Deoxyribonucleic acid sequence effects on molecular structure

The deoxyribonucleic acid (DNA) duplex shows polymorphism depending on the base sequence and the environment. The base sequence dependent variations in conformational properties of the synthesized oligonucleotides are studied by X-ray analysis and several physico-chemical techniques. The possible structures in solution were proposed by molecular dynamics (MD) simulation. 1) The several oligonucleotides which include the adenine or adenine-thiamine tract, have unique conformational characteristics with the base sequence dependent property. The junction-model structure for DNA bending was proposed by the combined method of nuclear magnetic resonance (NMR) observations and MD calculation. 2) The two different hydrogen bonding schemes of inosine-adenine base-pairing, anti/anti and anti/syn forms, are adopted in B-DNA structure. The preference of these forms depends on the base sequence. The MD calculation could offer the models consistent with NMR evidence. 3) Oligonucleotides containing cyclonucleosides with a high-anti (intermediate between anti and syn) glycosidic conformation adopt left-handed double-helical structures. A suitable model of this left-handed duplex was proposed by calculation with energy minimization.