Conformation and interaction of short nucleic acid double-stranded helices. II. Proton magnetic resonance studies on the hydrogen-bonded NH-N protons of ribosyl ApApGpCpUpU helix.

Biochemistry
L S KanP O Ts'o

Abstract

A self-complementary ribohexanucleotide, ApApGpCpUpU, was synthesized and its NH-N hydrogen-bonded protons were studied by proton magnetic resonance. At 1 degree C, 0.17 M Na+, pH 7.6 with 10 mM phosphate-0.1 mM EDTA in H2O, three proton resonances are found in the low-field region with the following chemical shifts and line widths at half-height: 13.2 ppm (80 Hz), 13.5 ppm (30 Hz), and 14.2 ppm (44 Hz). The existence of these resonances indicates the formation of a self-complementary, hydrogen-bonded duplex under these conditions. Upon elevation of temperature, these three resonances sequentially broaden and finally all disappear near 35 degrees C. Unambiguous assignments of these three resonances can be made to the terminal A(1)-U(6) pairs, interior A(2)-U(5) pairs, and to the middle G(3)-C(4) pairs. The assignments were based on (i) the differential sensitivities of the line widths of these resonances to thermal variation, as well as on (ii) a comparison of the computed chemical shifts with the observed chemical shifts. The quantitative aspects of the NH proton transfer between helix, coil, and water are discussed in relationship to the line widths of these resonances and the lifetime of the helix state. The computed chemica...Continue Reading

Citations

Nov 1, 1976·Biopolymers·C Giessner-PrettreP O Ts'o
May 1, 1977·Quarterly Reviews of Biophysics·N R Kallenbach, H M Berman
Nov 1, 1987·Quarterly Reviews of Biophysics·C Giessner-Prettre, B Pullman
Aug 1, 1986·Journal of Biomolecular Structure & Dynamics·G KotovychJ P Tong
Dec 9, 1985·Nucleic Acids Research·D E Wemmer, A S Benight
Sep 25, 1987·Nucleic Acids Research·G LancelotN T Thuong
Mar 1, 1983·Biopolymers·B W Shum, D M Crothers
Jul 29, 1976·Nature·G T RobillardH J Berendsen

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