Nuclear magnetic resonance study of hydrogen-bonded ring protons in oligonucleotide helices involving classical and nonclassical base pairs

N. R. Kallenbach, W. E. Daniel, M. A. Kaminker

Research output: Contribution to journalArticle

Abstract

A study of the exchangeable ring nitrogen protons in aqueous solutions of oligonucleotide complexes involving Watson-Crick base pairs as well as Hoogsteen pairs and other nonclassical hydrogen bonding schemes shows that resolvable resonances in the low-field (-10 to -16 ppm from sodium 4,4-dimethyl-4-silapentanesulfonate) region can be detected in a variety of structures other than double stranded helices. Ring nitrogen proton resonances arising from the following hydrogen-bonding situations are reported: (1) AT and GC Watson-Crick base pairs in a self-complementary octanucleotide, dApApApGpCpTpT-pT; (2) U·A·U base triples in complexes between oligo-U15 and AMP; (3) C·G·C+ base triples in complexes between oligo-C17 and GMP at acid pH; (4) s4U·A*s4U base triples in complexes between oligo-s4U15 and AMP, all of which involve both Watson-Crick and Hoogsteen base pairing to form triplexes; (5) C·C+ base pairing between protonated and unprotonated C residues in oligo-C17 at acid pH; and (6) I4 base quadruples in the four strand association among oligo-I at high salt. The behavior of the dA3G·CT3 helix is consistent with both fraying of the terminal base pairs and presence of intermediate states as the helix opens. In the monomer-oligomer complexes, under the conditions used here, the exchange appears to be governed by the dissociation rate of monomer from the complex. These findings suggest that those tertiary structure hydrogen bonds in tRNA involving ring nitrogen protons should have representative resonances in the low-field (11-16 ppm) proton NMR region in H2O.

Original languageEnglish (US)
Pages (from-to)1218-1224
Number of pages7
JournalBiochemistry
Volume15
Issue number6
StatePublished - 1976

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Oligonucleotides
Base Pairing
Protons
Hydrogen
Magnetic Resonance Spectroscopy
Nuclear magnetic resonance
Hydrogen bonds
Nitrogen
Adenosine Monophosphate
Hydrogen Bonding
Monomers
Acids
Transfer RNA
Oligomers
Ion exchange
Salts
Sodium
Association reactions

ASJC Scopus subject areas

  • Biochemistry

Cite this

Nuclear magnetic resonance study of hydrogen-bonded ring protons in oligonucleotide helices involving classical and nonclassical base pairs. / Kallenbach, N. R.; Daniel, W. E.; Kaminker, M. A.

In: Biochemistry, Vol. 15, No. 6, 1976, p. 1218-1224.

Research output: Contribution to journalArticle

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