UNUSUAL CONFORMATION OF A 3'-THIOFORMACETAL LINKAGE IN A DNA DUPLEX

The DNA.DNA duplex d(CGCGTT(SCH2O)TTGCGC).d(GCGCAAAACGCG) (designated duplex III) containing a 3'-thioformacetal (3'-TFMA) linkage in the ce nter of the sequence was characterized in detail by two- and three-dim ensional homonuclear NMR spectroscopy. The NMR results were analyzed a nd compared with those of two duplexes of the same sequence: One is an unmodified reference sequence and the other contains a formacetal (OC H2O) linkage at the central T^T step (designated duplex I and duplex I I, respectively). In general, the NMR spectra of duplex III closely re semble those of the analogous duplexes I and II, suggesting an overall B-type structure adopted by the 3'-TFMA-modified duplex III. Nonethel ess, the detection of several distinct spectral features originating f rom the protons at the T6(3'-SCH2O)T7 modification site is indicative of a local conformation that is clearly different from the correspondi ng region in duplexes I and II. The 3'-thioformacetal linker, in contr ast to the formacetal (FMA) linkage, cannot be accommodated in a confo rmation usually found in natural nucleic acid duplexes. As a consequen ce, the 3'-TFMA-modified T6 sugar adopts an 04'-endo form (an intermed iate structure between the usual C2'-endo and C3'-endo forms). This ch ange is accompanied by a change in the E (C4'-C3'-S3'-CH2) dihedral an gle and by subsequent adjustments of other torsion angles along the ba ckbone. Notably, this conformational readjustment at the T6-T7 backbon e linkage is localized; its collective result has negligible effect on base-base stacking of the T6 and T7 residues. A close examination of the COSY data in all three duplexes reveals a subtle variation in suga r geometry, with more S-type character adopted by the modified duplexe s II and III. The results of this study illustrate that, although the difference between FMA and 3'-TFMA linkages is merely in the substitut ion of the T6(O3') in the former by a sulfur atom in the latter, the s tereoelectronic difference in a single atom can induce significant loc al structural distortion in an otherwise well-structured oligonucleoti de duplex.