An NMR study of d(CTACTGCTTTAG).d(CTAAAGCAGTAG) showing hydration water molecules in the minor groove of a TpA step

The hydration properties of the non-palindromic duplex d(CTACTGCTTTAG). d(C TAAAGCAGTAG) were investigated by NMR spectroscopy. The oligonucleotide pos sesses a heterogeneous B-DNA structure. The H2(n)-H1'(m+1) distances reflec t a minor groove narrowing within the TTT/AAA segment (similar to 3.9 Angst rom) and a sudden widening at the T10:A15 base-pair (similar to 5.3 Angstro m), the standard B-DNA distance being similar to 5 Angstrom. The facing T10 pA1.1 and T14pA15 steps at the end of the TTTA/AAAT segment have completely different behaviors. Only A15 ending the AAA run displays NMR features com parable to those shown by adenines of TpA steps occupying the central posit ion of TnAn (n greater than or equal to 2) segments. These involve particul ar chemical shifts and line broadening of the H2 and H8 protons. Positive N OESY cross-peaks were measured between the water protons and the H2 protons of A15, A16 and A17 reflecting the occurrence of hydration water molecules with residence times longer than 500 picoseconds along the minor groove of the TTT/AAA segment. In contrast no water molecules with long residence ti mes were observed neither for A3, A20 and A23 nor for All ending the 5'TTTA run. We confirm thus that the binding of water molecules with long residen ce time to adenine residues correlates with the minor groove narrowing. In contrast, the widening of the minor groove at the A11:T14 base-pair ending the TTTA/TAAA segment, likely associated to a high negative propeller twist value at this base-pair, prevents the binding of a water molecule with lon g residence time to All but not to A15 of the preceding T10:AIS base-pair. Thus, in our non-palindromic oligonucleotide the water molecules bind diffe rently to All and A15 although both adenines are part of a TpA step. The sl ower motions occurring at A15 compared to All are also well explained by th e present results.