. 2023; 13(6):200.

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Real-time Detection and Monitoring of Loop Mediated Amplification (LAMP) Reaction Using Self-quenching and De-quenching Fluorogenic Probes.

Gadkar V, Goldfarb D, Gantt S, Tilley P Sci Rep. 2018; 8(1):5548.

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Detection of genetic variations in coagulopathy-related genes using ramified rolling circle amplification.

Smith J, Cui M, Zhang D, Beals T, Ye F Biomed Res Int. 2014; 2014:641090.

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Nucleic acid amplification: Alternative methods of polymerase chain reaction.

Fakruddin M, Bin Mannan K, Chowdhury A, Mazumdar R, Hossain M, Islam S J Pharm Bioallied Sci. 2013; 5(4):245-52.

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Detection of nucleic acid targets using ramified rolling circle DNA amplification: a single nucleotide polymorphism assay model.

Smith J, Beals T PLoS One. 2013; 8(5):e65053.

PMID: 23724122 PMC: 3664557. DOI: 10.1371/journal.pone.0065053.

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