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

Ligang Zhang, Hai Long, Grant E. Boldt, Kim D. Janda, George C Schatz, Frederick D. Lewis

Research output: Contribution to journalArticle

11 Citations (Scopus)

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 α- and β-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 β-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 π-stacking with the adjacent base-pair. The calculated structures for the internal stilbenosides show that the α- and β-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.

Original languageEnglish
Pages (from-to)314-322
Number of pages9
JournalOrganic and Biomolecular Chemistry
Volume4
Issue number2
DOIs
Publication statusPublished - 2006

Fingerprint

Stilbenes
stilbene
nucleosides
Base Pairing
Nucleosides
deoxyribonucleic acid
DNA
Spectrum Analysis
Circular dichroism spectroscopy
Molecular modeling
oligonucleotides
Molecular Dynamics Simulation
Circular Dichroism
Oligonucleotides
spectroscopy
dichroism
Molecular dynamics
excitons
molecular dynamics
preparation

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Chemistry(all)

Cite this

α- and β-Stilbenosides as base-pair surrogates in DNA hairpins. / Zhang, Ligang; Long, Hai; Boldt, Grant E.; Janda, Kim D.; Schatz, George C; Lewis, Frederick D.

In: Organic and Biomolecular Chemistry, Vol. 4, No. 2, 2006, p. 314-322.

Research output: Contribution to journalArticle

Zhang, Ligang ; Long, Hai ; Boldt, Grant E. ; Janda, Kim D. ; Schatz, George C ; Lewis, Frederick D. / α- and β-Stilbenosides as base-pair surrogates in DNA hairpins. In: Organic and Biomolecular Chemistry. 2006 ; Vol. 4, No. 2. pp. 314-322.
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