Rapid polymerase chain reaction and melting analysis

The PCR Revolution: Basic Technologies and Applications

Volumn , Issue , 2009, Pages 48-69

  Wittwer, Carl T ^a   Rasmussen, Randy P ^b   Ririe, Kirk M ^b  

^a UNIVERSITY OF UTAH HEALTH SCIENCES CENTER   (United States)

^b Idaho Technology Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77951734516     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1017/CBO9780511818974.006     Document Type: Chapter

References (75)

1. Wittwer CT, Reed GB, Ririe KM (1994) Rapid cycle DNA amplification. In: K Mullis, F Ferre, and R Gibbs (eds), The Polymerase Chain Reaction, pages 174–181. Deerfield Beach, FL: Springer-Verlag.
2. Wittwer CT, Fillmore GC, Hillyard DR (1989) Automated polymerase chain reaction in capillary tubes with hot air. Nucleic Acids Research 17: 4353–4357.
3. Wittwer CT, Fillmore GC, Garling DJ (1990) Minimizing the time required for DNA amplification by efficient heat transfer to small samples. Analytical Biochemistry 186: 328–331.
4. Wittwer CT, Garling DJ (1991) Rapid cycle DNA amplification: time and temperature optimization. BioTechniques 10: 76–83.
5. Wittwer CT, Marshall BC, Reed GH, Cherry JL (1993) Rapid cycle allele-specific amplification: studies with the cystic fibrosis delta F508 locus. Clinical Chemistry 39: 804–809.
6. Schoder D, Schmalwieser A, Schauberger G, Hoorfar J, Kuhn M, Wagner M (2005) Novel approach for assessing performance of PCR cyclers used for diagnostic testing. Journal of Clinical Microbiology 43: 2724–2728.
7. Herrmann MG, Durtschi JD, Wittwer CT, Voelkerding KV (2007) Expanded instrument comparison of amplicon DNA melting analysis for mutation scanning and genotyping. Clinical Chemistry 53: 1544–1548.
8. Herrmann MG, Durtschi JD, Bromley LK, Wittwer CT, Voelkerding KV (2006) Amplicon DNA melting analysis for mutation scanning and genotyping: cross-platform comparison of instruments and dyes. Clinical Chemistry 52: 494–503.
9. Raja S, El-Hefnawy T, Kelly LA, Chestney ML, Luketich JD, Godfrey TE (2002) Temperature-controlled primer limit for multiplexing of rapid, quantitative reverse transcription-PCR assays: application to intraoperative cancer diagnostics. Clinical Chemistry 48: 1329–1337.
10. Wittwer CT, Ririe KM, Andrew RV, David DA, Gundry RA, Balis UJ (1997) The Light-Cycler: a microvolume multisample fluorimeter with rapid temperature control. BioTechniques 22: 176–181.
11. Wittwer CT, Ririe KM, Rasmussen RP (1998) Fluorescence monitoring of rapid cycle PCR for quantification. In: F Ferre (ed), Gene Quantification, pages 129–144. New York: Birkhauser.
12. Elenitoba-Johnson O, David D, Crews N, Wittwer CT (2008) Plastic vs glass capillaries for rapid-cycle PCR. Bio Techniques 44: 487–488, 490, 492.
13. Roper MG, Easley CJ, Landers JP (2005) Advances in polymerase chain reaction on microfluidic chips. Analytical Chemistry 77: 3887–3893.
14. Zhang C, Xing D (2007) Miniaturized PCR chips for nucleic acid amplification and analysis: latest advances and future trends. Nucleic Acids Research 35: 4223–4237.
15. Cheng J, Shoffner MA, Hvichia GE, Kricka LJ, Wilding P (1996) Chip PCR. II. Investigation of different PCR amplification systems in microfabricated silicon-glass chips. Nucleic Acids Research 24: 380–385.
16. Woolley AT, Hadley D, Landre P, deMello AJ, Mathies RA, Northrup MA (1996) Functional integration of PCR amplification and capillary electrophoresis in a microfabricated DNA analysis device. Analytical Chemistry 68: 4081–4086.
17. Neuzil P, Zhang C, Pipper J, Oh S, Zhuo L (2006) Ultra fast miniaturized real-time PCR: 40 cycles in less than six minutes. Nucleic Acids Research 34: e77.
18. Oda RP, Strausbauch MA, Huhmer AF, Borson N, Jurrens SR, Craighead J, et al. (1998) Infrared-mediated thermocycling for ultrafast polymerase chain reaction amplification of DNA. Analytical Chemistry 70: 4361–4368.
19. Roper MG, Easley CJ, Legendre LA, Humphrey JA, Landers JP (2007) Infrared temperature control system for a completely noncontact polymerase chain reaction in microfluidic chips. Analytical Chemistry 79: 1294–1300.
20. Friedman NA, Meldrum DR (1998) Capillary tube resistive thermal cycling. Analytical Chemistry 70: 2997–3002.
21. Heap DM, Herrmann MG, Wittwer CT (2000) PCR amplification using electrolytic resistance for heating and temperature monitoring. BioTechniques 29: 1006–1012.
22. Kopp MU, Mello AJ, Manz A (1998) Chemical amplification: continuous-flow PCR on a chip. Science 280: 1046–1048.
23. Hashimoto M, Chen PC, Mitchell MW, Nikitopoulos DE, Soper SA, Murphy MC (2004) Rapid PCR in a continuous flow device. Lab on a Chip 4: 638–645.
24. Crews N, Wittwer C, Gale B (2008) Continuous-flow thermal gradient PCR. Biomedical Microdevices 10: 187–195.
25. Chiou JT, Matsudaira PT, Ehrlich DJ (2002) Thirty-cycle temperature optimization of a closed-cycle capillary PCR machine. BioTechniques 33: 557–558, 560, 562.
26. Frey O, Bonneick S, Hierlemann A, Lichtenberg J (2007) Autonomous microfluidic multi-channel chip for real-time PCR with integrated liquid handling. Biomedical Microdevices 9: 711–718.
27. Chen J, Wabuyele M, Chen H, Patterson D, Hupert M, Shadpour H, et al. (2005) Electrokinetically synchronized polymerase chain reaction microchip fabricated in polycarbonate. Analytical Chemistry 77: 658–666.
28. Sun Y, Kwok YC, Nguyen NT (2007) A circular ferrofluid driven microchip for rapid polymerase chain reaction. Lab on a Chip 7: 1012–1017.
29. Agrawal N, Hassan YA, Ugaz VM (2007) A pocket-sized convective PCR thermocycler. Angewandte Chemie (International ed. in English) 46: 4316–4319.
30. Zhang C, Xu J, Ma W, Zheng W (2006) PCR microfluidic devices for DNA amplification. Biotechnology Advances 24: 243–284.
31. Wheeler EK, Benett W, Stratton P, Richards J, Chen A, Christian A, et al. (2004) Convectively driven polymerase chain reaction thermal cycler. Analytical Chemistry 76: 4011–4016.
32. Belgrader P, Benett W, Hadley D, Long G, Mariella R Jr, Milanovich F, et al. (1998) Rapid pathogen detection using a microchip PCR array instrument. Clinical Chemistry 44: 2191–2194.
33. Wilhelm J, Hahn M, Pingoud A (2000) Influence of DNA target melting behavior on real-time PCR quantification. Clinical Chemistry 46: 1738–1743.
34. Zuna J, Muzikova K, Madzo J, Krejci O, Trka J (2002) Temperature non-homogeneity in rapid airflow-based cycler significantly affects real-time PCR. BioTechniques 33: 508, 510, 512.
35. von Kanel T, Adolf F, Schneider M, Sanz J, Gallati S (2007) Sample number and denaturation time are crucial for the accuracy of capillary-based LightCyclers. Clinical Chemistry 53: 1392–1394.
36. Wittwer CT, Herrmann MG (1999) Rapid thermal cycling and PCR kinetics. In: M Innis, D Gelfand, and J Sninsky (eds), PCR Methods Manual, pages 211–229. San Diego: Academic Press.
37. Wittwer CT, Reed GH, Gundry CN, Vandersteen JG, Pryor RJ (2003) High-resolution genotyping by amplicon melting analysis using LCGreen. Clinical Chemistry 49: 853–860.
38. von Ahsen N, Wittwer CT, Schutz E (2001) Oligonucleotide melting temperatures under PCR conditions: nearest-neighbor corrections for Mg(2+), deoxynucleotide triphosphate, and dimethyl sulfoxide concentrations with comparison to alternative empirical formulas. Clinical Chemistry 47: 1956–1961.
39. Ririe KM, Rasmussen RP, Wittwer CT (1997) Product differentiation by analysis of DNA melting curves during the polymerase chain reaction. Analytical Biochemistry 245: 154–160.
40. Wittwer CT, Herrmann MG, Moss AA, Rasmussen RP (1997) Continuous fluorescence monitoring of rapid cycle DNA amplification. BioTechniques 22: 130–131, 134–138.
41. Weis JH, Tan SS, Martin BK, Wittwer CT (1992) Detection of rare mRNAs via quantitative RT-PCR. Trends in Genetics 8: 263–264.
42. Brown RA, Lay MJ, Wittwer CT (1998) Rapid cycle amplification for construction of competitive templates. In: RM Horton and RC Tait (eds), Genetic Engineering with PCR, pages 57–70. Norfolk: Horizon Scientific Press.
43. Wittwer CT, Kusukawa N (2004) Real-time PCR. In: DH Persing, FC Tenover, J Versalovic, YW Tang, ER Unger, DA Relman, et al. (eds), DiagnosticMolecular Microbiology: Principles and Applications, pages 71–84. Washington, DC: ASM Press.
44. Higuchi R, Dollinger G, Walsh PS, Griffith R (1992) Simultaneous amplification and detection of specific DNA sequences. Biotechnology (NY)10: 413–417.
45. Morrison TB, Weis JJ, Wittwer CT (1998) Quantification of low-copy transcripts by continuous SYBR Green I monitoring during amplification. BioTechniques 24: 954–958, 960, 962.
46. Gundry CN, Vandersteen JG, Reed GH, Pryor RJ, Chen J, Wittwer CT (2003) Amplicon melting analysis with labeled primers: a closed-tube method for differentiating homozygotes and heterozygotes. Clinical Chemistry 49: 396–406.
47. Reed GH, Kent JO, Wittwer CT (2007) High-resolution DNAmelting analysis for simple and efficient molecular diagnostics. Pharmacogenomics 8: 597–608.
48. Zhou L, Myers AN, Vandersteen JG, Wang L, Wittwer CT (2004) Closed-tube genotypingwith unlabeled oligonucleotide probes and a saturating DNA dye. Clinical Chemistry 50: 1328–1335.
49. Liew M, Pryor R, Palais R, Meadows C, Erali M, Lyon E, et al. (2004) Genotyping of single-nucleotide polymorphisms by high-resolution melting of small amplicons. Clinical Chemistry 50: 1156–1164.
50. Palais RA, Liew MA, Wittwer CT (2005) Quantitative heteroduplex analysis for single nucleotide polymorphism genotyping. Analytical Biochemistry 346: 167–175.
51. Graham R, Liew M, Meadows C, Lyon E, Wittwer CT (2005) Distinguishing different DNA heterozygotes by high-resolution melting. Clinical Chemistry 51: 1295–1298.
52. Vandersteen JG, Bayrak-Toydemir P, Palais RA, Wittwer CT (2007) Identifying common genetic variants by high-resolution melting. Clinical Chemistry 53: 1191–1198.
53. Montgomery J, Wittwer CT, Kent JO, Zhou L (2007) Scanning the cystic fibrosis transmembrane conductance regulator gene using high-resolution DNA melting analysis. Clinical Chemistry 53: 1891–1898.
54. Liew M, Nelson L, Margraf R, Mitchell S, Erali M, Mao R, et al. (2006) Genotyping of human platelet antigens 1 to 6 and 15 by high-resolution amplicon melting and conventional hybridization probes. The Journal of Molecular Diagnostics 8: 97–104.
55. Seipp MT, Durtschi JD, Liew MA, Williams J, Damjanovich K, Pont-Kingdon G, et al. (2007) Unlabeled oligonucleotides as internal temperature controls for genotyping by amplicon melting. The Journal of Molecular Diagnostics 9: 284–289.
56. Seipp MT, Pattison D, Durtschi JD, Jama M, Voelkerding KV, Wittwer CT (2008) Quadruplex genotyping of F5, F2, and MTHFR variants in a single closed tube by high-resolution amplicon melting. Clinical Chemistry 54: 108–115.
57. Liew M, Seipp M, Durtschi J, Margraf RL, Dames S, Erali M, et al. (2007) Closed-tube SNP genotyping without labeled probes/a comparison between unlabeled probe and amplicon melting. American Journal of Clinical Pathology 127: 1–8.
58. Zhou L, Vandersteen J, Wang L, Fuller T, Taylor M, Palais B, et al. (2004) Highresolution DNA melting curve analysis to establish HLA genotypic identity. Tissue Antigens 64: 156–164.
59. Reed GH, Wittwer CT (2004) Sensitivity and specificity of single-nucleotide polymorphism scanning by high-resolution melting analysis. Clinical Chemistry 50: 1748–1754.
60. Chou LS, Lyon E, Wittwer CT (2005) A comparison of high-resolution melting analysis with denaturing high-performance liquid chromatography for mutation scanning: cystic fibrosis transmembrane conductance regulator gene as amodel. American Journal of Clinical Pathology 124: 330–338.
61. Laurie AD, Smith MP, George PM (2007) Detection of Factor VIII gene mutations by high-resolution melting analysis. Clinical Chemistry 53: 2211–2214.
62. Dujols VE, Kusukawa N, McKinney JT, Dobrowolski SF, Wittwer CT (2006) Highresolution melting analysis for scanning and genotyping. In: MT Dorak (ed), Real-Time PCR, pages 157–171. New York: Garland Science.
63. Gingeras TR, Higuchi R, Kricka LJ, Lo YM, Wittwer CT (2005) Fifty years of molecular (DNA/RNA) diagnostics. Clinical Chemistry 51: 661–671.
64. Wittwer CT, Kusukawa N (2005) Nucleic acid techniques. In: C Burtis, E Ashwood, and D Bruns (eds), Tietz Textbook of Clinical Chemistry and Molecular Diagnostics. Fourth edition, pages 1407–1449. New York: Elsevier.
65. Lay MJ, Wittwer CT (1997) Real-time fluorescence genotyping of factor V Leiden during rapid-cycle PCR. Clinical Chemistry 43: 2262–2267.
66. Bernard PS, Ajioka RS, Kushner JP, Wittwer CT (1998) Homogeneous multiplex genotyping of hemochromatosis mutationswith fluorescent hybridization probes. American Journal of Pathology 153: 1055–1061.
67. Wittwer CT, Herrmann MG, Gundry CN, Elenitoba-Johnson KS (2001) Real-time multiplex PCR assays. Methods 25: 430–442.
68. Herrmann MG, Dobrowolski SF, Wittwer CT (2000) Rapid beta-globin genotyping by multiplexing probe melting temperature and color. Clinical Chemistry 46: 425–428.
69. von Ahsen N (2003) Labeled primers for mutation scanning: making diagnostic use of the nucleobase quenching effect. Clinical Chemistry 49: 355–356.
70. Crockett AO, Wittwer CT (2001) Fluorescein-labeled oligonucleotides for real-time PCR: using the inherent quenching of deoxyguanosine nucleotides. Analytical Biochemistry 290: 89–97.
71. Dames SA, Margraf RL, Pattison D, Wittwer CT, Voelkerding KV (2007) Characterization of aberrant melting peaks in unlabeled probe assays. The Journal of Molecular Diagnostics 9: 290–296.
72. Poulson MD, Wittwer CT (2007) Closed-tube genotyping of apolipoprotein E by isolated-probe PCR with multiple unlabeled probes and high-resolution DNA melting analysis. BioTechniques 43: 87–91.
73. Margraf RL, Mao R, Wittwer CT (2006) Masking selected sequence variation by incorporating mismatches into melting analysis probes. Human Mutation 27: 269–278.
74. Zhou L, Wang L, Palais R, Pryor R, Wittwer CT (2005) High-resolution DNA melting analysis for simultaneous mutation scanning and genotyping in solution. Clinical Chemistry 51: 1770–1777.
75. Erali M, Palais B, Wittwer C (2008) SNP genotyping by unlabeled probe melting analysis. In: O Seitz and A Marx (eds), Molecular Beacons – Signaling Nucleic Acid Probes, Methods and Protocols, pp. 199–206 (Methods in Molecular Biology Series, Vol. 429). Totowa, NJ: Humana Press.