ISSN:
0020-7608
Keywords:
Computational Chemistry and Molecular Modeling
;
Atomic, Molecular and Optical Physics
Source:
Wiley InterScience Backfile Collection 1832-2000
Topics:
Chemistry and Pharmacology
Notes:
Double-helical polynucleotide conformations, poly(dA)·poly(dT), poly(d(A-T))·poly(d(T-A))·poly(dG)·poly(dC), and poly(d(G-C))·poly(d(C-G)) are analyzed by the atom-atom potential method. The energy optimization is carried out in the space of eight independent geometric parameters using analytical procedures for the constraints, taking into account the flexibility of the β-D-deoxyribose rings. At the first stage, the full screening of atomic partial charges was assumed. The structures of the calculated B and the A forms of DNA are characterized by low energy and absence of short contacts; the dihedral angles are near the average values in the monomers. With the typical energy difference of 3-5 kcal/mol nucleotide pairs in all cases, the B form is more preferable as compared to the A form. At the final step the effect of the Coulomb term is evaluated for poly(dA)·poly(dT) using various values of the effective dielectric constant (ε = 28, 24, 20, 18, 14, 12, 10, 8, 6, 4, and 1). If ε ≤24, the energy optimization leads A to B. We discuss the stereochemical details of the intermediate conformations on the A-B path and hypothesize the nature of stability of the A and the B forms and the mechanism of the A-B transition.
Additional Material:
3 Tab.
Type of Medium:
Electronic Resource
URL:
http://dx.doi.org/10.1002/qua.560170215
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