| The effects of transverse cross-relaxation have long been ignored in analyzing J-couplings in biopolymers. One-dimensional and two dimensional COSY simulations for 3-and 4-spin systems modeling the H1{dollar}prime{dollar}-H2{dollar}prime{dollar}R-H2{dollar}prime{dollar}S and H1{dollar}prime{dollar}-H2{dollar}prime{dollar}R-H2{dollar}prime{dollar}S- H3{dollar}prime{dollar}, respectively, have been carried out explicitly including the effect of cross-relaxation. The results show that cross-relaxation has a very strong effect on the multiplet structure and the COSY cross-peak pattern of DNA sugar protons when the correlation time is longer than {dollar}sim{dollar} 2 ns; this effect cannot be ignored in DNA sugar conformational analysis.; An improved NOESY simulation program BIRDER, has been developed, which takes into account incomplete Z-magnetization recovery and differential external relaxation rates. This program greatly reduces the NMR spectrometer time required for the acquisition of NOESY spectra.; The solution structures of the chimeric hybrid-DNA-hybrid duplex (r(cgcg)d({eth}it TATACGCG)) {dollar}sb2{dollar} and the Eco RI DNA duplex, {9B}d(CGCGAATTCGCG)) {dollar}sb2{dollar} have been solved. The structural features of the chimeric duplex are very different from those reported for the X-ray crystal structure of the similar sequence (r(gcg)d(TATACGC)) {dollar}sb2.{dollar} A detailed comparison between the X-ray crystal structure of the ({eth}it d(CGCGAATTCGCG)) {dollar}sb2{dollar} sequence and the solution structure of this sequence is presented.; A new structural motif containing the trinucleotide (GPu{dollar}sb1{dollar}A): (GPu{dollar}sb2{dollar}A) has been determined. In this novel structure, the central purines on opposite strands do not pair, but intercalate with each other in a sandwich between two sheared GA mismatches to form a stable antiparallel duplex with excellent stacking. Sequences that can form this kind of structure have been found extensively in the human centromere and this unusual structure is undoubtedly of great biological importance. |
