SOLUTION STRUCTURE OF N-(2-DEOXY-D-ERYTHRO-PENTOFURANOSYL)UREA FRAMESHIFTS, ONE INTRAHELICAL AND THE OTHER EXTRAHELICAL, BY NUCLEAR-MAGNETIC-RESONANCE AND MOLECULAR-DYNAMICS

The presence of a N-(2-deoxy-D-erythro pentofuranosyl)urea (henceforth referred to as deoxyribosylurea) residue, ring fragmentation product of a thymine, in a frameshift situation in the sequence 5'd(AGGACCACG) .d(CGTGGurTCCT) has been studied by H-1 and P-31 nuclear magnetic reso nance and molecular dynamics. At equilibrium, two species are found in slow exchange. We observe that the deoxyribosylurea residue can be ei ther intra-or extrahelical within structures which otherwise do not de viate strongly from that of a B-DNA as observed by NMR. Our study sugg ests that this is determined by the nature and number of hydrogen bond s which this residue can form as a function of two possible isomers, T here are two possible structures for the urea side chain, either cis o r trans for the urido bond which significantly changes the hydrogen bo nding geometry of the residue. In the intrahelical species, the cis is omer can form two good hydrogen bonds with the bases on the opposite s trand in the intrahelical species, A4 and C5, which is not the case fo r the trans isomer, This results in a kink in the helical axis. For th e major extrahelical species, the situation is reversed. The trans iso mer is able to form two good hydrogen bonds, with G13 on the same stra nd and A7 on the opposite strand. For the extrahelical species, the ci s isomer can form only one hydrogen bond. In this major structure the NMR data show that the bases which are on either side of the deoxyribo sylurea residue in the sequence, G14 and T16, are stacked over each ot her in a way similar to a normal B-DNA structure. This requires the fo rmation of a loop for the backbone between these two residues. This lo op can belong to one of two families, right-or left-handed. In a previ ous study of an abasic frameshift [Cuniasse et al. (1989) Biochemistry 28, 2018-2026], a left-handed loop was observed, whereas in this stud y a right-handed loop is found for the first time in solution. The deo xyribosylurea residue lies in the minor groove and can form both an in tra- and an interstrand hydrogen bond.