Heat capacity changes associated with DNA duplex formation: Salt- and sequence-dependent effects

Biochemistry

Volumn 45, Issue 2, 2006, Pages 604-616

  Mikulecky, Peter J ^a   Feig, Andrew L ^a  

^a INDIANA UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CALORIMETRY; DNA; PROTEINS; SALTS; SPECTROSCOPIC ANALYSIS; THERMODYNAMICS; TITRATION;

DNA DUPLEX FORMATION; ISOTHERMAL TITRATION CALORIMETRY (ITC); NUCLEIC ACID FOLDING; SINGLE STRAND MELTING;

SPECIFIC HEAT;

DOUBLE STRANDED DNA; SODIUM CHLORIDE;

ARTICLE; DNA DETERMINATION; HEATING; IONIC STRENGTH; ISOTHERMAL TITRATION CALORIMETRY; MELTING POINT; NUCLEIC ACID ANALYSIS; PHASE TRANSITION; PRIORITY JOURNAL; PROTEIN FOLDING; SOLVATION;

BASE SEQUENCE; CALORIMETRY; CALORIMETRY, DIFFERENTIAL SCANNING; CIRCULAR DICHROISM; DNA; HEAT; KINETICS; NUCLEIC ACID HETERODUPLEXES; PURINES; SALTS;

EID: 30744467696     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi0517178     Document Type: Article

References (60)

1. Cooper, A. (2000) Heat capacity of hydrogen-bonded networks: an alternative view of protein folding thermodynamics, Biophys. Chem. 85, 25-39.
2. Cooper, A., Johnson, C. M., Lakey, J. H., and Nollmann, M. (2001) Heat does not come in different colours: entropy-enthalpy compensation, free energy windows, quantum confinement, pressure perturbation calorimetry, solvation and the multiple causes of heat capacity effects in biomolecular interactions, Biophys. Chem. 93, 215-230.
3. Sharp, K. (2001) Entropy-enthalpy compensation: Fact or artifact?, Protein Sci. 10, 661-667.
4. Makhatadze, G. I. (1998) Heat capacities of amino acids, peptides and proteins, Biophys. Chem. 71, 133-156.
5. Mikulecky, P. J., and Feig, A. L. (2006) Heat capacity changes associated with nucleic acid folding, Biopolymers (in press).
6. Rouzina, I., and Bloomfield, V. A. (1999) Heat capacity effects on the melting of DNA. 1. General aspects, Biophys. J. 77, 3242-3251.
7. Privalov, P. L. (1990) Cold denaturation of proteins, Crit. Rev. Biochem. Mol. Biol. 25, 281-305.
8. Tamura, A., Kimura, K., Takahara, H., and Akasaka, K. (1991) Cold denaturation and heat denaturation of Streptomyces subtilisin inhibitor. 1. CD and DSC studies, Biochemistry 30, 11307-11313.
9. Hallerbach, B., and Hinz, H. J. (1999) Protein heat capacity: inconsistencies in the current view of cold denaturation, Biophys. Chem. 76, 219-227.
10. Mikulecky, P. J., and Feig, A. L. (2002) Cold denaturation of the hammerhead ribozyme, J. Am. Chem. Soc. 124, 890-891.
11. Mikulecky, P. J., and Feig, A. L. (2004) Heat capacity changes in RNA folding: application of perturbation theory to hammerhead ribozyme cold denaturation, Nucleic Acids Res. 32, 3967-3976.
12. Suurkuusk, J., Alvarez, J., Freire, E., and Biltonen, R. (1977) Calorimetric determination of the heat capacity changes associated with the conformational transitions of polyriboadenylic acid and polyribouridylic acid, Biopolymers 16, 2641-2652.
13. Petersheim, M., and Turner, D. H. (1983) Base-stacking and base-pairing contributions to helix stability-thermodynamics of double-helix formation with CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp, and ACCGGUp, Biochemistry 22, 256-263.
14. Sugimoto, N., Kierzek, R., Freier, S. M., and Turner, D. H. (1986) Energetics of internal GU mismatches in ribooligonucleotide helixes, Biochemistry 25, 5755-5759.
15. Freier, S. M., Sugimoto, N., Sinclair, A., Alkema, D., Neilson, T., Kierzek, R., Caruthers, M. H., and Turner, D. H. (1986) Stability of XGCGCp, GCGCYp, and XGCGCYp helixes: an empirical estimate of the energetics of hydrogen bonds in nucleic acids, Biochemistry 25, 3214-3219.
16. 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.
17. Kamiya, M., Torigoe, H., Shindo, H., and Sarai, A. (1996) Temperature dependence and sequence specificity of DNA triplex formation: An analysis using isothermal titration calorimetry, J. Am. Chem. Soc. 118, 4532-4538.
18. Plum, G. E. (1997) Thermodynamics of oligonucleotide triple helices, Biopolymers 44, 241-256.
19. Cao, W., and Lai, L. H. (1999) A thermodynamic study on the formation and stability of DNA duplex at transcription site for DNA binding proteins GCN4, Biophys. Chem. 80, 217-226.
20. Holbrook, J. A., Capp, M. W., Saecker, R. M., and Record, M. T. (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.
21. 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.
22. Ross, P. D., and Howard, F. B. (2003) The thermodynamic contribution of the 5-methyl group of thymine in the two- and three-stranded complexes formed by poly(dU) and poly(dT) with poly(dA), Biopolymers 68, 210-222.
23. Gomez, J., Hilser, V. J., Xie, D., and Freire, E. (1995) The heat capacity of proteins, Proteins 22, 404-412.
24. 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.
25. 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.
26. Chalikian, T. V. (2001) Structural thermodynamics of hydration, J. Phys. Chem. B 105, 12566-12578.
27. Madan, B., and Sharp, K. A. (2001) Hydration heat capacity of nucleic acid constituents determined from the random network model, Biophys. J. 81, 1881-1887.
28. Williams, M. C., Wenner, J. R., Rouzina, I., and Bloomfield, V. A. (2001) Entropy and heat capacity of DNA melting from temperature dependence of single molecule stretching, Biophys. J. 80, 1932-1939.
29. 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.
30. P, J. Am. Chem. Soc. 126, 16387-16394.
31. Hallerbach, B., and Hinz, H. J. (2000) Protein heat capacity reflects the dynamics of enthalpy exchange between the single macromolecule and the surroundings, Proteins: Struct., Funct., Genet., 86-92.
32. Prabhu, N. V., and Sharp, K. A. (2005) Heat capacity in proteins, Annu. Rev. Phys. Chem. 56, 521-548.
33. Robertson, A. D., and Murphy, K. P. (1997) Protein structure and the energetics of protein stability, Chem. Rev. 97, 1251-1267.
34. Chalikian, T. V., and Breslauer, K. J. (1998) Volumetric properties of nucleic acids, Biopolymers 48, 264-280.
35. Gallagher, K., and Sharp, K. (1998) Electrostatic contributions to heat capacity changes of DNA-ligand binding, Biophys. J. 75, 769-776.
36. Madan, B., and Sharp, K. (1996) Heat capacity changes accompanying hydrophobic and ionic solvation: A Monte Carlo and random network model study, J. Phys. Chem. 100, 7713-7721.
37. Sharp, K. A., and Madan, B. (1997) Hydrophobic effect, water structure, and heat capacity changes, J. Phys. Chem. B 101, 4343-4348.
38. Gallagher, K. R., and Sharp, K. A. (2003) A new angle on heat capacity changes in hydrophobic solvation, J. Am. Chem. Soc. 125, 9853-9860.
39. Eftink, M. R., Anusiem, A. C., and Biltonen, R. L. (1983) Enthalpy-entropy compensation and heat capacity changes for protein-ligand interactions-General thermodynamic models and data for the binding of nucleotides to ribonuclease A, Biochemistry 22, 3884-3896.
40. Lane, A. N., and Jenkins, T. C. (2000) Thermodynamics of nucleic acids and their interactions with ligands, Q. Rev. Biophys. 33, 255-306.
41. Thirumalai, D., Lee, N., Woodson, S. A., and Klimov, D. (2001) Early events in RNA folding, Annu. Rev. Phys. Chem. 52, 751-762.
42. Serra, M. J., and Turner, D. H. (1995) Predicting thermodynamic properties of RNA, Methods Enzymol. 259, 242-261.
43. SantaLucia, J., and Turner, D. H. (1997) Measuring the thermodynamics of RNA secondary structure formation, Biopolymers 44, 309-319.
44. 2+ ions, Biophys. J. 75, 3041-3056.
45. 2+ ions, J. Biomol. Struct. Dyn. 20, 275-290.
46. Takach, J. C., Mikulecky, P. J., and Feig, A. L. (2004) Salt-dependent heat capacity changes for RNA duplex formation, J. Am. Chem. Soc. 126, 6530-6531.
47. (1975) CRC Handbook of Biochemistry and Molecular Biology, Vol. 1, 3rd ed., CRC Press LLC, Boca Raton, FL.
48. Mizoue, L. S., and Tellinghuisen, J. (2004) The role of backlash in the "first injection anomaly" in isothermal titration calorimetry, Anal. Biochem. 326, 125-127.
49. Wiseman, T., Williston, S., Brandts, J. F., and Lin, L. N. (1989) Rapid measurement of binding constants and heats of binding using a new titration calorimeter, Anal. Biochem. 179, 131-137.
50. 2, Proc. Natl. Acad. Sci. U.S.A. 88, 1551-1555.
51. SantaLucia, J., Jr., and Hicks, D. (2004) The thermodynamics of DNA structural motifs, Annu. Rev. Biophys. Biomol. Struct. 33, 415-440.
52. Appleby, D. W., and Kallenbach, N. R. (1973) Theory of oligonucleotide stabilization. 1. Effect of single-strand stacking, Biopolymers 12, 2093-2120.
53. Wu, P., and Sugimoto, N. (2000) Transition characteristics and thermodynamic analysis of DNA duplex formation: a quantitative consideration for the extent of duplex association, Nucleic Acids Res. 28, 4762-4768.
54. Dimitrov, R. A., and Zuker, M. (2004) Prediction of hybridization and melting for double-stranded nucleic acids, Biophys. J. 87, 215-226.
55. Markham, N. R., and Zuker, M. (2005) DINAMelt web server for nucleic acid melting prediction, Nucleic Acids Res. 33, W577-W581.
56. Zuker, M. (2003) Mfold web server for nucleic acid folding and hybridization prediction, Nucleic Acids Res. 31, 3406-3415.
57. Diamond, J. M., Turner, D. H., and Mathews, D. H. (2001) Thermodynamics of three-way multibranch loops in RNA, Biochemistry 40, 6971-6981.
58. Mathews, D. H., and Turner, D. H. (2002) Experimentally derived nearest-neighbor parameters for the stability of RNA three- and four-way multibranch loops, Biochemistry 41, 869-880.
59. Doshi, K. J., Cannone, J. J., Cobaugh, C. W., and Gutell, R. R. (2004) Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction, BMC Bioinformatics 5.
60. Fang, X. W., Golden, B. L., Littrell, K., Shelton, V., Thiyagarajan, P., Pan, T., and Sosnick, T. R. (2001) The thermodynamic origin of the stability of a thermophilic ribozyme, Proc. Natl. Acad. Sci. U.S.A. 98, 4355-4360.