Influencing factors of dsDNA dye (high-resolution) melting curves and improved genotype call based on thermodynamic considerations

Analytical Biochemistry

Volumn 385, Issue 1, 2009, Pages 143-152

  Schütz, Ekkehard ^a,b   von Ahsen, Nicolas ^c  

^a Chronix Biomedical   (Germany)

^b Institute of Veterinary Medicine   (Germany)

^c UNIVERSITY MEDICAL CENTER GÖTTINGEN   (Germany)

Author keywords

DNA dyes; High resolution melting; LightCycler; Thermodynamics

Indexed keywords

COMPUTERIZED TOMOGRAPHY; COST EFFECTIVENESS; ENTHALPY; POLYMERASE CHAIN REACTION; SCANNING; THERMODYNAMICS;

HIGH RESOLUTION; LIGHTCYCLER; MELTING CURVES; MODEL CALCULATIONS; MUTATION DETECTION; ROBUST MEASURES; TEMPERATURE RESOLUTION; TRANSITION ENTHALPY;

MELTING;

DOUBLE STRANDED DNA; DYE; MULTIDRUG RESISTANCE PROTEIN 1; RESOLIGHT; SODIUM CHLORIDE; UNCLASSIFIED DRUG;

ANIMAL TISSUE; ARTICLE; CONCENTRATION (PARAMETERS); CONTROLLED STUDY; DOG; ENTHALPY; GENE MUTATION; GENOTYPE; MATHEMATICAL ANALYSIS; MELTING POINT; MUTATIONAL ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SIMULATION; STAINING; TEMPERATURE MEASUREMENT; THERMODYNAMICS;

EID: 57749189098     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2008.10.045     Document Type: Article

References (41)

1. Wittwer C.T., Reed G.H., Gundry C.N., Vandersteen J.G., and Pryor R.J. High-resolution genotyping by amplicon melting analysis using LCGreen. Clin. Chem. 49 (2003) 853-860
2. Gundry C.N., Vandersteen J.G., Reed G.H., Pryor R.J., Chen J., and Wittwer C.T. Amplicon melting analysis with labeled primers: a closed-tube method for differentiating homozygotes and heterozygotes. Clin. Chem. 49 (2003) 396-406
3. Zhou L., Myers A.N., Vandersteen J.G., Wang L., and Wittwer C.T. Closed-tube genotyping with unlabeled oligonucleotide probes and a saturating DNA dye. Clin. Chem. 50 (2004) 1328-1335
4. Reed G.H., Kent J.O., and Wittwer C.T. High-resolution DNA melting analysis for simple and efficient molecular diagnostics. Pharmacogenomics 8 (2007) 597-608
5. Montgomery J., Wittwer C.T., Kent J.O., and Zhou L. Scanning the cystic fibrosis transmembrane conductance regulator gene using high-resolution DNA melting analysis. Clin. Chem. 53 (2007) 1891-1898
6. Dames S., Margraf R.L., Pattison D.C., Wittwer C.T., and Voelkerding K.V. Characterization of aberrant melting peaks in unlabeled probe assays. J. Mol. Diagn. 9 (2007) 290-296
7. Hill C.E., Duncan A., Wirth D., and Nolte F.S. Detection and identification of cytochrome P-450 2C9 alleles *1, *2, and *3 by high-resolution melting curve analysis of PCR amplicons. Am. J. Clin. Pathol. 125 (2006) 584-591
8. Zhou L., Wang L., Palais R., Pryor R., and Wittwer C.T. High-resolution DNA melting analysis for simultaneous mutation scanning and genotyping in solution. Clin. Chem. 51 (2005) 1770-1777
9. Herrmann M.G., Durtschi J.D., Wittwer C.T., and Voelkerding K.V. Expanded instrument comparison of amplicon DNA melting analysis for mutation scanning and genotyping. Clin. Chem. 53 (2007) 1544-1548
10. Herrmann M.G., Durtschi J.D., Bromley L.K., Wittwer C.T., and Voelkerding K.V. Amplicon DNA melting analysis for mutation scanning and genotyping: cross-platform comparison of instruments and dyes. Clin. Chem. 52 (2006) 494-503
11. Monis P.T., Giglio S., and Saint C.P. Comparison of SYTO9 and SYBR Green I for real-time polymerase chain reaction and investigation of the effect of dye concentration on amplification and DNA melting curve analysis. Anal. Biochem. 340 (2005) 24-34
12. Marziliano N., Pelo E., Minuti B., Passerini I., Torricelli F., and Da Prato L. Melting temperature assay for a UGT1A gene variant in Gilbert syndrome. Clin. Chem. 46 (2000) 423-425
13. von Ahsen N., Oellerich M., and Schutz E. Limitations of genotyping based on amplicon melting temperature. Clin. Chem. 47 (2001) 1331-1332
14. Krypuy M., Ahmed A.A., Etemadmoghadam D., Hyland S.J., DeFazio A., Fox S.B., Brenton J.D., Bowtell D.D., and Dobrovic A. High resolution melting for mutation scanning of TP53 exons 5-8. BMC Cancer 7 (2007) 168
15. Hsia A.P., Wen T.J., Chen H.D., Liu Z., Yandeau-Nelson M.D., Wei Y., Guo L., and Schnable P.S. Temperature gradient capillary electrophoresis (TGCE)-a tool for the high-throughput discovery and mapping of SNPs and IDPs. Theor. Appl. Genet. 111 (2005) 218-225
16. Gut I.G. DNA analysis by MALDI-TOF mass spectrometry. Hum. Mutat. 23 (2004) 437-441
17. Kristensen V.N., Kelefiotis D., Kristensen T., and Borresen-Dale A.L. High-throughput methods for detection of genetic variation. Biotechniques 30 (2001) 318-322 324, 326 passim
18. Marky L.A., and Breslauer K.J. Calculating thermodynamic data for transitions of any molecularity from equilibrium melting curves. Biopolymers 26 (1987) 1601-1620
19. Marky L.A., Blumenfeld K.S., Kozlowski S., and Breslauer K.J. Salt-dependent conformational transitions in the self-complementary deoxydodecanucleotide d(CGCAATTCGCG): evidence for hairpin formation. Biopolymers 22 (1983) 1247-1257
20. Schildkraut C. Dependence of the melting temperature of DNA on salt concentration. Biopolymers 3 (1965) 195-208
21. SantaLucia Jr. J. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl. Acad. Sci. USA 95 (1998) 1460-1465
22. SantaLucia Jr. J., Allawi H.T., and Seneviratne P.A. Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry 35 (1996) 3555-3562
23. Schütz E., and von Ahsen N. Spreadsheet software for thermodynamic melting point prediction of oligonucleotide hybridization with and without mismatches. Biotechniques 27 (1999) 1218-1222 1224
24. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31 (2003) 3406-3415
25. McTigue P.M., Peterson R.J., and Kahn J.D. Sequence-dependent thermodynamic parameters for locked nucleic acid (LNA)-DNA duplex formation. Biochemistry 43 (2004) 5388-5405
26. Manning G.S. On the application of polyelectrolyte "limiting laws" to the helix-coil transition of DNA. II. The effect of Mg++ counterions. Biopolymers 11 (1972) 951-955
27. Record Jr. M.T., Woodbury C.P., and Lohman T.M. Na+ effects on transition of DNA and polynucleotides of variable linear charge density. Biopolymers 15 (1976) 893-915
28. Blake R.D., and Delcourt S.G. Thermal stability of DNA. Nucleic Acids Res. 26 (1998) 3323-3332
29. Seipp M.T., Durtschi J.D., Liew M.A., Williams J., Damjanovich K., Pont-Kingdon G., Lyon E., Voelkerding K.V., and Wittwer C.T. Unlabeled oligonucleotides as internal temperature controls for genotyping by amplicon melting. J. Mol. Diagn. 9 (2007) 284-289
30. Douthart R.J., Burnett J.P., Beasley F.W., and Frank B.H. Binding of ethidium bromide to double-stranded ribonucleic acid. Biochemistry 12 (1973) 214-220
31. Anshelevich V.V., Vologodskii A.V., Lukashin A.V., and Frank-Kamenetskii M.D. Slow relaxational processes in the melting of linear biopolymers: a theory and its application to nucleic acids. Biopolymers 23 (1984) 39-58
32. Breslauer K.J., Frank R., Blocker H., and Marky L.A. Predicting DNA duplex stability from the base sequence. Proc. Natl. Acad. Sci. USA 83 (1986) 3746-3750
33. Allawi H.T., and SantaLucia Jr. J. Thermodynamics and NMR of internal G.T mismatches in DNA. Biochemistry 36 (1997) 10581-10594
34. Owczarzy R., You Y., Moreira B.G., Manthey J.A., Huang L., Behlke M.A., and Walder J.A. Effects of sodium ions on DNA duplex oligomers: improved predictions of melting temperatures. Biochemistry 43 (2004) 3537-3554
35. SantaLucia Jr. J., and Turner D.H. Measuring the thermodynamics of RNA secondary structure formation. Biopolymers 44 (1997) 309-319
36. Förster T. Energiewanderung und Fluoreszenz. Naturwissenschaften 6 (1946) 166-175
37. Förster T. Zwischenmolekulare Energiewanderung und Floureszenz. Annal. Phys. 437 (1948) 55-75
38. Cardullo R.A., Agrawal S., Flores C., Zamecnik P.C., and Wolf D.E. Detection of nucleic acid hybridization by nonradiative fluorescence resonance energy transfer. Proc. Natl. Acad. Sci. USA 85 (1988) 8790-8794
39. von Ahsen N., Wittwer C.T., and Schütz E. Oligonucleotide melting temperatures under PCR conditions: nearest-neighbor corrections for Mg(2+), deoxynucleotide triphosphate, and dimethyl sulfoxide concentrations with comparison to alternative empirical formulas. Clin. Chem. 47 (2001) 1956-1961
40. Pont-Kingdon G., Margraf R.L., Sumner K., Millson A., Lyon E., and Schütz E. Design and application of noncontinuously binding probes used for haplotyping and genotyping. Clin. Chem. 54 (2008) 990-999
41. Gordon P.M., and Sensen C.W. Osprey: a comprehensive tool employing novel methods for the design of oligonucleotides for DNA sequencing and microarrays. Nucleic Acids Res. 32 (2004) e133