Improvement of base selectivity and binding affinity by controlling hydrogen bonding motifs between nucleobases and isoxanthopterin: Application to the detection of T/C mutation

Burki Rajendar, Yusuke Sato, Seiichi Nishizawa, Norio Teramae

Research output: Contribution to journalArticlepeer-review

21 Citations (Scopus)

Abstract

At an abasic site in an oligo-DNA duplex, isoxanthopterin (IX)†IX and 3-MIX was obtained from Sigma-Aldrich Co. (USA) and Enamine Ltd, (Ukraine), respectively. can bind to thymine (T) and cytosine (C) with strong affinity compared to adenine and guanine, but the base selectivity for T against C is moderate. In order to improve both binding affinity and base selectivity for T against C, a methyl group is introduced to IX, which is known as 3-methyl isoxanthopterin (3-MIX), by which binding affinity for C is expected to decrease. Indeed, 3-MIX specifically binds to T more strongly than IX and loses its binding affinity for C. The improved binding ability of 3-MIX for T would be suitable for the practical use in SNP typing related to T.

Original languageEnglish
Pages (from-to)3682-3685
Number of pages4
JournalBioorganic and Medicinal Chemistry Letters
Volume17
Issue number13
DOIs
Publication statusPublished - 2007 Jul 1

Keywords

  • AP site
  • Methyl group
  • T/C SNP
  • p53 Gene

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Medicine
  • Molecular Biology
  • Pharmaceutical Science
  • Drug Discovery
  • Clinical Biochemistry
  • Organic Chemistry

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