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Possible B-conformations of DNA fragments with alternating purine-pyrimidine sequences

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

Molekuliarnaia Biologiia 32(4): 668-677

1998

ISSN/ISBN: 0026-8984
PMID: 9785573
Document Number: 484151
Search for low energy conformartions of oligonucleotide duplexes d(ATATATA) and d(GCGCGCG) was conducted to study conformational potentials of DNA fragments containing alternating purine-pyrimidine sequences. Calculations made it possible to find an area that included 6 energy minimums corresponding with the conformation of sugar rings, average values of spiral rotation angle, ratios between the spiral parameters of purine-pyrimidine and pyrimidine-purine steps. Under the conditions of coordinated changes in several structural parameters, conformational transitions between these types can be carried out through insignificant potential barriers. However, some of the parameters can change also in each type within rather wide limits without noticeable changes in energy. Ranges of changes in conformation parameters for duplexes d(ATATATA) and d(GCGCGCG) differ. Many of the conformations of duplexes with alternating purine-pyrimidine sequences described in experimental studies belong to the area of low energy conformations. Other conformations, for example, such as those similar to DNA D-form, possess energy which is higher than that of low energy conformations and can exist only at the account of intermolecular interactions. Experimental structures are still unknown for some parts of the low energy conformation area.

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