SOLUTION CONFORMATION OF AN ABASIC DNA UNDECAMER DUPLEX D(CGCACXCACGC)-D(GCGTGTGTGCG) - THE UNPAIRED THYMINE STACKS INSIDE THE HELIX

The three-dimensional structural analysis of DNA undecamer 1)G(2)C(3)A (4)C(5)X(6)C(7)A(8)C(9)G(10)C(11))(3'), G(20)T(19)G(18)T(17)G(16)T(15) G(14)C(13)G(12))(5') duplex in which the X residue is a modified abasi c site [3-hydroxy-2-(hydroxymethyl)tetrahydrofuran] has been performed using NOESY, DQFCOSY, TOCSY, and P-31-H-1 HSQC-TOCSY spectra in relat ion with molecular dynamics simulations. A total of 249 distances and 224 dihedral angles were used for construction. The optimal distances were calculated using the complete relaxation matrix method from hybri d matrices which were built with the experimental NOE intensities and additional data derived from either standard A- or B-DNA. Six independ ent refined structures starting from canonical A- and B-DNA were deter mined on the basis of the NMR data, and all converged to a single fami ly with average rms deviations below 0.6 Angstrom and final NOE R-x fa ctors of 0.055 +/- 0.03. A satisfactory agreement was obtained between measured NOE intensities and those resulting from full relaxation mat rix calculations. A single intrahelical form of right-handed DNA duple x is observed; the aromatic base of residue T17 opposite the abasic si te is stacked inside the helix. No clear correlation was detected betw een the C5 and C7 residues, excluding their proximity and the looping out of the abasic site. The abasic site induces a kink of about 30 deg rees in the DNA duplex. This kink allows the formation of a bifurcated hydrogen bond between the amino protons of C5 and the O4 oxygen of T1 7. A detailed analysis of the final structures and their comparison wi th previous studies of abasic site lesions are described.