Salt-Dependent stability of poly(dG) · poly(dC) with potential of mean force coulomb interactions
✍ Scribed by Y. Z. Chen; W. Zhuang; E. W. Prohofsky
- Book ID
- 101719121
- Publisher
- Wiley (John Wiley & Sons)
- Year
- 1992
- Tongue
- English
- Weight
- 404 KB
- Volume
- 32
- Category
- Article
- ISSN
- 0006-3525
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✦ Synopsis
In earlier work we have showed that the modified selfconsistent phonon approximation (MSPA) could be used to describe a system in which hydrogen-bond breaking and base-pair separation could be analyzed by statistical methods.'-4 We calculated the probability of the breakdown of the interbase H bonds of the DNA homopolymers caused by thermal fluctuations. We showed that the approach gave reasonable values for the fluctuational H-bond opening in the premelting region and could show the correct cooperative behavior for melting in the critical transition region. That work did not contain factors explicitly dependent on ionic environment or effects due to static Coulomb interactions. The theory looked only at excitations from an assumed low temperature stable configuration. The force constants and Morse parameters that went into the calculations were extracted from Raman and ir measurements on samples under "physiological salt conditions." The theory is, then, presumed valid for the same conditions. Experimentally, however, DNA denatures at low salt c ~n c e n t r a t i o n , ~-~ and inclusion of Coulomb forces causes instabilities in simulation (A. X. Garcia, private communication).
In this communication we show that explicit salt dependence can be incorporated into the MSPA quasi-equilibrium calculation by including tensions developed in the system due to Coulomb interactions. The Coulomb interactions are included as a potential of mean force ( P M F ) in which there is explicit salt dependence. We carry out this calculation in the homopolymer poly( dG) * poly( dC). We find that the helix is stable at room temperature for "physiological" NaCl concentration (C, -0.05M NaCl) .