Conformation and interaction of short nucleic acid double-stranded helices. I. Proton magnetic resonance studies on the nonexchangeable protons of ribosyl ApApGpCpUpU

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

Research output: Contribution to journalArticle

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Abstract

1H nuclear magnetic resonance (NMR) spectra of a self-complementary ribosyl hexanucleotide, A2GCU2, are investigated as a function of temperature and ionic strength in D2O. Seventeen nonexchangeable base and ribose-H1′ resonances are resolved, and unequivocally assigned by a systematic comparison with the spectra of a series of oligonucleotide fragments of the A2GCU2 sequence varying in chain length from 2 to 5. Changes in the chemical shifts of the 17 protons from the hexamer as well as the six H1′-H2′ coupling constants are followed throughout a thermally induced helix-coil transition. These δ vs. T and J vs. T (°C) profiles indicate that the transition is not totally cooperative and that substantial populations of partially bonded structures must exist at intermediate temperatures, with the central G·C region being most stable. Transitions in chemical shift for protons in the same base pair exhibit considerable differences in their Tm values as the data reflect both thermodynamic and local magnetic field effects in the structural transition, which are not readily separable. However, an average of the Tm values agrees well with the value predicted from studies of the thermally induced transition made by optical methods. The values of J1′-2′ for all six residues become very small (<1.5 Hz) at low temperatures indicating that C3′-endo is the most heavily populated furanose conformation in the helix. The 6 values of protons in the duplex were compared with those calculated from the ring current magnetic anisotropies of nearest and next-nearest neighboring bases using the geometrical parameters of the A′-RNA and B-DNA models. The δ values of the base protons in the duplex calculated assuming the A′-RNA geometry agree (±∼0.1 ppm) with the observed values much more accurately than those calculated on the basis of B-DNA geometry. The measured δ values of the H1′ are not accurately predicted from either model. The synthesis of 35 mg of A2GCU2 using primer-dependent polynucleotide phosphorylase is described in detail with extensive discussion in the microfilm edition.

Original languageEnglish (US)
Pages (from-to)4847-4863
Number of pages17
JournalBiochemistry
Volume14
Issue number22
StatePublished - 1975

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Nucleic Acids
Conformations
Protons
Magnetic Resonance Spectroscopy
Nuclear magnetic resonance
B-Form DNA
Chemical shift
Temperature
Polyribonucleotide Nucleotidyltransferase
Microfilm
RNA
Magnetic field effects
Ribose
Geometry
Magnetic anisotropy
Anisotropy
Magnetic Fields
Ionic strength
Chain length
Thermodynamics

ASJC Scopus subject areas

  • Biochemistry

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Conformation and interaction of short nucleic acid double-stranded helices. I. Proton magnetic resonance studies on the nonexchangeable protons of ribosyl ApApGpCpUpU. / Borer, Philip N.; Kan, Lou S.; Ts'o, Paul O P.

In: Biochemistry, Vol. 14, No. 22, 1975, p. 4847-4863.

Research output: Contribution to journalArticle

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abstract = "1H nuclear magnetic resonance (NMR) spectra of a self-complementary ribosyl hexanucleotide, A2GCU2, are investigated as a function of temperature and ionic strength in D2O. Seventeen nonexchangeable base and ribose-H1′ resonances are resolved, and unequivocally assigned by a systematic comparison with the spectra of a series of oligonucleotide fragments of the A2GCU2 sequence varying in chain length from 2 to 5. Changes in the chemical shifts of the 17 protons from the hexamer as well as the six H1′-H2′ coupling constants are followed throughout a thermally induced helix-coil transition. These δ vs. T and J vs. T (°C) profiles indicate that the transition is not totally cooperative and that substantial populations of partially bonded structures must exist at intermediate temperatures, with the central G·C region being most stable. Transitions in chemical shift for protons in the same base pair exhibit considerable differences in their Tm values as the data reflect both thermodynamic and local magnetic field effects in the structural transition, which are not readily separable. However, an average of the Tm values agrees well with the value predicted from studies of the thermally induced transition made by optical methods. The values of J1′-2′ for all six residues become very small (<1.5 Hz) at low temperatures indicating that C3′-endo is the most heavily populated furanose conformation in the helix. The 6 values of protons in the duplex were compared with those calculated from the ring current magnetic anisotropies of nearest and next-nearest neighboring bases using the geometrical parameters of the A′-RNA and B-DNA models. The δ values of the base protons in the duplex calculated assuming the A′-RNA geometry agree (±∼0.1 ppm) with the observed values much more accurately than those calculated on the basis of B-DNA geometry. The measured δ values of the H1′ are not accurately predicted from either model. The synthesis of 35 mg of A2GCU2 using primer-dependent polynucleotide phosphorylase is described in detail with extensive discussion in the microfilm edition.",
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N2 - 1H nuclear magnetic resonance (NMR) spectra of a self-complementary ribosyl hexanucleotide, A2GCU2, are investigated as a function of temperature and ionic strength in D2O. Seventeen nonexchangeable base and ribose-H1′ resonances are resolved, and unequivocally assigned by a systematic comparison with the spectra of a series of oligonucleotide fragments of the A2GCU2 sequence varying in chain length from 2 to 5. Changes in the chemical shifts of the 17 protons from the hexamer as well as the six H1′-H2′ coupling constants are followed throughout a thermally induced helix-coil transition. These δ vs. T and J vs. T (°C) profiles indicate that the transition is not totally cooperative and that substantial populations of partially bonded structures must exist at intermediate temperatures, with the central G·C region being most stable. Transitions in chemical shift for protons in the same base pair exhibit considerable differences in their Tm values as the data reflect both thermodynamic and local magnetic field effects in the structural transition, which are not readily separable. However, an average of the Tm values agrees well with the value predicted from studies of the thermally induced transition made by optical methods. The values of J1′-2′ for all six residues become very small (<1.5 Hz) at low temperatures indicating that C3′-endo is the most heavily populated furanose conformation in the helix. The 6 values of protons in the duplex were compared with those calculated from the ring current magnetic anisotropies of nearest and next-nearest neighboring bases using the geometrical parameters of the A′-RNA and B-DNA models. The δ values of the base protons in the duplex calculated assuming the A′-RNA geometry agree (±∼0.1 ppm) with the observed values much more accurately than those calculated on the basis of B-DNA geometry. The measured δ values of the H1′ are not accurately predicted from either model. The synthesis of 35 mg of A2GCU2 using primer-dependent polynucleotide phosphorylase is described in detail with extensive discussion in the microfilm edition.

AB - 1H nuclear magnetic resonance (NMR) spectra of a self-complementary ribosyl hexanucleotide, A2GCU2, are investigated as a function of temperature and ionic strength in D2O. Seventeen nonexchangeable base and ribose-H1′ resonances are resolved, and unequivocally assigned by a systematic comparison with the spectra of a series of oligonucleotide fragments of the A2GCU2 sequence varying in chain length from 2 to 5. Changes in the chemical shifts of the 17 protons from the hexamer as well as the six H1′-H2′ coupling constants are followed throughout a thermally induced helix-coil transition. These δ vs. T and J vs. T (°C) profiles indicate that the transition is not totally cooperative and that substantial populations of partially bonded structures must exist at intermediate temperatures, with the central G·C region being most stable. Transitions in chemical shift for protons in the same base pair exhibit considerable differences in their Tm values as the data reflect both thermodynamic and local magnetic field effects in the structural transition, which are not readily separable. However, an average of the Tm values agrees well with the value predicted from studies of the thermally induced transition made by optical methods. The values of J1′-2′ for all six residues become very small (<1.5 Hz) at low temperatures indicating that C3′-endo is the most heavily populated furanose conformation in the helix. The 6 values of protons in the duplex were compared with those calculated from the ring current magnetic anisotropies of nearest and next-nearest neighboring bases using the geometrical parameters of the A′-RNA and B-DNA models. The δ values of the base protons in the duplex calculated assuming the A′-RNA geometry agree (±∼0.1 ppm) with the observed values much more accurately than those calculated on the basis of B-DNA geometry. The measured δ values of the H1′ are not accurately predicted from either model. The synthesis of 35 mg of A2GCU2 using primer-dependent polynucleotide phosphorylase is described in detail with extensive discussion in the microfilm edition.

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