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Review

Rolling-circle amplification in DNA diagnostics: the power of simplicity

Pages 542-548 | Published online: 09 Jan 2014

References

  • Fire A, Xu S-Q. Rolling replication of short DNA circles. Proc. Natl Acad. Sc]. USA 92, 4641–4645 (1995).
  • ••Pioneering paper on RCA that describedall major features of linear reactions.
  • Daubendiek SL, Ryan K, Kool ET. Rolling- circle RNA synthesis: circular oligonucleotides as efficient substrates for T7 RNA polymerase. J. Am Chem. Soc. 117,77818-7819 (1995).
  • ••Pioneering paper on RCA that describedall major features of linear reactions.
  • Liu D, Daubendiek SL, Zillman MA eta]. Rolling circle DNA synthesis: small circular oligonucleotides as efficient templates for DNA polymerases. A/17. Chem. Soc. 118, 1587–1594 (1996).
  • ••Pioneering paper on RCA that describedall major features of linear reactions.
  • Lizardi PM, Huang X, Zhu Z eta]. Mutation detection and single-molecule counting using isothermal rolling-circle amplification. Nature Genet. 19,225–232 (1998).
  • ••Pioneering paper on geometric RCA thatdemonstrated the remarkable sensitivity of these reactions in DNA diagnostics.
  • Zhang DY, Brandwein M, Hsuih TCH, Li H. Amplification of target-specific, ligation-dependent circular probe. Gene 211,277–285 (1998).
  • ••Pioneering paper on geometric RCA thatdemonstrated the remarkable sensitivity of these reactions in DNA diagnostics.
  • Banér J, Nilsson M, Mendel-Hartvig M, Landegren U. Signal amplification of padlock probes by rolling circle replication. Nucleic Acids Res. 26,5073–5078 (1998).
  • •Aroused the controversy about the ability of polymerase enzymes to function on DNA minicircles linked to target molecules.
  • Thomas DC, Nardone GA, Randall SK. Amplification of padlock probes for DNA diagnostics by cascade rolling circle amplification or the polymerase chain reaction. Arch. Pallid Lab. Med. 123, 1170–1176 (1999).
  • Kwoh DY, Davis GR, Whitfield KM etal. Transcription-based amplification system and detection of amplified human immunodeficiency virus Type 1 with a bead-based sandwich hybridization format. Pox. Nat/Acad. Li USA 86,1173–1177 (1989).
  • Walker GT, Little MC, Nadeau JG, Shank DD. Isothermal in vitm amplification of DNA by a restriction enzyme/DNA polymerase system. Proc. Natl Acad. Sc]. USA 89,392–396 (1992).
  • Walker GT, Fraiser MS, Schram JL etal Strand displacement amplification — an isothermal, in vitro DNA amplification technique. Nucleic Acids Res. 20,1691-1696 (1992). iiUrdea MS, Running JA, Horn T et al A novel method for the rapid detection of specific nucleotide sequences in crude biological samples without blotting or radioactivity; application to the analysis of hepatitis B virus in human serum. Gene 61,253–264 (1987).
  • Shchepinov MS, Udalova IA, Bridgman AJ, Southern EM. Oligonucleotide dendrimers: synthesis and use as polylabelled DNA probes. Nucleic Acids Res. 25,4447–4454 (1997).
  • Hall JG, Eis PS, Law SM etal Sensitive detection of DNA polymorphisms by the serial invasive signal amplification reaction. Proc. Natl Acad. Sc]. USA 97,8272–8277 (2000).
  • Lyamichev VI, Kaiser MW, Lyamicheva NE etal Experimental and theoretical analysis of the invasive signal amplification reaction. Biochemistry39, 9523–9532 (2000).
  • Notomi T, Okayama H, Masubuchi H etal Loop-mediated isothermal amplification of DNA. Nucleic Acids Res. 28, e63 (2000).
  • Nagamine K, Kuzuhara Y, Notomi T Isolation of single-stranded DNA from loop-mediated isothermal amplification products. Biochem. Biophys. Res. Commun. 290,1195–1198 (2002).
  • Hawkins TL, Defter JC, Richardson PM. Whole genome amplification — applications and advances. CU17: Opin. Biotechnol 13, 65–67 (2002).
  • Andras SC, Power JB, Cocking EC, Davey MR. Strategies for signal amplification in nucleic acid detection. Mal Biotechnol 19, 29–44 (2001).
  • Banér J, Nilsson M, Isaksson A etal. More keys to padlock probes: mechanisms for high-throughput nucleic acid analysis. Cun: Opin. Biotechnol 12, 11–15 (2001).
  • Schweitzer B, Kingsmore S. Combining nucleic acid amplification and detection. Cun: Opin. Biotechnol 12,21–27 (2001).
  • Shi MM. Enabling large-scale pharmacogenetic studies by high-throughput mutation detection and genotyping technologies. Gun. Chem. 47, 164–172 (2001).
  • Kool ET Synthetically modified DNAs as substrates for polymerases. Cutr Opin. Chem. Biol. 4,602–608 (2000).
  • Isaksson A, Landegren U. Accessing genomic information: alternatives to PCR. Curt: Opin. Biotechnol 10,11–15 (1999).
  • Kiechle FL. DNA technology in the clinical laboratory. Arch. Athol Lab. Med. 123, 1151–1153 (1999).
  • Kool ET Recognition of DNA, RNA and proteins by circular oligonucleotides. Arc. Chem. Res. 31,502–510 (1998).
  • Kuhn H, Demidov W, Frank-Kamenetskii MD. Topological links between duplex DNA and a circular DNA single strand. Angew Chem. Int. Eri. 38,1446–1449 (1999).
  • •DNA topological labeling exhibiting superior stability and specificity is developed.
  • Kuhn H, Demidov VV, Frank-Kamenetskii MD. An earring for the double helix: assembly of topological links comprising duplex DNA and a circular oligodeoxynucleotide. j Biomol Struct. Dyn. S2,221-225 (2000).
  • Kuhn H, Frank-Kamenetskii MD, Demidov W. High-purity preparation of a large DNA dumbbell. Antisense Nucleic Acid Drug Dev 11, 149–153 (2001).
  • Demidov VV, Kuhn H, Lavrentyeva- Smolina IV, Frank-Kamenetskii MD. Peptide nucleic acid-assisted topological labeling of duplex DNA. Methods 23, 123–131 (2001).
  • Demidov VV. PD-loop technology: PNA openers at work. Expert Rev Mal Diagn. 1, 343–351 (2001).
  • Kuhn H, Demidov VV, Frank-Kamenetskii MD. Rolling-circle amplification undertopological constraints. Nucleic Acids Res. 30,574–580 (2002).
  • •Ability of DNA polymerases to run RCA directly on target-linked probes is proved.
  • Frieden M, Pedroso E, Kool ET Tightening the belt on polymerases: evaluating the physical constraints on enzyme substrate size. Angew Chem Int. Ed 38,3654–3657 (1999).
  • •Ability of polymerase enzymes to run RCA on very short circular DNAs is shown.
  • Sabanayagam CR, Berkey C, Lavi U eta]. Molecular DNA switches and DNA chips. In: SPIE Proceeding Series 3606: Micro-, and Nanofabricatecl Structuirs, and Devices for Biomedical and Environmental Applications II Ferrari M (Ed.), SPIE Proc., San José, CA, USA, 90–97 (1999).
  • Zhang DY, Zhang W, Li X, Konomi Y. Detection of rare DNA targets by isothermal ramification amplification. Gene 274, 209–216 (2001).
  • Zhang DY, Brandwein M, Hsuih T, Li HB. Ramification amplification: a novel isothermal DNA amplification method. Mal Diagn. 6, 141–150 (2001).
  • Lee J, Chastain PD 2nd, Kusakabe T eta]. Co-ordinated leading and lagging strand DNA synthesis on a minicircular template. Mal Cell, 1001–1010 (1998).
  • Ulanovsky L, Bodner M, Trifonov EN, Choder M. Curved DNA: design, synthesis and circularization. Proc. Nati Acad. Sci USA 83, 862–866 (1986).
  • Hagerman PJ. Flexibility of DNA. Ann. Rev Biophys. Biophys. Chem. 17, 265–286 (1988).
  • Koo HS, Drak J, Rice JA, Crothers DM. Determination of the extent of DNA bending by an adenine — thymine tract. Biochemistry29, 4227–4234 (1990).
  • Nallur G, Luo C, Fang L etal Signal amplification by rolling circle amplification on DNA microarrays. Nucleic Acids Res. 29, e118 (2001).
  • Schweitzer B, Wiltshire S, Lambert J et al Immunoassays with rolling circle DNA amplification: a versatile platform for ultrasensitive antigen detection. Pmc. Natl Acad. Sci USA 97, 10113–10119 (2000).
  • Hatch A, Sano T, Misasi J, Smith CL. Rolling circle amplification of DNA immobilized on solid surfaces and its application to multiplex mutation detection. Genet. Anal. 15, 35–40 (1999).
  • Christian AT, Pattee MS, Affix CM etal Detection of DNA point mutations and mRNA expression levels by rolling circle amplification in individual cells. Proc. Natl Acad. Li. USA 98, 14238–14243 (2001).
  • Ladner DP, Leamon JH, Hamann S et al Multiplex detection of hotspot mutations by rolling circle-enabled universal microarrays. Lab. Invest. 81, 1079–1086 (2001).
  • Zhong XB, Lizardi PM, Huang XH etal Visualization of oligonucleotide probes and point mutations in interphase nuclei and DNA fibers using rolling circle DNA amplification. Proc. Nati Acad. Li. USA 98, 3940–3945 (2001).
  • Voisey J, Hafner GJ, Morris CP etal Interrogation of multimeric DNA amplification products by competitive primer extension using Bst DNA polymerase (large fragment). Bio7echniques 31, 1122–1129 (2001).
  • Qi X, Bakht S, Devos KM etal L-RCA (ligation-rolling circle amplification): a general method for genotyping of single nucleotide polymorphisms (SNPs). Nucleic Acids Res. 29, e116 (2001).
  • Faruqi AF, Hosono S, Driscoll MD eta]. High-throughput genotyping of single nucleotide polymorphisms with rolling circle amplification. BMC Genomics 2(1), 4 (2001).
  • Pickering J, Bamford A, Godbole V etal Integration of DNA ligation and rolling circle amplification for the homogeneous, end point detection of single nucleotide polymorphisms. Nucleic Adds Res 30, e60 (2002).
  • Dean FB, Nelson JR, Giesler TL, Lasken RS. Rapid amplification of plasmid and phage DNA using Ph129 DNA polymerase and multiply-primed rolling circle amplification. Genome Res. 11, 1095–1099 (2001).
  • •Robust RCA-based method for amplification of recombinant plasmids is developed featuring the ability to operate directly with biological samples.
  • Schweitzer B, Roberts S, Grimwade B eta]. Multiplexed protein profiling on microarrays by rolling-circle amplification. Nature Biotechnol 20, 359–365 (2002).
  • ••Utility of RCA for chip-based high-throughput analyses of protein expression is demonstrated.
  • Ohmichi T, Maki A, Kool ET Efficient bacterial transcription of DNA nanocircle vectors with optimized single-stranded promoters. Proc. Nati Acad. Sci. USA 99, 54–59 (2002).
  • •New approach to gene therapy is described based on the in vivo rolling transcription of synthetic circular DNAs into biologically active RNAs.

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