This Article Figures Only Full Text Full Text (PDF) Supporting Information Alert me when this article is cited Alert me if a correction is posted Citation Map Services Email this article to a colleague Similar articles in this journal Similar articles in ISI Web of Science Similar articles in PubMed Alert me to new issues of the journal Add to My File Cabinet Download to citation manager Request Copyright Permission Citing Articles Citing Articles via CrossRef Google Scholar Articles by Ye, J.-D. Articles by Piccirilli, J. A. PubMed PubMed Citation Articles by Ye, J.-D. Articles by Piccirilli, J. A. Pubmed/NCBI databases Compound via MeSH Substance via MeSH Hazardous Substances DB MAGNESIUM COMPOUNDS MAGNESIUM, ELEMENTAL Social Bookmarking                What's this?

 Previous Article  | Table of Contents |  Next Article 

BIOLOGICAL SCIENCES / BIOCHEMISTRY
Synthetic antibodies for specific recognition and crystallization of structured RNA

Jing-Dong Ye^*, Valentina Tereshko, John K. Frederiksen, Akiko Koide, Frederic A. Fellouse, Sachdev S. Sidhu, Shohei Koide^,, Anthony A. Kossiakoff^,, and Joseph A. Piccirilli^*,,

*Department of Chemistry, Howard Hughes Medical Institute, and Department of Biochemistry and Molecular Biology, University of Chicago, 929 East 57th Street, Chicago, IL 60637; and Department of Protein Engineering, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080

Edited by Alan M. Lambowitz, University of Texas, Austin, TX, and approved November 12, 2007 (received for review September 24, 2007)

Antibodies that bind protein antigens are indispensable in biochemical research and modern medicine. However, knowledge of RNA-binding antibodies and their application in the ever-growing RNA field is lacking. Here we have developed a robust approach using a synthetic phage-display library to select specific antigen-binding fragments (Fabs) targeting a large functional RNA. We have solved the crystal structure of the first Fab–RNA complex at 1.95 Å. Capability in phasing and crystal contact formation suggests that the Fab provides a potentially valuable crystal chaperone for RNA. The crystal structure reveals that the Fab achieves specific RNA binding on a shallow surface with complementarity-determining region (CDR) sequence diversity, length variability, and main-chain conformational plasticity. The Fab–RNA interface also differs significantly from Fab–protein interfaces in amino acid composition and light-chain participation. These findings yield valuable insights for engineering of Fabs as RNA-binding modules and facilitate further development of Fabs as possible therapeutic drugs and biochemical tools to explore RNA biology.

antigen-binding fragments | x-ray crystallography

The authors declare no conflict of interest.

This article is a PNAS Direct Submission.

Data deposition: The atomic coordinates and structure factors have been deposited in the Protein Data Bank, www.pdb.org (PDB ID code 2R8S).

This article contains supporting information online at www.pnas.org/cgi/content/full/0709082105/DC1.

To whom correspondence may be addressed. E-mail: jpicciri{at}uchicago.edu, koss{at}bsd.uchicago.edu, or skoide{at}uchicago.edu

© 2008 by The National Academy of Sciences of the USA

CiteULike    Complore    Connotea    Del.icio.us    Digg    What's this?

Current Issue | Archives | Online Submission | Info for Authors | Editorial Board | About Subscribe | Advertise | Contact | Site Map Copyright © 2008 by the National Academy of Sciences