title: NMR proton chemical shift prediction of C·C mismatches in B-DNA.
abstract: Accurate prediction of DNA chemical shifts facilitates resonance assignment and allows recognition of different conformational features. Based on the nearest neighbor model and base pair replacement approach, we have determined a set of triplet chemical shift values and correction factors for predicting the proton chemical shifts of B-DNA containing an internal C·C mismatch. Our results provide a reliable chemical shift prediction with an accuracy of 0.07 ppm for non-labile protons and 0.09 ppm for labile protons. In addition, we have also shown that the correction factors for C·C mismatches can be used interchangeably with those for T·T mismatches. As a result, we have generalized a set of correction factors for predicting the flanking residue chemical shifts of pyrimidine·pyrimidine mismatches.
authors: Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong. Electronic address: linkksng@cuhk.edu.hk.
authors: Kui Sang
authors: KS
authors: Ng
authors: Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong. Electronic address: lams@cuhk.edu.hk.
authors: Sik Lok
authors: SL
authors: Lam
mesh_terms: D000465:Algorithms; D020137:Base Pair Mismatch / Q000235:genetics*; D059371:DNA, B-Form / Q000737:chemistry* / Q000235:genetics*; D066244:Proton Magnetic Resonance Spectroscopy / Q000379:methods*; D011743:Pyrimidines / Q000737:chemistry*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D059371:DNA, B-Form; D011743:Pyrimidines; C030986:pyrimidine
keywords: C·C mismatch; DNA; NMR; Prediction; Proton chemical shift