Hydration sites in purine·purine·pyrimidine and pyrimidine·purine·pyrimidine DNA triplexes in aqueous solution

Background DNA triplexes are higher-order nucleic acid structures with potential roles in gene regulation and hence biochemical and therapeutic applications. The stabilizing influence exerted by water molecules on the conformation of the DNA duplex is well known. However, the role of water molecules in the DNA triple helix has not been investigated. We have previously determined the solution structures of the purine·purine·pyrimidine (R·RY) and pyrimidine·purine·pyrimidine (Y·RY) structural motifs in DNA triplexes and identified both the global helical parameters, as well as local helical distortions associated with non-standard base triple pairing alignments. Results Here we have used homonuclear two-dimensional NMR spectroscopy to define the hydration sites in R·RY and Y·RY DNA triplexes in aqueous solution. Long-lived hydration sites with residence times exceeding 1 nanosecond have been identified in the new groove formed by the Hoogsteen paired strands in both triplexes. Distinctive patterns of hydration are displayed by each triplex in the remaining two grooves. Conclusions The role played by water molecules in DNA triplexes appears to be similar to that played in duplexes. By binding to specific sites, particularly in the narrow groove formed by the Hoogsteen paired strands whose phosphate groups are in close proximity, water molecules may stabilize the triplex by shielding it against unfavorable electrostatic interactions.