Correcting for heat capacity and 5′-TA type terminal nearest neighbors improves prediction of DNA melting temperatures using nearest-neighbor thermodynamic models

Biochemistry

Volumn 50, Issue 13, 2011, Pages 2642-2649

  Hughesman, Curtis B ^a,b   Turner, Robin F B ^a,b   Haynes, Charles ^a,b  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^b UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURATE PREDICTION; BASE PAIRS; BROAD TEMPERATURE RANGES; DNA DUPLEXES; DNA MELTING; HEAT CAPACITIES; HEAT CAPACITY CHANGE; HELIX-TO-COIL TRANSITIONS; HYBRIDIZATION THERMODYNAMICS; MELTING TEMPERATURES; NEAREST NEIGHBORS; NEW APPROACHES; REFERENCE TEMPERATURE; TEMPERATURE DEPENDENCE; THERMODYNAMIC DATA; THERMODYNAMIC MODEL;

DIFFERENTIAL SCANNING CALORIMETRY; DNA; FORECASTING; MELTING POINT; METAL MELTING; NUCLEIC ACIDS; PHASE TRANSITIONS; SPECIFIC HEAT; THERMOANALYSIS;

THERMODYNAMICS;

DOUBLE STRANDED DNA;

ARTICLE; DIFFERENTIAL SCANNING CALORIMETRY; DNA DENATURATION; DNA HYBRIDIZATION; DNA LIBRARY; PRIORITY JOURNAL; TEMPERATURE; TERMINAL SEQUENCE; THERMODYNAMICS;

ALGORITHMS; BASE SEQUENCE; CALORIMETRY, DIFFERENTIAL SCANNING; DNA; HOT TEMPERATURE; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; OLIGODEOXYRIBONUCLEOTIDES; THERMODYNAMICS; TRANSITION TEMPERATURE;

EID: 79953207302     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi101653z     Document Type: Article

References (33)

1. Rychlik, W., Spencer, W. J., and Rhoads, R. E. (1990) Optimization of the annealing temperature for DNA amplification in vitro Nucleic Acids Res. 18, 6409-6412
2. Rouillard, J. M., Zuker, M., and Gulari, E. (2003) OligoArray 2.0: Design of oligonucleotide probes for DNA microarrays using a thermodynamic approach Nucleic Acids Res. 31, 3057-3062 (Pubitemid 37441764)
3. Matveeva, O. V., Shabalina, S. A., Nemtsov, V. A., Tsodikov, A. D., Gesteland, R. F., and Atkins, J. F. (2003) Thermodynamic calculations and statistical correlations for oligo-probes design Nucleic Acids Res. 31, 4211-4217 (Pubitemid 37442300)
4. Matveeva, O. V., Mathews, D. H., Tsodikov, A. D., Shabalina, S. A., Gesteland, R. F., Atkins, J. F., and Freier, S. M. (2003) Thermodynamic criteria for high hit rate antisense oligonucleotide design Nucleic Acids Res. 31, 4989-4994 (Pubitemid 37441865)
5. Zimm, B. H. (1960) Theory of "Melting" of the Helical Form in Double Chains of the DNA Type J. Chem. Phys. 33, 1349-1356
6. Gray, D. M. and Tinoco, I., Jr. (1970) A new approach to the study of sequence-dependent properties of polynucleotides Biopolymers 9, 223-244
7. Breslauer, K. J., Frank, R., Blocker, H., and Marky, L. A. (1986) Predicting DNA duplex stability from the base sequence Proc. Natl. Acad. Sci. U.S.A. 83, 3746-3750 (Pubitemid 16062362)
8. SantaLucia, J., Jr., Allawi, H. T., and Seneviratne, P. A. (1996) Improved nearest-neighbor parameters for predicting DNA duplex stability Biochemistry 35, 3555-3562 (Pubitemid 26092574)
9. Sugimoto, N., Nakano, S., Yoneyama, M., and Honda, K. (1996) Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes Nucleic Acids Res. 24, 4501-4505 (Pubitemid 26388637)
10. Bruylants, G., Boccongelli, M., Snoussi, K., and Bartik, K. (2009) Comparison of the thermodynamics and base-pair dynamics of a full LNA:DNA duplex and of the isosequential DNA:DNA duplex Biochemistry 48, 8473-8482
11. Holbrook, J. A., Capp, M. W., Saecker, R. M., and Record, M. T., Jr. (1999) Enthalpy and heat capacity changes for formation of an oligomeric DNA duplex: Interpretation in terms of coupled processes of formation and association of single-stranded helices Biochemistry 38, 8409-8422
12. Jelesarov, I., Crane-Robinson, C., and Privalov, P. L. (1999) The energetics of HMG box interactions with DNA: Thermodynamic description of the target DNA duplexes J. Mol. Biol. 294, 981-995 (Pubitemid 30000389)
13. Mikulecky, P. J. and Feig, A. L. (2006) Heat capacity changes associated with DNA duplex formation: Salt- and sequence-dependent effects Biochemistry 45, 604-616 (Pubitemid 43100425)
14. Tikhomirova, A., Beletskaya, I. V., and Chalikian, T. V. (2006) Stability of DNA duplexes containing GG, CC, AA, and TT mismatches Biochemistry 45, 10563-10571 (Pubitemid 44320472)
15. Wu, P., Nakano, S., and Sugimoto, N. (2002) Temperature dependence of thermodynamic properties for DNA/DNA and RNA/DNA duplex formation Eur. J. Biochem. 269, 2821-2830 (Pubitemid 34754009)
16. Chalikian, T. V., Volker, J., Plum, G. E., and Breslauer, K. J. (1999) A more unified picture for the thermodynamics of nucleic acid duplex melting: A characterization by calorimetric and volumetric techniques Proc. Natl. Acad. Sci. U.S.A. 96, 7853-7858 (Pubitemid 29328371)
17. p J. Am. Chem. Soc. 126, 16387-16394 (Pubitemid 40081936)
18. Mikulecky, P. J. and Feig, A. L. (2006) Heat capacity changes associated with nucleic acid folding Biopolymers 82, 38-58
19. Rouzina, I. and Bloomfield, V. A. (1999) Heat capacity effects on the melting of DNA. 2. Analysis of nearest-neighbor base pair effects Biophys. J. 77, 3252-3255
20. Allawi, H. T. and SantaLucia, J., Jr. (1997) Thermodynamics and NMR of internal G•T mismatches in DNA Biochemistry 36, 10581-10594 (Pubitemid 27374152)
21. SantaLucia, J., Jr. (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics Proc. Natl. Acad. Sci. U.S.A. 95, 1460-1465 (Pubitemid 28103414)
22. Chavali, S., Mahajan, A., Tabassum, R., Maiti, S., and Bharadwaj, D. (2005) Oligonucleotide properties determination and primer designing: A critical examination of predictions Bioinformatics 21, 3918-3925 (Pubitemid 41535508)
23. SantaLucia, J., Jr. and Hicks, D. (2004) The thermodynamics of DNA structural motifs Annu. Rev. Biophys. Biomol. Struct. 33, 415-440 (Pubitemid 38829966)
24. Erali, M., Voelkerding, K. V., and Wittwer, C. T. (2008) High resolution melting applications for clinical laboratory medicine Exp. Mol. Pathol. 85, 50-58
25. Vossen, R. H., Aten, E., Roos, A., and den Dunnen, J. T. (2009) High-resolution melting analysis (HRMA): More than just sequence variant screening Hum. Mutat. 30, 860-866
26. Levin, J. D., Fiala, D., Samala, M. F., Kahn, J. D., and Peterson, R. J. (2006) Position-dependent effects of locked nucleic acid (LNA) on DNA sequencing and PCR primers Nucleic Acids Res. 34, e142
27. McTigue, P. M., Peterson, R. J., and Kahn, J. D. (2004) Sequence-dependent thermodynamic parameters for locked nucleic acid (LNA)-DNA duplex formation Biochemistry 43, 5388-5405 (Pubitemid 38620931)
28. Owczarzy, R., You, Y., Moreira, B. G., Manthey, J. A., Huang, L., Behlke, M. A., and Walder, J. A. (2004) Effects of sodium ions on DNA duplex oligomers: Improved predictions of melting temperatures Biochemistry 43, 3537-3554 (Pubitemid 38391709)
29. Owczarzy, R. (2005) Melting temperatures of nucleic acids: Discrepancies in analysis Biophys. Chem. 117, 207-215 (Pubitemid 41253595)
30. Ramprakash, J., Lang, B., and Schwarz, F. P. (2008) Thermodynamics of single strand DNA base stacking Biopolymers 89, 969-979
31. Vesnaver, G. and Breslauer, K. J. (1991) The contribution of DNA single-stranded order to the thermodynamics of duplex formation Proc. Natl. Acad. Sci. U.S.A. 88, 3569-3573 (Pubitemid 21916664)
32. Rouzina, I. and Bloomfield, V. A. (1999) Heat capacity effects on the melting of DNA. 1. General aspects Biophys. J. 77, 3242-3251
33. Zhou, Y., Hall, C. K., and Karplus, M. (1999) The calorimetric criterion for a two-state process revisited Protein Sci. 8, 1064-1074 (Pubitemid 29211744)