Complete assignment and conformational analysis of a deoxyribotetranucleotide, d(TAAT). A 360 and 500 MHz NMR study

Abstract

A proton NMR study at 360 MHz and 500 MHz was carried out on the tetranucleoside triphosphate d(TAAT) at a temperature of 27°C. Extensive decoupling experiments allowed a complete and unambiguous spectral assignment. The data are interpreted in terms of the N and S deoxyribose pseudorotational ranges. From the observed proton-proton coupling constants it is calculated that (a) the populations of deoxyribose S-form are as follows: dT(1)-, 85%; -dA(2)-, 97%; -dA(3)-, 81%; -dT(4), 64%; and (b) the g⁺ populations (backbone notation) along the exocyclic C4′-C5′ bond in -dA(2)-, dA(3)- and -dT(4) are 82%, 86% and 78%, respectively. From these values, combined with chemical shift considerations, it is concluded that the central -dA(2)-dA(3)- part of the molecule occurs preferentially as a mixture of two right-handed single-helical conformations, denoted S-S and S-N, in a ratio of approximately 8 : 2. This situation closely mimics that found for the 3′-end of d(A-A-A) (Olsthoorn, C.S.M., Bostelaar, L.J., Van Boom, J.H. and Altona, C. (1980) Eur. J. Biochem. 112, 95–110). Similarly, the conformational behaviour of the dT(1)-dA(2)- and -dA(3)-dT(4) terminals appears roughly identical to that displayed by the corresponding dinucleoside monophosphates. The molecule as a whole does not show signs of cooperativity of stacking.