Comparative study of ribonucleotide, deoxyribonucleotide, and hybrid oligonucleotide helices by nuclear magnetic resonance

Abstract

The nonexchangeable base protons and the hydrogen-bonding NH--N imino protons were used to study the conformations and the helix--coil transitions in the following oligonucleotides: (I) dCT5G + dCA5G, (II) rCU5G + rCA5G, (III) dCT5 G + rCA5G, (IV) rCU5G + dCA5G. The first three mixtures all form stable double-helical structures at 5 degrees C, whereas IV forms a triple strand with an rCU5G:dCA5G 2:1 ratio. The chemical shifts of the imino protons in the double strands indicate that I, II, and III have different conformations in solution. For example, the hydrogen-bonded proton of one of the C.G base pairs is more deshielded (a 0.4-ppm downfield shift) in helix I than in helix II or III. This implies a significant change in helical parameters, such as the winding angle, the distance between base pairs, or overlap of the bases. The coupling constants of the H1' sugar protons show that helix I has 90% 2'-endo sugar conformation, whereas helix III has greater than 85% 3'-endo conformation for the observed sugar rings. The sugar pucker data are consistent with helix I having B-family geometry; III has A-family geometry. The chemical shifts of the nonexchangeable base protons in system I were followed with increasing temperature. The midpoints for the transitions, Tm's, for all the base protons were 28--30 degrees C; this indicates an all-or-none transition.