Single base mismatches in DNA long- and short-range structure probed by analysis of axis trajectory and local chemical reactivity

Abstract

We have devised a procedure to generate any single base mismatch in a constant sequence context, and have studied these from two points of view. 1. (1) We have examined electrophoretic mobility of 458 base-pair fragments containing approximately centrally located single mismatches, in polyacrylamide gels, compared to fully matched DNA fragments. We found that no single mismatch caused a significant perturbation of gel mobility, and we conclude that all the mismatches may be accommodated within a helical geometry such that there is no alteration of the path of the helix axis in a straight DNA molecule. 2. (2) We have studied all the single mismatches with respect to reactivity to a number of chemical probes. We found that: 2.1. (a) No mispaired adenine bases are reactive to diethyl pyrocarbonate and are therefore not simply unpaired such that N-7 is exposed. 2.2. (b) A number of mispaired thymine bases are reactive to osmium tetroxide, and cytosine bases to hydroxylamine. 2.3. (c) Where crystal or nuclear magnetic resonance structures are available, the reactivity correlates with exposure of the pyrimidine 5,6 double bonds to attack in the major groove as a result of wobble base-pair formation. This is particularly clear for G·T and I·T base-pairs. 2.4. (d) Reactivity of bases in mismatched pairs can be dependent on sequence context. 2.5. (e) Reactivity of the C·C mismatch to hydroxylamine is suppressed at low pH, suggesting that a rearrangement of base-pairing occurs on protonation. The results overall are consistent with the formation of stacked intrahelical base-pairs wherever possible, resulting in no global distortion of the DNA structure, but specific enhancement of chemical reactivity in some cases.