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Nucleic Acids Research Advance Access originally published online on November 14, 2007
Nucleic Acids Research 2008 36(1):157-167; doi:10.1093/nar/gkm1006
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Nucleic Acids Research, 2008, Vol. 36, No. 1 157-167
© 2007 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.

Chemistry

Characterization and use of an unprecedentedly bright and structurally non-perturbing fluorescent DNA base analogue

Peter Sandin1, Karl Börjesson1, Hong Li2, Jerker Mårtensson1, Tom Brown2, L. Marcus Wilhelmsson1,* and Bo Albinsson1

1Department of Chemical and Biological Engineering/Physical Chemistry, Chalmers University of Technology, SE-41296 Gothenburg, Sweden and 2School of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, UK

*To whom correspondence should be addressed. Tel: +46 (0) 31 7723051; Fax: +46 (0) 31 7723858; Email: mawi{at}chembio.chalmers.se

Received September 21, 2007. Revised October 23, 2007. Accepted October 23, 2007.

This article presents the first evidence that the DNA base analogue 1,3-diaza-2-oxophenoxazine, tCO, is highly fluorescent, both as free nucleoside and incorporated in an arbitrary DNA structure. tCO is thoroughly characterized with respect to its photophysical properties and structural performance in single- and double-stranded oligonucleotides. The lowest energy absorption band at 360 nm ({varepsilon} = 9000 M–1 cm–1) is dominated by a single in-plane polarized electronic transition and the fluorescence, centred at 465 nm, has a quantum yield of 0.3. When incorporated into double-stranded DNA, tCO shows only minor variations in fluorescence intensity and lifetime with neighbouring bases, and the average quantum yield is 0.22. These features make tCO, on average, the brightest DNA-incorporated base analogue so far reported. Furthermore, it base pairs exclusively with guanine and causes minimal perturbations to the native structure of DNA. These properties make tCO a promising base analogue that is perfectly suited for e.g. photophysical studies of DNA interacting with macromolecules (proteins) or for determining size and shape of DNA tertiary structures using techniques such as fluorescence anisotropy and fluorescence resonance energy transfer (FRET).


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