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Miscellaneous

Detection of target nucleic acids and proteins by amplification of circularizable probes

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Pages 237-248 | Published online: 09 Jan 2014

References

  • Nilsson M, Malmgren H, Samiotaki M eta]. Padlock probes: circularizing oligonucleotides for localized DNA detection. Science 265,2085–2088 (1994).
  • ••First paper describing the used of C-probefor target detection.
  • Zhang DY, Brandwein M, Hsuih TC, Li H. Amplification of target-specific, ligation-dependent circular probe. Gene 211,277–285 (1998).
  • •First paper describing amplification of C-probe by PCR and RAM.
  • Kool ET. Circular oligonucleotides: new concepts in oligonucleotide design. Ann. Rev. Biophys. Biomol Shutt 25,1–28 (1996).
  • Wang S, Kool ET Circular RNA oligonucleotides. Synthesis, nucleic acid binding properties and a comparison with circular DNAs. Nucleic Acids Res. 22,2326–2333 (1994).
  • Hsuih TC, Park YN, Zaretsky C eta]. Novel, ligation-dependent PCR assay for detection of hepatitis C virus in serum. J. Gun. Microbial. 34(3), 501–507 (1996).
  • Faruqi AF, Hosono S, Driscoll MD et al High-throughput genotyping of single nucleotide polymorphisms with rolling circle amplification. BMC Genomics 2 (1), 4 (2001).
  • ••Use of RCA and Arnplifluor for SNP detection.
  • Christian AT, Pattee MS, Attix CM, Reed BE, Sorensen KJ, Tucker JD. Detection of DNA point mutations and mRNA expression levels by rolling circle amplification in individual cells. Proc. Natl Acad. Li. USA 98(25), 14238–14243 (2001).
  • •Description of in situ RCA.
  • Nilsson M, Barbany G, Antson DO, Gertow K, Landegren U. Enhanced detection and distinction of RNA by enzymatic probe ligation. Nature Biotechnol 18(7), 791–793 (2000).
  • Luo J, Beig,iiium DE, Barmy F. Improving the fidelity of Thermus thermophilus DNA ligase. IVucleic Acid s Res. 24(14), 3071–3078 (1996).
  • Nilsson M, Krejci K, Koch J, Kwiatkowski M, Gustavsson P, Landegren U. Padlock probes reveal single-nucleotide differences, parent of origin and in situ distribution of centromeric sequences in human chromosomes 13 and 21. Nature Genet. 16(3), 252–255 (1997).
  • Baner J, Nilsson M, Mendel-Hartvig M, Landegren U. Signal amplification of padlock probes by rolling circle replication. Nucleic Acids Res. 26,5073–5078 (1998).
  • Lizardi PM, Huang X, Zhu Z, Bray-Ward P, Thomas DC, Ward DC. Mutation detection and single-molecule counting using isothermal rolling-circle amplification. Nature Genet. 19,225–232 (1998).
  • Zhang DY, Zhang W, Li X, Konomi Y. Detection of rare DNA targets by isothermal ramification amplification. Gene 274,209–216 (2001).
  • ••Detailed description of RAM assaycondition and optimization.
  • Fire A, Xu S. Rolling replication of short DNA circles. Proc. Natl Acad. Li. USA 92, 4641–4645 (1995).
  • Perler FB, Kumar S, Kong H. Thermostable DNA polymerases. In: Advances in Protein Chemistry 48,377–435 (1996).
  • Ausubel FM, Brent R, Kingston RE eta] (Eds) 6.117-ent Protocols in Molecular Biology (Vol )). John Wiley & Sons, Hoboken, NJ, USA (1995).
  • Zhang DY, Brandwein M, Hsuih T, Li HB. Ramification amplification: a novel isothermal DNA amplification methods. Mal Diagnosis 6(2), 141–150 (2001).
  • •Use of in situ RAM to detect DNA target in a cell.
  • Schweitzer B, Wiltshire S, Lambert J eta]. Immunoassays with rolling circle DNA amplification: a versatile platform for ultrasensitive antigen detection. Proc. Natl Acad. Li. USA 97(18), 10113–10119 (2000).
  • ••Description of imrnunoRCA
  • 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).
  • Baer RJ, Bankier AT, Biggin MD et al DNA sequence and expression of the B95-8 Epstein-Barr virus genome. Nature 310, 207–211 (1984).
  • Kuhn H, Demidov VV, Frank-Kamenetskii M. Rolling-circle amplification under topological constraints. Nucleic Adds Res. 30(2), 574–580 (2002).
  • Thomas D, Nardone G, Randall S. Amplification of padlock probes for DNA diagnostics by cascade rolling circle amplification or the polymerase chain reaction. Arch. Pathol Lab. Med. 123(12), 1170–1176 (1999).
  • Varadaraj K, Skinner DM. Denaturants or cosolvents improve the specificity of PCR amplification of a G+C-rich DNA using genetically engineered DNA polymerases. Gene 140,1–5 (1994).
  • Morris CF, Sinha NK, Alberts BM. Reconstruction of bacteriophage T4 DNA replication apparatus from purified components: rolling circle replication follwoing de novo chain initiation on a single-stranded circular DNA template. Proc. Natl Acad. Sri USA 72,4800–4804 (1975).
  • Nuovo GJ. PCRin situ Hybridization: Protocols and Applications. (Second Ed.). Raven Press, New York, NY, USA (1994).
  • Park YN, Abe K, Li H, Hsuih T, Thung SN, Zhang DY. Detection of hepatitis C virus RNA using ligation-dependent polymerase chain reaction in formalin-fixed, paraffin-embedded liver tissues. Am. J. Pathol. 149(5), 1485–1491 (1996).
  • Gerry NP, Witowski NE, Day J, Hammer RP, Barany G, Barany E Universal DNA microarray method for multiplex detection of low abundance point mutations. J Mal Biol. 292,251–62 (1999).
  • 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 Acids Res. 30(12), e60 (2002).
  • Ladner DP, Leamon JH, Hamann S etal Multiplex detection of hotspot mutations by rolling circle-enabled universal microarrays. Lab. Invest. 81,1079–1086 (2001).
  • Sano T, Smith CL, Cantor CR. Immuno- PCR: very sensitive antigen detection by means of specific antibody-DNA conjugates. Science 258,120–122 (1992).
  • Joerger RD, Truby TM, Hendrickson ER, Young RM, Ebersole RC. Analyte detection with DNA-labeled antibodies and polymerase chain reaction. Clin. Chem. 41, 1371–1377 (1995).
  • Schweitzer B, Roberts S, Grimwade B eta]. Multiplexed protein profiling on microarrays by rolling-circle amplification. Nature Biotechnol. 20(4), 359–365 (2002).
  • Gusev Y, Sparkowski J, Raghunathan A etal Rolling circle amplification: a new approach to increase sensitivity for immunohistochemistry and flow cytometry. AIR I Pathol 159(1), 63–69 (2001).
  • Anthony RM, Brown TJ, French GL. DNA array technology and diagnostic microbiology. Expert Rev Mal Diagn.1(1), 30–38 (2001).
  • Nallur G, Luo C, Fang L etal Signal amplification by rolling circle amplification on DNA microarrays. Nucleic Acids Res. 29, E118 (2001). Use of RCA for on-chip signal amplification to detect nucleic acids.
  • Dean FB, Hosono S, Fang L etal Comprehensive human genome amplification using multiple displacement amplification. Proc. Natl Acad. Sri USA 99(8), 5261–5266 (2002).
  • ••Use of RCA for whole genomic DNA amplification.
  • Li F eta Detection of E. Coli 0157:H7 and other Shiga toxin-producing E. coil in clinical specimens. J Clin. Mcrobiol. (2003) (In Press).
  • Nilsson M, Gullberg M, Dahl F, Szuhai K, Raap AK. Real-time monitoring of rolling-circle amplification using a modified molecular beacon design. Nucleic Acids Res. 30, e66 (2002).
  • Tyagi S, Kramer FR. Molecular beacons: probes that fluoresce upon hybridization. Nature Biotechn. 14(3), 303–308 (1996).
  • Zhang W, Cohenford M, Lentrichia B eta]. Detection of Chlamydia trachomatis by isothermal ramification amplification method: a feasibility study. J Clin. Mcrobiol. 40,128-132 (2002).
  • Wiltshire S, O'Malley S, Lambert J etal Detection of multiple allergen-specific IgEs on microarrays by immunoassay with rolling circle amplification. Clin. Chem. 46(12), 1990–1993 (2000).

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