Sequence and conformational effects on imino proton exchange in A · T‐ and A · U‐containing DNA and RNA duplexes

1 H‐nmr relaxation has been used to study the effect of sequence and conformation on imino proton exchange in adenine–thymine (A · T) and adenine–uracil (A · U) containing DNA and RNA duplexes. At low temperature, relaxation is caused by dipolar interactions between the imino and the adenine amino and AH2 protons, and at higher temperature, by exchange with the solvent protons. Although room temperature exchange rates vary between 3 and 12s −1 , the exchange activation energies ( E α ) are insensitive to changes in the duplex sequence (alternating vs homopolymer duplexes), the conformation (B‐form DNA vs A‐form RNA), and the identity of the pyrimidine base (thymine vs uracil). The average value of the activation energy for the five duplexes studied, poly[d(A‐T)], poly[d(A) · d(T)], poly[d(A‐U)], Poly[d(A) · d(U)], and poly[r(A) · r(U)], was 16.8 ± 1.3 kcal/mol. In addition, we find that the average E α for the A.T base pairs in a 43‐base‐pair restriction fragment is 16.4 ± 1.0 kcal/mol. This result is to be contrasted with the observation that the E α of cytosine‐containing duplexes depends on the sequence, conformation, and substituent groups on the purine and pyrimidine bases. Taken together, the data indicate that there is a common low‐energy pathway for the escape of the thymine (uracil) imino protons from the double helix. The absolute values of the exchange rates in the simple sequence polymers are typically 3–10 times faster than in DNAs containing both A · T and G · C base pairs.