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Synthesis and DNA binding properties of iminodiacetic acid-linked polyamides: characterization of cooperative extended 2 : 1 side-by-side parallel binding

Academic Article
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Overview

authors

  • Woods, C. R.
  • Ishii, T.
  • Boger, Dale

publication date

  • September 2002

journal

  • Journal of the American Chemical Society  Journal

abstract

  • A series of iminodiacetic acid (IDA)-linked polyamides (DpPyPyPy-IDA-PyPyPyDp) were prepared and constitute polyamides joined head-to-head by a functionalizable five-atom linker. It was found that the IDA linker exerts a unique influence over the DNA binding conformation differing from both the beta-alanine (extended) or gamma-aminobutyric acid (hairpin) linkers, resulting in cooperative parallel side-by-side 2:1 binding in an extended conformation most likely with a staggered versus stacked alignment. A generalized variant of a fluorescent intercalator displacement (FID) assay conducted on a series of hairpin deoxyoligonucleotides containing a systematically varied A/T-rich binding-site size was used to distinguish between the binding modes of the IDA-linked polyamides.

subject areas

  • Base Sequence
  • DNA
  • Imino Acids
  • Kinetics
  • Nucleic Acid Conformation
  • Nylons
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Identity

International Standard Serial Number (ISSN)

  • 0002-7863

Digital Object Identifier (DOI)

  • 10.1021/ja026588m

PubMed ID

  • 12207521
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Additional Document Info

start page

  • 10676

end page

  • 10682

volume

  • 124

issue

  • 36

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