Monoplex/multiplex linear-after-the-exponential-pcr assays combined with primesafe and dilute-‘n’-go sequencing

Nature Protocols

Volumn 2, Issue 10, 2007, Pages 2429-2438

  Rice, John E ^a   Sanchez, J Aquiles ^a   Pierce, Kenneth E ^a   Reis, Arthur H ^a   Osborne, Adam ^a   Wangh, Lawrence J ^a  

^a BRANDEIS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DYES, REAGENTS, INDICATORS, MARKERS AND BUFFERS; ORGANIC COMPOUND; PRIMER DNA; SINGLE STRANDED DNA; SYBR GREEN I; UNCLASSIFIED DRUG;

ARTICLE; DNA SEQUENCE; KINETICS; METHODOLOGY; POLYMERASE CHAIN REACTION; TEMPERATURE;

DNA; DNA PRIMERS; DNA, SINGLE-STRANDED; INDICATORS AND REAGENTS; KINETICS; ORGANIC CHEMICALS; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA; TEMPERATURE;

EID: 38449116138     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2007.362     Document Type: Article

References (26)

1. Surdhar, G.K. Cycle sequencing of PCR products. Methods Mol. Biol. 187, 65-72 (2002).
2. Gyllensten, U.B. & Erlich, H.A.: Generation of single-stranded DNA by the polymerase chain reaction and its application to direct sequencing of the HLA-DQA locus. Proc. Natl. Acad. Sci. USA 85, 7652-7656 (1988).
3. Shyamala, V. & Ames, G.F. Amplification ofbacterial genomic DNA bythe polymerase chain reaction and direct sequencing after asymmetric amplification: application to the study of periplasmic permeases. J. Bactenol. 171, 1602-1608 (1989).
4. Innis, M.A. et al. DNA sequencing with Thermus aquaticus DNA polymerase and direct sequencing of polymerase chain reaction-amplified DNA. Proc. Natl. Acad. Sd. USA 85, 9436-9440 (1988).
5. Mazars, G.R. & Theillet, C. Direct sequencing by thermalasymmetric PCR. Methods Mol. Biol. 226, 355-360 (2003).
6. Sanchez, J.A. etal. Linear-after-the-exponential (LATE)-PCR: an advanced method of asymmetric PCR and its uses in quantitative real-time analysis. Proc. Natl. Acad. Sd. USA 101, 1933-1938 (2004).
7. Pierce, K.E. et al. Linear-after-the-exponential (LATE)-PCR: primer design criteria for high yields ofspecific single-stranded DNA and improved real-time detection. Proc. Natl. Acad. Sd. USA 102, 8609-8614 (2005).
8. Pierce, K.E. & Wangh, L.J. LATE-PCR and allied technologies: real-time detection strategies for rapid, reliable diagnosis from single cells. in Single Cell Di agnostics, Methods in Molecular Medicine Series (ed. Thornhill, A.) (Humana Press, Totowa, New Jersey, USA, 2007) p65-85.
9. Chou, Q. etal. Prevention ofpre-PCR mis-primingand primerdimerization improves low-copy-number amplifications. Nucleic Acids Res. 20, 1717-1723 (1992).
10. Le Novere, N. MELTING, computing the melting temperature of nucleic acid duplex. Bioinformatics 17, 1226-1227 (2001).
11. Pierce, K.E. et al. Detection of cystic fibrosis alleles from single cells using molecular beacons and a novel method of asymmetric real-time PCR. Mol. Hum. Reprod. 9, 815-820 (2003).
12. Bustin, S.A.: Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays. J. Mol. Endocrinol. 25, 169-193 (2000).
13. Salk, J.J. et al. Direct amplification of single-stranded DNA for pyrosequencing using linear-after-the-exponential (LATE)-PCR. Anal. Biochem. 353, 124-132 (2006).
14. Henegariu, O. etal. Multiplex PCR: critical parameters and step-by-step protocol. Biotechniques 23, 504-511 (1997).
15. Elnifro, E.M. etal. Multiplex PCR: optimization and application in diagnostic virology. Clin. Microbiol. Rev. 13, 559-570 (2000).
16. Markoulatos, P. et al. Multiplex polymerase chain reaction: a practical approach. J. Clin. Lab. Anal. 16, 47-51 (2002).
17. Tyagi, S. & Kramer, F.R. Molecular beacons: probes that fluoresce upon hybridization. Nat. Biotechnol. 14, 303-308 (1996).
18. Lee, M.A., Siddle, A.L. & Page, R.H. ResonSense: simple linear fluorescent probes for quantitative homogeneous rapid polymerase chain reaction. Anal. Chim. Acta 457, 61-70 (2002).
19. Sanchez, J.A. etal. Two-temperature LATE-PCR endpoint genotyping. BMC Biotechnol. 6, 44 (2006).
20. McCombie, W.R. et al. Rapid and reliable fluorescent cycle sequencing of doublestranded templates. DNA Seq. 2, 289-296 (1992).
21. Rosenthal, A. et al. Large-scale production of DNA sequencing templates by microtitre format PCR. Nucleic Acids Res. 21, 173-174 (1993).
22. Dowton, M. & Austin, A.D. Direct sequencing of double-stranded PCR products withoutintermediate fragment purification; digestion with mung bean nuclease. Nucleic Acids Res. 21, 3599-3600 (1993).
23. Hanke, M. & Wink, M. Direct DNA sequencing of PCR-amplified vector inserts following enzymatic degradation of primer and dNTPs. Biotechniques 17, 858-860 (1994).
24. Werle, E. et al. Convenient single-step, one tube purification of PCR products for direct sequencing. Nucleic Acids Res. 22, 4354-4355 (1994).
25. Hashimoto, M. et al. On-line integration of PCR and cycle sequencing in capillaries: from human genomic DNA directly to called bases. Nucleic Acids Res. 31, e41 (2003).
26. Pierce, K.E. etal. QuantiLyse: reliable DNA amplification from single cells. Biotechniques 32, 1106-1111 (2002).