NMR studies of abasic sites in DNA duplexes: deoxyadenosine stacks into the helix opposite the cyclic analogue of 2-deoxyribose.

摘要: Proton and phosphorus NMR studies are reported for the complementary d(C-A-T-G-A-G-T-A-C).d(G-T-A-C-F-C-A-T-G) nonanucleotide duplex (designated APF 9-mer duplex) which contains a stable abasic site analogue, F, in center of helix. This oligodeoxynucleotide modified tetrahydrofuran moiety, isosteric with 2-deoxyribofuranose, serves as structural analogue natural apurinic/apyrimidinic [Takeshita, M., Chang, C.N., Johnson, F., Will, S., & Grollman, A.P. (1987) J. Biol. Chem. 262, 10171-10179]. Exchangeable nonexchangeable base sugar protons, including those located at site, have been assigned by recording analyzing two-dimensional phase-sensitive NOESY data sets H2O D2O solution low temperature (0 degrees C). These indicate that A5 inserts into helix opposite F14 stacks flanking G4.C15 G6.C13 Watson-Crick pairs. Base-sugar proton NOE connectivities were measured through G4-A5-G6 on unmodified strand between protons C15 5'-flanking residue strand. establish all glycosidic torsion angles anti is right-handed adjacent to duplex. Two 16 phosphodiester groups exhibit resonances outside normal spectral dispersion indicative altered two phosphate backbone