Proton nuclear magnetic resonance studies on bulge-containing DNA oligonucleotides from a mutational hot-spot sequence

Sarah A. Woodson, Donald M. Crothers

Research output: Contribution to journalArticle

Abstract

A series of bulge-containing and normal double-helical synthetic oligodeoxyribonucleotides, of sequence corresponding to a frame-shift mutational hot spot in the λ CI gene, are compared by proton magnetic resonance spectroscopy at 500 MHz. The imino proton resonances of d(GATGGGCAG)·d(CTGCCCATC), d(GATGGGCAG)·d(CTGCCCCATC), and d(GATGGGCAG)-d(CTGACCCATC) are assigned by one-dimensional nuclear Overhauser effect spectroscopy. Nonselective T1 inversion-recovery experiments are used to determine exchangeable proton lifetimes and to compare helix stability and dynamics of the three duplexes. An extra adenosine flanking the internal G·C base pairs has a strongly localized effect on helix stability, but the destabilizing effect of an extra cytidine in a C tract is delocalized over the entire G·C run. These data lead to the conclusion that the position of the bulge migrates along the run in the fast-exchange limit on the NMR time scale. Rapid migration of the bulge defect in homopolymeric sequences may help rationalize both frame-shift mutagenesis and translational frame shifting. We estimate that the unfavorable free energy of a localized bulge defect is 2.9-3.2 kcal/mol, in good agreement with earlier estimates for RNA helices.

Original languageEnglish (US)
Pages (from-to)904-912
Number of pages9
JournalBiochemistry®
Volume26
Issue number3
StatePublished - 1987
Externally publishedYes

Fingerprint

Oligonucleotides
Protons
Magnetic Resonance Spectroscopy
Nuclear magnetic resonance
Magnetic resonance spectroscopy
Cytidine
Mutagenesis
Defects
Oligodeoxyribonucleotides
DNA
Base Pairing
Adenosine
Free energy
Spectrum Analysis
Genes
Spectroscopy
RNA
Recovery
Experiments
Proton Magnetic Resonance Spectroscopy

ASJC Scopus subject areas

  • Biochemistry

Cite this

Proton nuclear magnetic resonance studies on bulge-containing DNA oligonucleotides from a mutational hot-spot sequence. / Woodson, Sarah A.; Crothers, Donald M.

In: Biochemistry®, Vol. 26, No. 3, 1987, p. 904-912.

Research output: Contribution to journalArticle

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