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

A proton chemical shift prediction scheme for B-DNA duplexes containing a T center dot T mismatch has been established. The scheme employs a set of T center dot T mismatch triplet chemical shift values, 5'- and 3'-correction factors extracted from reference sequences, and also the B-DNA chemical shift values predicted by Altona et al. The prediction scheme was tested by eight B-DNA duplexes containing T center dot T mismatches. Based on 560 sets of predicted and experimental proton chemical shift values, the overall prediction accuracy for non-labile protons was determined to be 0.07 ppm with an excellent correlation coefficient of 0.9996. In addition, the prediction accuracy for 96 sets of labile protons was found to be 0.22 ppm with a correlation coefficient of 0.9961. The prediction scheme developed herein can facilitate resonance assignments of B-DNA duplexes containing T center dot T mismatches and be generalized for the chemical shift prediction of other DNA mismatches. Our chemical shift data will also be useful for establishing structure-chemical shift information in B-DNA containing mismatches. (C) 2013 Elsevier Inc. All rights reserved.