title: Triphenylmethane dyes as fluorescent probes for G-quadruplex recognition.
abstract: Triphenylmethane (TPM) dyes normally render rather weak fluorescence due to easy vibrational deexcitation. However, when they stack onto the two external G-quartets of a G-quadruplex (especially intramolecular G-quadruplex), such vibrations will be restricted, resulting in greatly enhanced fluorescence intensities. Thus, TPM dyes may be developed as sensitive G-quadruplex fluorescent probes. Here, fluorescence spectra and energy transfer spectra of five TPM dyes in the presence of G-quadruplexes, single- or double-stranded DNAs were compared. The results show that the fluorescence spectra of four TPM dyes can be used to discriminate intramolecular G-quadruplexes from intermolecular G-quadruplexes, single- and double-stranded DNAs. The energy transfer fluorescence spectra and energy transfer fluorescence titration can be used to distinguish G-quadruplexes (including intramolecular and intermolecular G-quadruplexes) from single- and double-stranded DNAs. Positive charges and substituent size in TPM dyes may be two important factors in influencing the binding stability of the dyes and G-quadruplexes.
authors.affiliation: Research Centre for Analytical Sciences, Department of Chemistry, Nankai University, Tianjin, PR China.
authors.forename: Jun-Hong
authors.initials: JH
authors.lastname: Guo
authors.forename: Li-Na
authors.initials: LN
authors.lastname: Zhu
authors.forename: De-Ming
authors.initials: DM
authors.lastname: Kong
authors.forename: Han-Xi
authors.initials: HX
authors.lastname: Shen
mesh_terms: D004247:DNA / Q000737:chemistry; D004277:DNA, Single-Stranded / Q000737:chemistry; D004735:Energy Transfer; D005456:Fluorescent Dyes / Q000737:chemistry*; D054856:G-Quadruplexes; D007700:Kinetics; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry; D013050:Spectrometry, Fluorescence / Q000379:methods*; D014320:Triphenylmethyl Compounds / Q000737:chemistry*
chemical_list: D004277:DNA, Single-Stranded; D005456:Fluorescent Dyes; D009841:Oligonucleotides; D014320:Triphenylmethyl Compounds; C046945:triphenylmethane; D004247:DNA