SOLUTION STRUCTURE OF THE EXOCYCLIC 1,N(2)-PROPANODEOXYGUANOSINE ADDUCT OPPOSITE DEOXYADENOSINE IN A DNA NONAMER DUPLEX AT PH 8 .9. MODEL OF PH-DEPENDENT CONFORMATIONAL TRANSITION

The solution structure of the complementary 6-T7-A8-C9).d(G10-T11-A12- C13-A14-C15-A16-T17-G18) DNA duplex (designated X.A 9-mer), which cont ains a 1,N2-propanodeoxyguanosine exocyclic adduct X5 opposite deoxyad enosine A14 at the center, is pH dependent [Kouchakdjian, M., Eisenber g, M., Live, D., Marinelli, E., Grollman, A., & Patel, D. J. (I 990) B iochemistry 29, 4456-4465]. In our previous paper [Huang, P., & Eisenb erg, M. (1992) Biochemistry 31, 6518-6532] we established the three-di mensional structure of this X.A 9-mer duplex at pH 5.8 by use of restr ained molecular dynamics followed by NOE-based back-calculation refine ment. The present paper discusses the structure at pH 8.9 and the pH-d ependent conformational transition between the structures at pH 5.8 an d at pH 8.9. The structure at pH 8.9 is calculated starting from five different conformations. The final structures converge and agree well with the experimental NOE intensities. These structures are essentiall y B-type DNA (with X5 and A14 in the B(II) conformation while the othe r residues are in the most commonly described B(I) conformation) and d isplay an approximate 27-degrees kink at the center of the helix. At t he kink site, X5 is positioned in the major groove with the exocyclic ring directed toward the G6.C13 base pair, unstacked from the flanking base G6 and exposed to the solvent. A14, opposite the lesion, remains stacked with its neighbor C15, but not with C13. The kinked helix can accommodate the rotation of the bulky X5 about its glycosidic bond. W e propose here a model for the pH-dependent transition. Our model expl ains the conformational change, which includes the anti and syn rotati on of the bulky adduct around its glycosidic bond, with a minimal ener gy barrier and with an overall kink of the DNA helix. These new findin gs, fully consistent with the NMR experimental data, were revealed onl y after restrained dynamics refinement. Distance-restrained energy min imization by itself was insufficient, as shown by the previous NMR stu dy.