TCB Publications - Abstract

Dorina Kosztin, Richard Gumport, and Klaus Schulten. Probing the role of structural water in a duplex oligodeoxyribonucleotide containing a water-mimicking base analogue. Nucleic Acids Research, 27:3550-3556, 1999. (PMC: 148600)

KOSZ99A Molecular dynamics simulations were performed on models of the dodecamer DNA double-stranded segment, [d(CGCGAATTCGCG)]$_{2}$, in which each of the adenine residues, individually or jointly, was replaced by the water-mimicking analogue 2'-deoxy-7-(hydroxymethyl)-7-deazaadenosine (hm$^{7}c^{7}$dA). The simulations, when compared to those of the dodecamer itself, show that incorporation of the analogue affects neither the overall DNA structure nor its hydrogen-bonding and stacking interactions when a single individual base is replaced by the analogue. Furthermore, the water molecules near the bases in the singly-substituted oligonucleotides are similarly unaffected. Double substitutions lead to differences in all the aforementioned parameters with respect to the reference sequence. The results suggest that the analogue provides a good mimic of specific ``ordered" water molecules observed in contact with DNA itself and at the interface between protein and DNA in specific complexes.

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