Fluorescence of Unmodified Oligonucleotides: A Tool to Probe G-Quadruplex DNA Structure

Fluorescence of unmodified oligonucleotides has not been exploited for guanine-quadruplex (G-quadruplex) characterization. We observe that G-rich sequences fluoresce more strongly than duplex or single-stranded DNA but much more weakly than fluorophores like fluorescein. This increase in the intrinsic fluorescence is not due to an increase in absorption at the excitation wavelength but rather to a change in the quantum yield. We show that unlabeled oligonucleotides that form G-quadruplexes can be differentiated on the basis of their emission spectra from similar sequences that do not contain consecutive guanines. Intermolecular quadruplexes formed by the oligonucleotides 5'-T(4)G(n)T(4)-3' (n = 4-10) display a nonlinear, but continuous, increase in emission intensity as the G content increases. The sequence 5'-GGGT-3', which has been proposed to form a monomeric quadruplex and an interlocked quadruplex (Krishnan-Ghosh et al. J Am Chem Soc 2004, 126, 11009), was compared with the similar sequence 5'-TGGG-3', the structure of which has not been characterized. Both the maximum emission intensity and the spectral shape differ for these oligonucleotides as a function of sample preparation, indicating that different types of quadruplexes form for both sequences. Our work is the first to demonstrate that the suprastructure of G-rich sequences can be probed using fluorescence signatures of unmodified oligonucleotidcs. (C) 2009 Wiley Periodicals, Inc. Biopolyiners 91: 841-850, 2009.