Characterization of Aptamer-Protein Complexes by X-ray Crystallography and Alternative Approaches

V.J.B. Ruigrok, M. Levisson, J. Hekelaar, H. Smidt, B.W. Dijkstra, J. van der Oost

Research output: Contribution to journalArticleAcademicpeer-review

26 Citations (Scopus)

Abstract

Aptamers are oligonucleotide ligands, either RNA or ssDNA, selected for high-affinity binding to molecular targets, such as small organic molecules, proteins or whole microorganisms. While reports of new aptamers are numerous, characterization of their specific interaction is often restricted to the affinity of binding (K(D)). Over the years, crystal structures of aptamer-protein complexes have only scarcely become available. Here we describe some relevant technical issues about the process of crystallizing aptamer-protein complexes and highlight some biochemical details on the molecular basis of selected aptamer-protein interactions. In addition, alternative experimental and computational approaches are discussed to study aptamer-protein interactions
Original languageEnglish
Pages (from-to)10537-10552
JournalInternational Journal of Molecular Sciences
Volume13
Issue number8
DOIs
Publication statusPublished - 2012

Keywords

  • angstrom crystal-structure
  • nf-kappa-b
  • streptavidin-binding aptamers
  • rna structure prediction
  • dna aptamer
  • high-affinity
  • nucleic-acid
  • molecular recognition
  • alpha-thrombin
  • crystallization

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