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α- and β-Stilbenosides as base-pair surrogates in DNA hairpins

Academic Article
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Overview

related to degree

  • Boldt, Grant E, Ph.D. in Chemical Biology, Scripps Research 2004 - 2007

authors

  • Zhang, L. G.
  • Long, H.
  • Boldt, Grant E
  • Janda, Kim
  • Schatz, G. C.
  • Lewis, F. D.

publication date

  • January 2006

journal

  • Organic & Biomolecular Chemistry  Journal

abstract

  • The synthesis, structure, and optical spectroscopy of hairpin oligonucleotide conjugates possessing synthetic stilbene C-nucleosides (stilbenosides) are reported. Synthetic methods for selective preparation of both the alpha- and beta-stilbenosides have been developed. Both anomers are effective in stabilizing hairpin structures when used as capping groups at the open end of the hairpin base-pair domain. However, only the beta-anomer effectively stabilizes the hairpin structure when located in the interior of the base-pair domain opposite an abasic site. Similar results are obtained for hairpins possessing two stilbenosides, either adjacent to each other or with one intervening base-pair. Molecular dynamics simulations are employed to obtain averaged structures for these conjugates. The calculated structures for the capped hairpins formed with either anomer show effective pi-stacking with the adjacent base-pair. The calculated structures for the internal stilbenosides show that the alpha- and beta-anomers form extrahelical and intrahelical structures, respectively. The relative orientations of the two stilbenes in the bis-stilbenosides have been studied using a combination of exciton-coupled circular dichroism spectroscopy and molecular modeling.

subject areas

  • Base Pairing
  • Circular Dichroism
  • DNA
  • Models, Molecular
  • Nucleic Acid Conformation
  • Nucleosides
  • Stilbenes
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Identity

International Standard Serial Number (ISSN)

  • 1477-0520

Digital Object Identifier (DOI)

  • 10.1039/b513694f

PubMed ID

  • 16391774
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Additional Document Info

start page

  • 314

end page

  • 322

volume

  • 4

issue

  • 2

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