Conformational Peculiarities and Biological Role of Some Nucleotide Sequences
A conclusion about the dependence of the conformational behavior of nucleic acids on nucleotide sequences has been made on the basis of nonbonded interaction energy calculations using the classical potential functions. The potential functions have been chosen by comparing the results of calculations for model systems (crystals, associates) with the experimental data and with the results of the most rigorous quantum mechanical calculations. Potentials proposed by other authors and the possibilities of further refinement of potential functions are considered.
To study conformational patterns of different nucleotide sequences we have calculated the energy of interaction between base pairs (all combinations have been considered) as a function of the parameters determining their mutual position in the double helix. The calculations have shown, in accordance with the experimental data, that there are sequences for which the energy preferred conformations are the A-like ones (e. g. GG, AT, AC) while for other sequences the preferred conformations are the B-like ones (e. g. AA, TA, CA).
Theoretical conformational analysis of a regular double-helical polynucleotide has shown the existence of two regions of minimal energy values corresponding to the A- and B-families of nucleic acid conformations. Taking into account the possible biological role of sequences containing repeating adenines in one chain and repeating thymines in the other one, we have considered other possible regular conformations of poly(dA) • poly(dT). Two more regions of minimal energy values have been revealed which correspond to the A-like conformation of one chain and the B-like conformation of the other one. The relative energetic advantages of the four regions depends on phosphate group charge neutralization.
KeywordsDouble Helix Mutual Position Nonbonded Interaction Conformational Parameter Helix Axis
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