The role of water H-bond imbalances in B-DNA substate transitions and peptide recognition revealed by time-resolved FTIR spectroscopy

The conformational substates BI and BII of the phosphodiester backbone in B-DNA are thought to contribute to DNA flexibility and protein recognition. We have studied by rapid scan FTIR spectroscopy the isothermal BI-BII transition on its intrinsic time scale. Correlation analysis of IR absorption changes occurring within seconds after a reversible incremental growth of the DNA hydration shell identifies water populations w₁ (PO₂--bound) and w₂ (non-PO₂--bound) exhibiting weaker and stronger H-bonds, respectively, than those dominating in bulk water. The BII substate is stabilized by w₂. The water H-bond imbalance of 3-4 kJ mol^-1 is equalized at little enthalpic cost upon formation of a contiguous water network (at 12-14 H₂O molecules per DNA phosphate) of reduced n(OH) band width. In this state, hydration water cooperatively stabilizes the BI conformer via the entropically favored replacement of w₂-DNA interactions by additional w₂-water contacts, rather than binding to BI-specific hydration sites. Such water rearrangements contribute to the recognition of DNA by indolicidin, an antimicrobial 13-mer peptide from bovine neutrophils which, despite little intrinsic structure, preferentially binds to the BI conformer in a water-mediated induced fit. The FTIR spectra resolve sequential steps leading from PO₂--solvation to substate transition and eventually to base stacking changes in the complex. In combination with CD-spectral titrations, the data indicate that in the absence of a bulk aqueous phase, as in molecular crowded environments, water relocation within the DNA hydration shell allows for entropic contributions similar to those assigned to water upon DNA ligand recognition in solution.