We analysed close contacts between the neighbouring base pairs in available oligonucleotide crystal structures and found that they mostly involved the amino groups of bases. Mutual amino group close contacts are abundant at the ApT steps in B-DNA but they also occur on the minor and major groove sides of the CpG steps in B-DNA. The close amino group contacts are much more frequent than the known bifurcated hydrogen bonds between the amino and carbonyl groups. The present empirical analysis indicates a previously unknown attractive interaction between the amino groups of bases in DNA which may significantly contribute to the base sequence-dependent variations of DNA architecture.

Institute of Biophysics Czech Academy of Sciences Brno

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Critical effect of the N2 amino group on structure, dynamics, and elasticity of DNA polypurine tracts