Conformational implications of some nucleotide sequences

The conformational properties of some nucleotide sequences result in their ability to bind specifically some ligands or tobe recognized by specific proteins. In order to investigate the dependence of conformational behavior of the DNA duplex on nucleotide sequence, we analyzed the interaction energy of nucleic acid bases as a function of conformational parameters and base sequence. Extended regions of minimum energy values were found for different sequences. Although these regions (valleys) largely overlap, each one shows specificity for a particular sequence. This suggests that a specific pathway of changes in conformational parameters exists for each sequence. the changes may be accompanied by considerable shifts (2–3 Å) of the atom positions and an only slight variation (1–2 kcal/mol) of energy. Even small shifts in other directions can cause a drastic energy increase. For some nucleotide sequences, the energetically preferable conformations are the B‐like ones (e.g., ApA, TpA), whereas for others the A‐like ones are preferable (e.g., GpG, ApT). IN general, Pyr‐Pur sequences have a tendency to a larger τ and smaller H and D than Pur‐Pyr sequences. A large body of experimental data on nucleic acid structure in fibers and in solutions can be explained by results obtained.