NMR proton chemical shift prediction of T·T mismatches in B-DNA duplexes

NMR proton chemical shift prediction of C·C mismatches in B-DNA

“…In our previous study in developing the chemical shift prediction method for TÁT mismatches [31], a set of 15-mer reference hairpin sequences containing a 6-base pair stem and a 3-nucleotide GAA loop was used. Owing to the loop effect, the 3 0 -flanking base of the mismatched T in the top strand was located in a more deshielded region, thus leading to systematic errors in the predicted chemical shifts of the 3 0 -flanking nucleotides.…”

“…Supplementary Information S4-S7). The prediction accuracies, expressed as the root-mean-square-deviations (RMSDs), were re-determined using the same set of experimental chemical shifts from the testing sequences [31]. As shown in Supplementary Information S8, the prediction accuracies of non-labile proton chemical shifts using the triplet chemical shifts, 5 0 and 3 0 -correction factors from the new 17-mer references (0.05, 0.06 and 0.08 ppm, respectively) was as good as those from the 15- …”

“…Accurate prediction of chemical shifts can facilitate resonance assignment of biomolecules, recognition of conformational features, and identification of the interactions with drugs, ligands, and other molecules [11][12][13][14][15][16]. Therefore, chemical shift prediction protocols have been established for proteins [17][18][19], RNAs [20][21][22], and DNAs [23][24][25][26][27][28][29][30][31] with specific structures and sequence contexts. For DNA chemical shifts, prediction methods for random coil [27][28][29], complementary B-DNA [23][24][25][26], and B-DNA containing an internal AÁA [30] or TÁT mismatch [31] have been developed.…”

“…For the second one which uses a sequence-based approach, chemical shifts can be predicted by the empirical values extracted from a set of reference sequences adopting a known structure. By considering simply the effects from the nearest neighbors of a particular residue, the triplet model has been successfully used to predict chemical shifts of random coil and double helical DNAs with good accuracies [26][27][28][29][30][31]. For predicting the chemical shifts of B-DNA containing an AÁA or TÁT mismatch, the nearest neighbor model and base pair replacement approach have also been used successfully [30,31].…”

“…By considering simply the effects from the nearest neighbors of a particular residue, the triplet model has been successfully used to predict chemical shifts of random coil and double helical DNAs with good accuracies [26][27][28][29][30][31]. For predicting the chemical shifts of B-DNA containing an AÁA or TÁT mismatch, the nearest neighbor model and base pair replacement approach have also been used successfully [30,31]. The method is based on the assumption that only the nearest neighboring nucleotides are involved in significantly affecting the chemical shifts of a particular residue, where nucleotides farther away from the triplet have negligible contribution to the chemical shifts of the residue.…”