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Hairpin versus extended DNA binding of a substituted beta-alanine linked polyamide

Academic Article
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Overview

authors

  • Woods, C. R.
  • Ishii, T.
  • Wu, B.
  • Bair, K. W.
  • Boger, Dale

publication date

  • March 2002

journal

  • Journal of the American Chemical Society  Journal

abstract

  • A series of alpha-substituted beta-alanine (beta) linked polyamides (DbaPyPyPy-beta*-PyPyPy) were prepared and examined. This resulted in the observation that while most substituents disrupt DNA binding, (R)-alpha-methoxy-beta-alanine (beta((R)-OMe)) maintains strong binding affinity and preferentially adopts a hairpin versus extended binding mode, providing an alternative hairpin linker to gamma-aminobutyric acid (gamma). A generalized variant of a fluorescent intercalator displacement assay conducted on a series of hairpin deoxyoligonucleotides containing a systematically varied A/T-rich binding site size was developed to distinguish between the extended binding of the parent beta-alanine 1 (DbaPyPyPy-beta-PyPyPy) and the hairpin binding of 3 (DbaPyPyPy-beta((R)-OMe)-PyPyPy).

subject areas

  • Alanine
  • Cross-Linking Reagents
  • DNA
  • Intercalating Agents
  • Models, Molecular
  • Nucleic Acid Conformation
  • Nylons
  • Pyrroles
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Identity

International Standard Serial Number (ISSN)

  • 0002-7863

Digital Object Identifier (DOI)

  • 10.1021/ja0122039

PubMed ID

  • 11878968
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Additional Document Info

start page

  • 2148

end page

  • 2152

volume

  • 124

issue

  • 10

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