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A free energy analysis of nucleic acid base stacking in aqueous solution
Open accessAbstract
This paper reports a theoretical study of the free energy contributions to nucleic acid base stacking in aqueous solution. Electrostatic interactions are treated by using the finite difference Poisson-Boltzmann method and nonpolar effects are treated with explicit calculation of van der Waals interactions and/or free energy-surface area relationships. Although for some pairs of bases there is a favorable Coulombic interaction in the stacked conformation, generally the net effect of electrostatic interactions is to oppose stacking. This result is caused by the loss of favorable base-solvent electrostatic interactions, that accompany the partial removal of polar atoms from water in the stacked conformation. Nonpolar interactions, involving the hydrophobic effect and enhancement of van der Waals interactions caused by close-packing, drive stacking. The calculations qualitatively reproduce the experimental dependence of stacking free energy on purine-pyrimidine composition.
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Cited by
Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics
Cramer, C. J., & Truhlar, D. G. (1999) · Chemical Reviews · doi:10.1021/cr960149m · Cited by 2,308
Factors Contributing to Aromatic Stacking in Water: Evaluation in the Context of DNA
Guckian, K. M., Schweitzer, B. A., Ren, R. X.-F., Sheils, C. J., Tahmassebi, D. C., & Kool, E. T. (2000) · Journal of the American Chemical Society · doi:10.1021/ja9934854 · Cited by 434
Active Site Tightness and Substrate Fit in DNA Replication
Kool, E. T. (2002) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.71.110601.135453 · Cited by 350
Tan, Z.-J., & Chen, S.-J. (2006) · Biophysical Journal · doi:10.1529/biophysj.105.070904 · Cited by 326
Protein and DNA Sequence Determinants of Thermophilic Adaptation
Zeldovich, K. B., Berezovsky, I. N., & Shakhnovich, E. I. (2007) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0030005 · Cited by 325
Metadata
- Authors
- Friedman, R. A., & Honig, B.
- Venue
- Biophysical Journal
- Publisher
- Elsevier BV
- Published
- 1995-10
- Volume
- 69
- Issue
- 4
- Pages
- 1528-1535
- ISSN
- 0006-3495 (ISSN-L)
- OpenAlex
- W1994418194
- Cited by
- 240
- References
- 0
- FWCI
- 2.25
- Type
- journal article
- Language
- en
- Open access
- hybrid
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- Friedman, R. A., & Honig, B. (1995). A free energy analysis of nucleic acid base stacking in aqueous solution. Biophysical Journal. https://doi.org/10.1016/s0006-3495(95)80023-8
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