A free energy analysis of nucleic acid base stacking in aqueous solution
نویسندگان
چکیده
منابع مشابه
Theoretical calculations of base-base interactions in nucleic acids: I. Stacking interactions in free bases.
Stacking interactions in free bases were computed on the basis of molecular association. The results of the calculations were compared with the stacking patterns observed in a few single crystals of nucleic acid components as examples. The following are the conclusions: (i) there can be two types of stacking pattern classified as normal and inverted types for any two interacting bases and both ...
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The potentials of mean force (PMF) for the association of purine, adenine, thymine, guanine, cytosine, and uracil in aqueous solution are investigated using ab initio MP2/6-31G(d-0.25) calculations (diffuse d-polarization functions were used) and Langevin dipoles solvation model. The entropy contributions to the free energies for stacking and hydrogen bonding are approximated using the linear r...
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The equilibrium of stacked and unstacked base pairs is of central importance for all nucleic acid structure formation processes. The stacking equilibrium is influenced by intramolecular interactions between nucleosides but also by interactions with the solvent. Realistic simulations on nucleic acid structure formation and flexibility require an accurate description of the stacking geometry and ...
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ژورنال
عنوان ژورنال: Biophysical Journal
سال: 1995
ISSN: 0006-3495
DOI: 10.1016/s0006-3495(95)80023-8