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The structure of cyanine 5 terminally attached to double-stranded DNA: implications for FRET studies

Iqbal, A. and Wang, L. and Thompson, Katherine C. and Lilley, D.M.J. and Norman, D.G. (2008) The structure of cyanine 5 terminally attached to double-stranded DNA: implications for FRET studies. Biochemistry 40 (30), pp. 7857-7862. ISSN 0006-2960.

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Official URL: http://dx.doi.org/10.1021/bi800773f

Abstract

Fluorescence resonance energy transfer, FRET, can be used to obtain long-range distance information for macromolecules and is particularly powerful when used in single-molecule studies. The determination of accurate distances requires knowledge of the fluorophore position with respect to the macromolecule. In this study we have used NMR to determine the structure of the commonly used fluorophore indocarbocyanine-5 (Cy5) covalently attached to the 5′-terminus of double-helical DNA. We find that Cy5 is predominantly stacked onto the end of the duplex, in a manner similar to an additional base pair. This is very similar to the behavior of Cy3 terminally attached to DNA and suggests that the efficiency of energy transfer between Cy3 and Cy5, that are attached to nucleic acids in this way, will exhibit significant dependence on fluorophore orientation.

Item Type: Article
School or Research Centre: Birkbeck Schools and Research Centres > School of Science > Biological Sciences
Depositing User: Administrator
Date Deposited: 04 Aug 2010 14:09
Last Modified: 17 Apr 2013 12:17
URI: http://eprints.bbk.ac.uk/id/eprint/1099

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