THE EFFECTS OF SEQUENCE CONTEXT ON BASE DYNAMICS AT TPA STEPS IN DNA STUDIED BY NMR

Base dynamics, heretofore observed only at TpA steps in DNA, were inve stigated as a function of sequence context by NMR spectroscopy, The la rge amplitude conformational dynamics have been previously observed in T(n)A(n) segments where n greater than or equal to 2. In order to det ermine whether the dynamic characteristics occur in more general seque nce contexts, we examined four self-complementary DNA sequences, [d(CT TTA-NATNTAAAG)(2)] (where N=A, C, T, G and N=complement of N). The ano malous broadening of the TpA adenine H2 resonance which is indicative of large amplitude base motion was observed in all nine unique four nu cleotide contexts. Furthermore, all the adenine H2 resonances experien ced a linewidth maximum as a function of temperature, which is a chara cteristic of the dynamic process, Interestingly, the temperature of th e linewidth maximum varied with sequence indicating that the thermodyn amics of TpA base dynamics are also sequence dependent. In one example , neither a T preceding nor an A trailing the TpA step was required fo r base dynamics. These results show that base dynamics, heretofore obs erved in only a few isolated sequences, occurs at all TpA steps which are either preceded or followed by a thymine or adenine, respectively, and may be characteristic of all TpA steps in DNA notwithstanding seq uence context.