[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.
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D000225:Adenine; D001483:Base Sequence; D004247:DNA; D007288:Inosine; D009682:Magnetic Resonance Spectroscopy; D008969:Molecular Sequence Data; D015394:Molecular Structure; D009841:Oligonucleotides; D014961:X-Ray Diffraction
D009841:Oligonucleotides; D007288:Inosine; D004247:DNA; D000225:Adenine