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Journal of Biomolecular Screening
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Article

Novel Approach to Analyzing RNA Aptamer-Protein Interactions: Toward Further Applications of Aptamers

Joonsung Hwang1 Satoshi Nishikawa2*

1 Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology, Higashi, Tsukuba, Ibaraki 305-8566, Japan.; National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases, Developmental Skin Biology Unit, Bethesda, Maryland.
2 Institute for Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology, Higashi, Tsukuba, Ibaraki 305-8566, Japan.; Age Dimension Research Center, National Institute of Advanced Industrial Science and Technology, Higashi, Tsukuba, Ibaraki 305-8566, Japan.

* To whom correspondence should be addressed. E-mail: satoshi-nishikawa{at}aist.go.jp.


  Abstract

Surface plasmon-resonance analysis using a Biacore biosensor is a powerful tool for the detailed study of biomolecular interactions. The authors examined the methods of immobilizing proteins on the surface of NTA, SA, and CM5 sensor chips to study RNA aptamer-protein interactions. RNA aptamers and their deletion variants were loaded onto a protein-immobilized sensor chip, and their binding affinities were analyzed. Immobilizing the protein on a CM5 sensor chip via an anti-His-tag antibody was the only strategy that clearly detected the kinetic parameters of the interactions. {Delta}NEO-III-14U, one of the deletion variants of the NS3 aptamer, had the highest binding affinity for the {Delta}NS3 protein in this study (KD = 4 x 10-8). Moreover, the 29-amino-acid spacer fragment was essential for protein immobilization using this strategy. This novel method will be useful in comparing the affinity of various RNA aptamers and selecting the most suitable candidates for a given target, as well as facilitating the in vitro selection procedure itself.

Key Words: RNA aptamers, immobilization, Biacore biosensor, surface plasmon-resonance analysis, SELEX technique

First published on June 7, 2006, doi:10.1177/1087057106288491

Journal of Biomolecular Screening 2006;11:599.

A more recent version of this article appeared on September 1, 2006

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