STRUCTURAL BEHAVIOR OF THE CPG STEP IN 2 RELATED OLIGONUCLEOTIDES REFLECTS ITS MALLEABILITY IN SOLUTION

We report on the determination of the solution structure of two sequen ce-related oligonucleotides, d(GTACGTAC)(2) and d(CATCGATG)(2). Result s have been obtained by using a combined approach of(a) two-dimensiona l NMR, including proton and phosphorus experiments, (b) restrained mol ecular mechanics performed with sugar phase angle, backbone epsilon an gle, and NOE distances as input, and (c) back-calculation refinements against the NOE spectra at various mixing times. The two oligonucleoti des adopt the B-DNA structure with, however, noticeable differences ce ntered on their core sequence and especially the CpG step. Due to the permutation of its flanking residues, the CpG step modifies its twist values and backbone epsilon value; globally, the CpG step appears more flexible within the tetranucleotide TCGA than ACGT. The solution stru cture of d(GTACGTAC)(2) differs from the previously reported X-ray str ucture, which was found to be A-form throughout [Takusagawa, F. (1990) J. Biomol. NMR 3, 547-568]. On the other hand, in the X-ray structure of d(CCAACGTTGG)(2) [Prive et al. (1991) J. Mel. Biol. 217, 177-199] the structure of the ACGT sequence is similar to that found in solutio n d(GTACGTAC)(2). Similarly, the central TCGA tetranucleotide of d(CAT CGATG)(2) presents a solution structure analogous to that observed on the X-ray structures of both d(CGATCGATCG)(2) [Grzeskowiak, et al. (19 91) J. Biol. Chem. 266, 8861-8883] and d(CGATCGmeATCG)a [Baikalov, et al. (1993) J. Mel. Biol. 231, 768-784]. At the end we discuss the poss ible biological significance of the particular structures exhibited by the ACGT and TCGA tetranucleotides.