Tracts of AT base pairs play important roles in DNA packing and DNA recognition by proteins. Recent crystallographic results have suggested the existence of a unique structural feature in these tracts, namely, bifurcated H-bonds from the N6-amino groups of adenine of the O4 of the thymine in the next base pair and in the opposite strand. The presence of these bifurcated H-bonds could explain properties of AT tracts such as binding of the helix axis and abnormal base-air opening kinetics. In this project , we are using 15N and 1H NMR spectroscopy to : (i) establish the existence of bifurcate H-bonds in AT tracts of the DANA in solution state, and (ii) characterize the effects of bifurcated H-bonds upon the local conformation and dynamics of the AT base pairs. We have synthesized, by chemical means, the DNA dodecamer 5(-d(CGCAAATTTGCG)-3( in which the N6-amino groups of all three adenines contain 15N. As a control, we have also synthesized the dodecamer 5(-d(CGCGAGCTCGCG)-3( in which only one adenine is present and 15N-labeled at the N6 amino group. The local environment at the adenine bases is investigated by monitoring the chemical shift of 15N and 1H resonances as a function of temperature. The dynamic properties of each adenine amino group are characterized by 1H-15N NOEs, 15N-edited 1H-1H NOEs, 15N and 1H relaxation rates, and the rates of exchange of amino protons with solvents protons. The results thus far indicate that 1H-15N NOEs and/or amino proton exchange rates for the first two adenines in the A3T3 tract differ from those in a single, isolated AT base pair. These findings support the presence of bifurcate H-bonds in these AT base pairs.
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