Base pairing configuration and stability of an oligonucleotide duplex containing a 5-chlorouracil-adenine base pair

Jacob A. Theruvathu, Cherine H. Kim, Daniel K. Rogstad, Jonathan W. Neidigh, Lawrence Sowers

Research output: Contribution to journalArticle

16 Citations (Scopus)

Abstract

Inflammation-mediated reactive molecules can damage DNA by oxidation and chlorination. The biological consequences of this damage are as yet incompletely understood. In this paper, we have constructed oligonucleotides containing 5-chlorouracil (ClU), one of the known inflammation damage products. The thermodynamic stability, base pairing configuration, and duplex conformation of oligonucleotides containing ClU paired opposite adenine have been examined. NMR spectra reveal that the ClU-A base pair adopts a geometry similar to that of the T-A base pair, and the ClU-A base pair-containing duplex adopts a normal B-form conformation. The line width of the imino proton of the ClU residue is substantially greater than that of the corresponding T imino proton; however, this difference is not attributed to a reduced thermal or thermodynamic stability or to an increased level of proton exchange with solvent. While the NMR studies reveal an increased level of chemical exchange for the ClU imino proton of the ClU-A base pair, the ClU residue is not a target for removal by the Escherichia coli mispaired uracil glycosylase, which senses damagerelated helix instability. The results of this study are consistent with previous reports indicating that the DNA of replicating cells can tolerate substantial substitution with ClU. The fraudulent, pseudo-Watson-Crick ClU-A base pair is sufficiently stable to avoid glycosylase removal and, therefore, might constitute a persistent form of cellular DNA damage.

Original languageEnglish (US)
Pages (from-to)7539-7546
Number of pages8
JournalBiochemistry
Volume48
Issue number31
DOIs
StatePublished - Aug 11 2009
Externally publishedYes

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Adenine
Oligonucleotides
Base Pairing
Protons
Thermodynamic stability
Conformations
DNA
Nuclear magnetic resonance
Thermodynamics
DNA Damage
Uracil
Chlorination
Linewidth
Escherichia coli
Inflammation
Substitution reactions
Halogenation
Cells
Oxidation
Molecules

ASJC Scopus subject areas

  • Biochemistry

Cite this

Base pairing configuration and stability of an oligonucleotide duplex containing a 5-chlorouracil-adenine base pair. / Theruvathu, Jacob A.; Kim, Cherine H.; Rogstad, Daniel K.; Neidigh, Jonathan W.; Sowers, Lawrence.

In: Biochemistry, Vol. 48, No. 31, 11.08.2009, p. 7539-7546.

Research output: Contribution to journalArticle

Theruvathu, Jacob A. ; Kim, Cherine H. ; Rogstad, Daniel K. ; Neidigh, Jonathan W. ; Sowers, Lawrence. / Base pairing configuration and stability of an oligonucleotide duplex containing a 5-chlorouracil-adenine base pair. In: Biochemistry. 2009 ; Vol. 48, No. 31. pp. 7539-7546.
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