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| Item Type: | Article |
|---|---|
| Title: | Analysis of the stability of looped-out and stacked-in conformations of an adenine bulge in DNA using a continuum model for solvent and ions |
| Creators Name: | Zacharias, M. and Sklenar, H. |
| Abstract: | A combination of conformational search, energy minimization, and energetic evaluation using a continuum solvent treatment has been employed to study the stability of various conformations of the DNA fragment d(CGCAGAA)/d(TTCGCG) containing a single adenine bulge. The extra-helical (looped-out) bulge conformation derived from a published x-ray structure and intra-helical (stacked bulge base) model structures partially based on nuclear magnetic resonance (NMR) data were used as start structures for the conformational search. Solvent-dependent contributions to the stability of the conformations were calculated from the solvent exposed molecular surface area and by using the finite difference Poisson-Boltzmann approach. Three classes (I-III) of bulge conformations with calculated low energies can be distinguished. The lowest-energy conformations were found in class I, corresponding to structures with the bulge base stacked between flanking helices, and class II, composed of structures forming a triplet of the bulge base and a flanking base pair. All extra-helical bulge structures, forming class III, were found to be less stable compared with the lowest energy structures of class I and II. The results are consistent with NMR data on an adenine bulge in the same sequence context indicating an intra-helical or triplet bulge conformation in solution. Although the total energies and total electrostatic energies of the low-energy conformations show only relatively modest variations, the energetic contributions to the stability were found to vary significantly among the classes of bulge structures. All intra-helical bulge structures are stabilized by a more favorable Coulomb charge-charge interaction but destabilized by a larger electrostatic reaction field contribution compared with all extra-helical and most triplet bulge structures. Van der Waals packing interactions and nonpolar surface-area-dependent contributions appear to favor triplet class II structures and to a lesser degree also the intra-helical stacked bulge conformations. The large conformational variation found for class III conformers might add a favorable entropic contribution to the stability of the extra-helical bulge form. |
| Keywords: | Adenine, Algorithms, Biophysical Phenomena, Biophysics, DNA, Ions, Magnetic Resonance Spectroscopy, Molecular Models, Nucleic Acid Conformation, Oligodeoxyribonucleotides, Solvents, Static Electricity, Thermodynamics, X-Ray Diffraction |
| Source: | Biophysical Journal |
| ISSN: | 0006-3495 |
| Publisher: | Biophysical Society |
| Volume: | 73 |
| Number: | 6 |
| Page Range: | 2990-3003 |
| Date: | December 1997 |
| Official Publication: | https://doi.org/10.1016/S0006-3495(97)78328-0 |
| PubMed: | View item in PubMed |
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