Crystal structures of DNA and protein-DNA complexes show the existence of """"""""fixed"""""""" water molecules in the minor and major groove of DNA and at the protein-DNA interface [87, 88]. We studied the effect of these water molecules on the structure and bending of DNA, as well as on the binding specificity, by using DNA with analogues*. It was argued theoretically, and supported experimentally, that a water molecule bridges between the N7 of the purine ring and the exocyclic amino group in adenine bases. The 2'-deoxy-7-hydroxymethyl-7-deazaadenosine analogue (hm7c7dA) [89] was suggested to mimic the role of structural water in the major groove of DNA. This analogue replaces the adenine base and the water molecule bound to it. Four distinct systems, based on the Dickerson dodecamer with d(CGCGAATTCGCG) sequence, were constructed: the dodecamer itself, the dodecamer with both adenine bases at position 5 and 6 mutated, the dodecamer with adenine base at position 5 mutated and the dodecamer with adenine base at position 6 mutated. DNA structure and dynamics are known to be sensitive to hydration, therefore, the DNA was embedded in a previously equilibrated cylinder of water molecules. To counterbalance the negative charge on the DNA backbone, 15 sodium ions were added by replacing 15 water molecules with the highest electrostatic energies of the oxygen atom. There are approximately 12,000 atoms in each system. The molecular dynamics program NAMD was used to run the simulations. For each system, 1ns of dynamics was performed: 250 ps of dynamics with soft constraints on the terminal base-pairs of the DNA and 750 ps of free dynamics in order to yield a better hydration of the DNA bases. The structural deviations of DNA from the initial X-ray crystal structure, evaluated on the basis of root mean square deviations (RMSD) for all four systems, show that the analogue does not affect the overall DNA conformation. Bending points develop in the axis of the DNA at the CG-AA and TT-CG steps in all the simulations. In addition, the analogue does not affect the hydrogen bonding and stacking interactions in either of the simulated structures. Since the (hm7c7dA) analogue does not disrupt the conformation and properties of B-form DNA, the interaction of proteins with DNA containing this analogue will be studied further to better delineate the role of water in protein-DNA interactions. The crystal structure of the trp-repressor bound to DNA [90] will be used as the starting point.
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