Proton chemical shift prediction of A.A mismatches in B-DNA duplexes.
A proton chemical shift prediction method has been developed for double helical DNAs containing A.A mismatches. This method makes use of the chemical shift prediction scheme for normal B-DNA duplexes developed by Altona and co-workers and a set of A.A mismatch triplet chemical shift values and corrections factors extracted from reference sequences. The triplet values are used for predicting chemical shifts of A.A mismatches whereas the normal B-DNA chemical shifts and correction factors are used for the flanking residues of A.A mismatches. Both 5'- and 3'-correction factors have been determined from the chemical shift differences upon replacing the A.A mismatch in a duplex with an A.T base pair. Based on 560 sets of predicted and experimental chemical shifts, the overall prediction accuracy for various types of protons has been determined to be 0.07 ppm with an excellent correlation coefficient of 0.9996.
Lam
Sik Lok
SL
Department of Chemistry, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong. lams@cuhk.edu.hk
Lai
Kin Fung
KF
Chi
Lai Man
LM
D024509:3' Flanking Region; D024506:5' Flanking Region; D020137:Base Pair Mismatch; D004247:DNA / Q000737:chemistry*; D009682:Magnetic Resonance Spectroscopy; D011522:Protons
D011522:Protons; D004247:DNA