Dynamic Structure of Pyrimidine-polyribonucleotides in Solution. 1H NMR Studies

Abstract

Abstract Temperature dependent conformations and molecular motions of pyrimidine polyribonucleotides, poly(C) and poly(U), have been studied in 2H2O solutions (pH 5.8±0.3, 5–72 °C by measuring 1H NMR intensities, chemical shifts, coupling constants, and spin-lattice relaxation times. Below 50 °C, poly(C) exists as a slowly exchanging mixture of double-stranded and single-stranded forms of which only the single-stranded form is observable by 1H NMR. In this temperature range, the single-stranded poly(C) shows a strong base-stacking with dominated C3′-endo anti conformation, whereas above 50 °C it takes partly C2′-endo conformation with destabilization of the helical structure. Poly(U) exists as single strand within the whole temperature range studied, and the bases are nearly unstacked with 58% of C2′-endo conformer. Poly(U) is more flexible than poly(C), which was characterized with rotational correlation times in the order of 10−9–10−10 s.