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Possible A-conformation and conformation intermediate between the A- and B-forms of DNA fragments with alternating purine-pyrimidine sequences

Nesterova, E.N.; Chuprina, V.P.; Poltev, V.I.

Molekuliarnaia Biologiia 33(5): 845-854

1999

ISSN/ISBN: 0026-8984
PMID: 10579189
Document Number: 511233
A search for low energy A-conformation of d(ATATATA) and d(GCGCGCG) duplexes was conducted to study the conformation potentials of DNA fragments containing alternating purine-pyrimidine sequences. Calculations made by means of CONAN program made it possible to identify an extended area among parameters characterizing conformations of dinucleotide steps. Possible pathways of changes in conformation parameters in the B-A transition were investigated. It was shown that the B-A transition could be a result of a simultaneous or subsequent change in sugar transformation and shift of base pairs from the axis of the helix. Potential barrier of transition from B- into A-family was found to be 1-3 ccal/mole of nucleotide pairs depending on the pathway of the transition.

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