Dinucleotides - Theoretical Structures

    Theoretical modeling of the dinucleotides (using the simulated annealing method described in the molecular mechanics section) predicts three conformational families with similar energies but significantly different collision cross sections. Examples of each family (for dAC) are shown at right.
    The stacked conformers, with the two nucleobases stacked, are the lowest-energy structures and have the smallest cross sections. The bases tend to stack so that a carbonyl oxygen on one base is directly over the NH₂ group (or NH on thymine) on the other base.
    The H-bonded conformers, with the two bases nearly planar with respect to one another and hydrogen bonded to each other, are the next-lowest-energy structures (by 1-2 kcal/mol) and have cross sections 10-12 Ų larger than the stacked conformers. The H-bonds typically involve the carbonyl oxygen or ring nitrogen on the 5' base and the amino group on the 3' base. As a result, no H-bonded conformers are observed for dAT, dCT, or dTT because the 3' T does not have an amino group and the CH₃ group is usually in the way. For dGT, however, the H-bonds between G and T involve the NH₂ group on the 5' G and the C=O group on the 3' T.
     The open conformers, with the two bases separated from each other, are the highest-energy structures (by 1-10 kcal/mol) and have cross sections 20-25 Ų larger than the stacked conformers.