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Thermodynamics and NMR of Internal G·T Mismatches in DNA

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Department of Chemistry, Wayne State University, Detroit, Michigan 48202
Cite this: Biochemistry 1997, 36, 34, 10581–10594
Publication Date (Web):August 26, 1997
https://doi.org/10.1021/bi962590c
Copyright © 1997 American Chemical Society
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Abstract

Thermodynamics of 39 oligonucleotides with internal G·T mismatches dissolved in 1 M NaCl were determined from UV absorbance versus temperature profiles. These data were combined with literature values of six sequences to derive parameters for 10 linearly independent trimer and tetramer sequences with G·T mismatches and Watson−Crick base pairs. The G·T mismatch parameters predict ΔG°37, ΔH°, ΔS°, and TM with average deviations of 5.1%, 7.5%, 8.0%, and 1.4 °C, respectively. These predictions are within the limits of what can be expected for a nearest-neighbor model. The data show that the contribution of a single G·T mismatch to helix stability is context dependent and ranges from +1.05 kcal/mol for AGA/TTT to −1.05 kcal/mol for CGC/GTG. Several tests of the applicability of the nearest-neighbor model to G·T mismatches are described. Analysis of imino proton chemical shifts show that structural perturbations from the G·T mismatches are highly localized. One-dimensional NOE difference spectra demonstrate that G·T mismatches form stable hydrogen-bonded wobble pairs in diverse contexts. Refined nearest-neighbor parameters for Watson−Crick base pairs are also presented.

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 Abstract published in Advance ACS Abstracts, August 1, 1997.

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One table showing experimental versus predicted (using Table 1) thermodynamics of 131 sequences with Watson−Crick base pairs; 10 figures showing 1/TM vs ln CT plots for the 33 sequences presented in Table 2 which are not shown in Figure 1; 11 figures showing the 1D-NOE difference spectra used for peak assignments listed in Table 6; two figures showing the 1D-NMR spectra at different temperatures for NTS-1 and NTS-2; one figure showing normalized melting curves for HP-1; and two figures showing plots of ΔH° vs ΔS° (31 pages). Ordering information is given on any current masthead page.

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