NMR studies of a deoxyribodecanucleotide containing an extrahelical thymidine surrounded by an oligo(dA) multiplied by oligo(dT) tract

One- and two-dimensional NMR experiments were carried out on a decamer, and on the same sequence with the addition of an unpaired thymidine which will be referred to as the T-bulge decamer. Evidence from one-dimensional NOE experiments on the exchangeable protons indicates that the unpaired thymidine is extrahelical. This conclusion is also supported by numerous cross-peaks in the two-dimensional NOESY spectrum of the nonexchangeable protons. Assignments for all of the resonances, with the exception of the H5' and H5" resonances, have been made for both oligonucleotide duplexes through the use of 2D NOESY, COSY, and relayed COSY experiments. Temperature dependence of the methyl resonance chemical shifts indicates that the unpaired thymidine shows unusual behavior compared to other thymidines in the duplex.