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

Lou S. Kan, Philip N. Borer, Paul O P Ts'o

Research output: Contribution to journalArticle

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Abstract

A self-complementary ribohexanucleotide, ApApGpCpUpU, was synthesized and its NH-N hydrogen-bonded protons were studied by proton magnetic resonance. At 1°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°. 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 life-time of the helix state. The computed chemical shifts of the NH-N resonances based on the A-RNA (or A′-RNA) model agree more closely with the observed chemical shifts than the computed values based on the B-DNA model. These results suggest that the helical duplex of A2GCU2 assumes a conformation similar to A-RNA (or A′-RNA) in aqueous solution. The results on both the NH-N resonances and the C-H resonances are summarized and discussed in terms of the helical conformation of ( A2GCU2)2.

Original languageEnglish (US)
Pages (from-to)4864-4869
Number of pages6
JournalBiochemistry
Volume14
Issue number22
StatePublished - 1975

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Nucleic Acids
Conformations
Protons
Hydrogen
Magnetic Resonance Spectroscopy
Nuclear magnetic resonance
RNA
Chemical shift
B-Form DNA
Linewidth
Edetic Acid
Hot Temperature
Phosphates
Temperature
Water
Proton transfer

ASJC Scopus subject areas

  • Biochemistry

Cite this

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. / Kan, Lou S.; Borer, Philip N.; Ts'o, Paul O P.

In: Biochemistry, Vol. 14, No. 22, 1975, p. 4864-4869.

Research output: Contribution to journalArticle

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title = "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",
abstract = "A self-complementary ribohexanucleotide, ApApGpCpUpU, was synthesized and its NH-N hydrogen-bonded protons were studied by proton magnetic resonance. At 1°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°. 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 life-time of the helix state. The computed chemical shifts of the NH-N resonances based on the A-RNA (or A′-RNA) model agree more closely with the observed chemical shifts than the computed values based on the B-DNA model. These results suggest that the helical duplex of A2GCU2 assumes a conformation similar to A-RNA (or A′-RNA) in aqueous solution. The results on both the NH-N resonances and the C-H resonances are summarized and discussed in terms of the helical conformation of ( A2GCU2)2.",
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T1 - 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

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AU - Borer, Philip N.

AU - Ts'o, Paul O P

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N2 - A self-complementary ribohexanucleotide, ApApGpCpUpU, was synthesized and its NH-N hydrogen-bonded protons were studied by proton magnetic resonance. At 1°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°. 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 life-time of the helix state. The computed chemical shifts of the NH-N resonances based on the A-RNA (or A′-RNA) model agree more closely with the observed chemical shifts than the computed values based on the B-DNA model. These results suggest that the helical duplex of A2GCU2 assumes a conformation similar to A-RNA (or A′-RNA) in aqueous solution. The results on both the NH-N resonances and the C-H resonances are summarized and discussed in terms of the helical conformation of ( A2GCU2)2.

AB - A self-complementary ribohexanucleotide, ApApGpCpUpU, was synthesized and its NH-N hydrogen-bonded protons were studied by proton magnetic resonance. At 1°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°. 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 life-time of the helix state. The computed chemical shifts of the NH-N resonances based on the A-RNA (or A′-RNA) model agree more closely with the observed chemical shifts than the computed values based on the B-DNA model. These results suggest that the helical duplex of A2GCU2 assumes a conformation similar to A-RNA (or A′-RNA) in aqueous solution. The results on both the NH-N resonances and the C-H resonances are summarized and discussed in terms of the helical conformation of ( A2GCU2)2.

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