pH-dependent configurations of a 5-chlorouracil-guanine base pair

Jacob A. Theruvathu, Cherine H. Kim, Agus Darwanto, Jonathan W. Neidigh, Lawrence Sowers

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

Hypochlorous acid (HOCl) from activated neutrophils at sites of inflammation can react with and damage biological molecules, including nucleic acids. The reaction of HOCl with cytosine analogues can generate multiple products, including 5-chlorouracil (ClU). In this paper, we have constructed oligonucleotides containing ClU paired opposite guanine (ClU-G). Melting studies indicate that oligonucleotide duplexes containing the ClU-G mispair are substantially less stable than those containing a ClU-A base pair. The melting temperature of the ClU-G mispair is not experimentally distinguishable from that of a T-G pair. NMR studies indicate that the ClU-G base pair adopts a wobble geometry at neutral pH, similar to a T-G mispair. The exchangeable protons of the ClU-G mispair broaden rapidly with an increase in temperature, indicating that the ClU-G mispair is less stable and opens more easily than the surrounding adjacent base pairs. Unlike the ClU-A base pair studied previously [Theruvathu, J. A., et al. (2009) Biochemistry 48, 7539-7546], the ClU-G mispair undergoes a pH-dependent structural change, assuming an ionized base pair configuration that approximates a Watson-Crick base pair at higher pH. Ionization of ClU in a DNA template could promote mispair formation and mutation, in accord with previous studies on other 5-halouracil analogues. The electron-withdrawing 5-chloro substituent facilitates ionization of the ClU N3 proton, promoting mispair formation, but it also renders the glycosidic bond susceptible to base cleavage by DNA repair glycosylases.

Original languageEnglish (US)
Pages (from-to)11312-11318
Number of pages7
JournalBiochemistry
Volume48
Issue number47
DOIs
StatePublished - Dec 1 2009
Externally publishedYes

Fingerprint

Guanine
Base Pairing
Hypochlorous Acid
Oligonucleotides
5-chlorouracil
Freezing
Ionization
Protons
DNA Glycosylases
Biochemistry
Temperature
Cytosine
DNA
DNA Repair
Nucleic Acids
Melting point
Melting
Neutrophils
Repair
Nuclear magnetic resonance

ASJC Scopus subject areas

  • Biochemistry

Cite this

Theruvathu, J. A., Kim, C. H., Darwanto, A., Neidigh, J. W., & Sowers, L. (2009). pH-dependent configurations of a 5-chlorouracil-guanine base pair. Biochemistry, 48(47), 11312-11318. https://doi.org/10.1021/bi901154t

pH-dependent configurations of a 5-chlorouracil-guanine base pair. / Theruvathu, Jacob A.; Kim, Cherine H.; Darwanto, Agus; Neidigh, Jonathan W.; Sowers, Lawrence.

In: Biochemistry, Vol. 48, No. 47, 01.12.2009, p. 11312-11318.

Research output: Contribution to journalArticle

Theruvathu, JA, Kim, CH, Darwanto, A, Neidigh, JW & Sowers, L 2009, 'pH-dependent configurations of a 5-chlorouracil-guanine base pair', Biochemistry, vol. 48, no. 47, pp. 11312-11318. https://doi.org/10.1021/bi901154t
Theruvathu JA, Kim CH, Darwanto A, Neidigh JW, Sowers L. pH-dependent configurations of a 5-chlorouracil-guanine base pair. Biochemistry. 2009 Dec 1;48(47):11312-11318. https://doi.org/10.1021/bi901154t
Theruvathu, Jacob A. ; Kim, Cherine H. ; Darwanto, Agus ; Neidigh, Jonathan W. ; Sowers, Lawrence. / pH-dependent configurations of a 5-chlorouracil-guanine base pair. In: Biochemistry. 2009 ; Vol. 48, No. 47. pp. 11312-11318.
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