NMR Evidence for Base Dynamics at all TpA Steps in DNA

Abstract

NMR evidence is presented indicating that the exceptional conformational dynamics found at TpA steps in DNA is general to all immediate sequence contexts. One easily tractable NMR parameter that is sensitive to TpA base dynamics is the resonance linewidth of the TpA adenine H2 proton. This resonance experiences a temperature-dependent broadening due to conformational dynamics. Unusual dynamics at TpA steps were originally observed in the sequence context (T)pTpTpApAp(A). We have since shown that the evidence for TpA dynamics persists when either the thymine preceding the TpA step or the adenine following the TpA step is preserved [McAteer et al., Nucleic Acids Res. 23 3962–3966 (1995)]. Here, in order establish whether or not exceptional TpA dynamics occurs in all DNA sequence contexts, we investigated a series of DNA sequences of the form GCN_aTAN_bN_bTAN_aGC, where N=A,T,C,G. In this family of sequences, all 16 possible immediate sequence context environments of the form N_aTAN_b were examined using 10 DNA sequences. Our NMR results show that the TpA adenine H2 resonance contains a temperature dependent excess linewidth indicative of dynamics in all 16 sequence context environments. By studying a complete set of sequence contexts, it was possible to recognize trends relating resonance parameters and sequence environment. For example, the magnitude of the maximum linewidth is largely determined by the identity of the nucleotide following the TpA step and the magnitude of the linewidth maximum is moderately correlated (r=0.56) with the temperature of the linewidth maximum. The physical basis for these correlations is discussed.