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

To study the possible conformations of DNA fragments containing alternating purine-pyrimidine sequences, a search was performed for low-energy conformations of oligonucleotide duplexes d(ATATATA) and d(GCGCGCG). The CONAN program was used for calculation of local energy minima within the space of structural variables characterizing the mutual position of bases, sugar ring conformations, and the glycoside angles of nucleotides. Calculations revealed an extensive region involving six types of energy minima corresponding to structures that differ in the conformations of sugar rings, average helix twist, and ratios between helical parameters of purine-pyrimidine and pyrimidine-purine steps. Conformational transitions between these types across low potential barriers are possible upon concerted changes of several structural parameters. Certain parameters may vary in a rather wide range and at virtually the same energy within each type. The ranges of changes in conformational parameters differ for duplexes d(ATATATA) and d(GCGCGCG), Many of experimentally studied conformations of duplexes with alternating purine-pyrimidine sequences belong to the region of low-energy conformations. Other conformations, e.g., D form of DNA, have energies several kcal/mol higher than low-energy ones and can exist only owing to intermolecular interactions. Some parts of the low-energy conformation region contain no experimentally shown structures.