title: Conquering 2-aminopurine's deficiencies: highly emissive isomorphic guanosine surrogate faithfully monitors guanosine conformation and dynamics in DNA.
abstract: The archetypical fluorescent nucleoside analog, 2-aminopurine (2Ap), has been used in countless assays, though it suffers from very low quantum yield, especially when included in double strands, and from the fact that its residual emission frequently does not represent biologically relevant conformations. To conquer 2Ap's deficiencies, deoxythienoguanosine (d(th)G) was recently developed. Here, steady-state and time-resolved fluorescence spectroscopy was used to compare the ability of 2Ap and d(th)G, to substitute and provide relevant structural and dynamical information on a key G residue in the (-) DNA copy of the HIV-1 primer binding site, (-)PBS, both in its stem loop conformation and in the corresponding (-)/(+)PBS duplex. In contrast to 2Ap, this fluorescent nucleoside when included in (-)PBS or (-)/(+)PBS duplex fully preserves their stability and exhibits a respectable quantum yield and a simple fluorescence decay, with marginal amounts of dark species. In further contrast to 2Ap, the fluorescently detected d(th)G species reflect the predominantly populated G conformers, which allows exploring their relevant dynamics. Being able to perfectly substitute G residues, d(th)G will transform nucleic acid biophysics by allowing, for the first time, to selectively and faithfully monitor the conformations and dynamics of a given G residue in a DNA sequence.
authors.affiliation: Laboratoire de Biophotonique et Pharmacologie, Faculté de Pharmacie, UMR 7213 CNRS, Université de Strasbourg , 74 route du Rhin, 67401 Illkirch, France.
authors.forename: Marianna
authors.initials: M
authors.lastname: Sholokh
authors.forename: Rajhans
authors.initials: R
authors.lastname: Sharma
authors.forename: Dongwon
authors.initials: D
authors.lastname: Shin
authors.forename: Ranjan
authors.initials: R
authors.lastname: Das
authors.forename: Olga A
authors.initials: OA
authors.lastname: Zaporozhets
authors.forename: Yitzhak
authors.initials: Y
authors.lastname: Tor
authors.forename: Yves
authors.initials: Y
authors.lastname: Mély
mesh_terms: D015075:2-Aminopurine / Q000737:chemistry* / Q000378:metabolism; D001665:Binding Sites; D004279:DNA, Viral / Q000737:chemistry* / Q000378:metabolism; D005454:Fluorescence Polarization; D006151:Guanosine / Q000737:chemistry / Q000378:metabolism*; D015497:HIV-1 / Q000378:metabolism*; D009692:Nucleic Acid Heteroduplexes / Q000737:chemistry / Q000378:metabolism; D011744:Pyrimidinones / Q000737:chemistry* / Q000378:metabolism; D013050:Spectrometry, Fluorescence / Q000379:methods; D013876:Thiophenes / Q000737:chemistry* / Q000378:metabolism
chemical_list: D004279:DNA, Viral; D009692:Nucleic Acid Heteroduplexes; D011744:Pyrimidinones; D013876:Thiophenes; D006151:Guanosine; D015075:2-Aminopurine