Theoretical calculations of conformational preferences in dinucleoside monophosphates Up-U and Ap-A. Significance of intramolecular base-backbone interaction.

Conformational preferences of dinucleoside monophosphates Up-U and Ap-A have been studied theoretically using the Quantum Chemical PCILO (Perturbative Configuration Interaction Using Localized Orbitals) method. The importance of intramolecular interactions between the bases and ribose phosphate backbone has been indicated. Additionally, a close similarity is predicted between overall Up-U and Ap-A conformational structures. Specific prefrences about the key conformation bonds are C4'-C5' (psi = 60 degrees), C5'-O5' (phi = 180 degrees), O5'-P (omega = 110 degrees), P-O3' (omega' = 310 degrees), O3'-C3' (phi' = 210 degrees), C1'-N (chi = 20 degrees), C2'-O2' (theta = 300 degrees) for nucleotidyl units with C3' -endo ribose pucker. Except for the O5'-P torsion angles (omega = 110 degrees), the remaining values fall in ranges observed for monomers and polynucleotides. Stabilization for this unique omega = 110 degrees preference is provided by intramolecular hydrogen bonding between the 3'-OH (hydroxyl group) and O2 (in uracil) or N3 (in adenine) of the second base from the 3'-terminal. The possibility of such interaction mechanisms at 3'-terminals of ribonucleic acids and polynucleotides is also discussed.