Int. J. Mol. Sci. 2012, 13(8), 10537-10552; doi:10.3390/ijms130810537
Review

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

Vincent J. B. Ruigrok 1,†,* email, Mark Levisson 1,† email, Johan Hekelaar 2 email, Hauke Smidt 1 email, Bauke W. Dijkstra 2 email and John van der Oost 1,* email
1 Laboratory of Microbiology, Wageningen University, Dreijenplein 10, Wageningen 6703 HB, The Netherlands 2 Laboratory of Biophysical Chemistry, University of Groningen, Nijenborgh 7, Groningen 9747 AG, The Netherlands † These authors contributed equally to this work.
* Authors to whom correspondence should be addressed.
Received: 31 May 2012; in revised form: 9 August 2012 / Accepted: 17 August 2012 / Published: 22 August 2012
(This article belongs to the Special Issue Protein Crystallography in Molecular Biology)
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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 (KD). 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.
Keywords: X-ray crystallography; aptamer; interaction; RNA/DNA-protein complex

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MDPI and ACS Style

Ruigrok, V.J.B.; Levisson, M.; Hekelaar, J.; Smidt, H.; Dijkstra, B.W.; van der Oost, J. Characterization of Aptamer-Protein Complexes by X-ray Crystallography and Alternative Approaches. Int. J. Mol. Sci. 2012, 13, 10537-10552.

AMA Style

Ruigrok VJB, Levisson M, Hekelaar J, Smidt H, Dijkstra BW, van der Oost J. Characterization of Aptamer-Protein Complexes by X-ray Crystallography and Alternative Approaches. International Journal of Molecular Sciences. 2012; 13(8):10537-10552.

Chicago/Turabian Style

Ruigrok, Vincent J. B.; Levisson, Mark; Hekelaar, Johan; Smidt, Hauke; Dijkstra, Bauke W.; van der Oost, John. 2012. "Characterization of Aptamer-Protein Complexes by X-ray Crystallography and Alternative Approaches." Int. J. Mol. Sci. 13, no. 8: 10537-10552.

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