Skip Navigation


Nucleic Acids Research Advance Access originally published online on January 9, 2009
Nucleic Acids Research 2009 37(3):e23; doi:10.1093/nar/gkn1012
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (2629K) Freely available
Right arrow Screen PDF (445K) Freely available
Right arrow Supplementary Data
Right arrowOA All Versions of this Article:
37/3/e23    most recent
gkn1012v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Shiohara, T.
Right arrow Articles by Inoue, T.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Shiohara, T.
Right arrow Articles by Inoue, T.
Related Collections
Right arrow Nucleic acid structure
Right arrow RNA characterisation and manipulation
Right arrow Miscellaneous/other
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2009, Vol. 37, No. 3 e23
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Methods Online

A designed RNA selection: establishment of a stable complex between a target and selectant RNA via two coordinated interactions

Tomoaki Shiohara1, Hirohide Saito1,2,* and Tan Inoue1,2,*

1Laboratory of Gene Biodynamics, Graduate School of Biostudies, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502 and 2ICORP, Japan Science and Technology Agency (JST), 5 Sanban-cho, Chiyoda-ku, Tokyo 102-0075, Japan

*To whom correspondence should be addressed. Tel: +81 75 753 3995; Fax: +81 75 753 3996; Email: h-saito{at}kuchem.kyoto-u.ac.jp

Correspondence may also be addressed to Tan Inoue. Email: tan{at}kuchem.kyoto-u.ac.jp

Received November 6, 2008. Accepted December 4, 2008.

In this paper, we describe a new method for selecting RNA aptamers that cooperatively bind to two specific sites within a target RNA. We designed a selection system in which two RNAs, a target RNA and a RNA pool, were assembled by employing a pre-organized GAAA tetraloop-11-nt receptor interaction. This allows us to select the binding sequence against a targeted internal loop as well as a linker region optimized for binding of the two binding sites. After the selection, the aptamers bound with dissociation constants in the nanomolar range, thereby forming a stable complex with the target RNA. Thus this method enables identification of aptamers for a specific binding site together with a linker for cooperative binding of the two RNAs. It appears that our new method can be applied generally to select RNAs that adhere tightly to a target RNA via two specific sites. The method can also be applicable for further engineering of both natural and artificial RNAs.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?




Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.