Article

Fluorescence of Size-Expanded DNA Bases:  Reporting on DNA Sequence and Structure with an Unnatural Genetic Set

Department of Chemistry, Stanford University, Stanford, California 94305
J. Am. Chem. Soc., 2008, 130 (12), pp 3989–3999
DOI: 10.1021/ja0782347
Publication Date (Web): March 1, 2008
Copyright © 2008 American Chemical Society

Abstract

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We recently described the synthesis and helix assembly properties of expanded DNA (xDNA), which contains base pairs 2.4 Å larger than natural DNA pairs. This designed genetic set is under study with the goals of mimicking the functions of the natural DNA-based genetic system and of developing useful research tools. Here, we study the fluorescence properties of the four expanded bases of xDNA (xA, xC, xG, xT) and evaluate how their emission varies with changes in oligomer length, composition, and hybridization. Experiments were carried out with short oligomers of xDNA nucleosides conjugated to a DNA oligonucleotide, and we investigated the effects of hybridizing these fluorescent oligomers to short complementary DNAs with varied bases opposite the xDNA bases. As monomer nucleosides, the xDNA bases absorb light in two bands:  one at ∼260 nm (similar to DNA) and one at longer wavelength (∼330 nm). All are efficient violet-blue fluorophores with emission maxima at ∼380−410 nm and quantum yields (Φfl) of 0.30−0.52. Short homo-oligomers of the xDNA bases (length 1−4 monomers) showed moderate self-quenching except xC, which showed enhancement of Φfl with increasing length. Interestingly, multimers of xA emitted at longer wavelengths (520 nm) as an apparent excimer. Hybridization of an oligonucleotide to the DNA adjacent to the xDNA bases (with the xDNA portion overhanging) resulted in no change in fluorescence. However, addition of one, two, or more DNA bases in these duplexes opposite the xDNA portion resulted in a number of significant fluorescence responses, including wavelength shifts, enhancements, or quenching. The strongest responses were the enhancement of (xG)n emission by hybridization of one or more adenines opposite them, and the quenching of (xT)n and (xC)n emission by guanines opposite. The data suggest multiple ways in which the xDNA bases, both alone and in oligomers, may be useful as tools in biophysical analysis and biotechnological applications.

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Received 27 October 2007
Published online 1 March 2008
Published in print 1 March 2008
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