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Nucleic Acids Research 2005 33(4):e37; doi:10.1093/nar/gni036
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Published online 24 February 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

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Novel cyanine-AMP conjugates for efficient 5' RNA fluorescent labeling by one-step transcription and replacement of [{gamma}-32P]ATP in RNA structural investigation

Na Li, Changjun Yu1 and Faqing Huang*

Department of Chemistry and Biochemistry, University of Southern Mississippi Hattiesburg MS 39406-5043, USA 1 AdeGenix, Inc. 870 S. Myrtle Avenue, Monrovia, CA 91016, USA

*To whom correspondence should be addressed. Tel: +1 601 266 4371; Fax: +1 601 266 6075; Email: faqing.h.huang{at}usm.edu

Received November 23, 2004. Revised February 4, 2005. Accepted February 4, 2005.

Two novel fluorescent cyanine-AMP conjugates, F550/570 and F650/670, have been synthesized to serve as transcription initiators under the T7 {varphi}2.5 promoter. Efficient fluorophore labeling of 5' RNA is achieved in a single transcription step by including F550/570 and F650/670 in the transcription solution. The current work makes fluorescently labeled RNA readily available for broad applications in biochemistry, molecular biology, structural biology and biomedicine. In particular, site-specifically fluorophore-labeled large RNAs prepared by the current method may be used to investigate RNA structure, folding and mechanism by various fluorescence techniques. In addition, F550/570 and F650/670 may replace [{gamma}-32P]ATP to prepare 5' labeled RNA for RNA structural and functional investigation, thereby eliminating the need for the unstable and radio-hazardous [{gamma}-32P]ATP.


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