title: Ultrafast site-specific fluorescence quenching of 2-aminopurine in a DNA hairpin studied by femtosecond down-conversion.
abstract: The ΔP(-)PBS analog of the DNA primary binding sequence (PBS) of the HIV-1 genome labeled at different positions by 2-aminopurine (2-AP) is investigated by a novel femtosecond fluorescence down-conversion experiment with 0.3-ps time resolution. The high signal-to-noise ratio of the fluorescence kinetics makes it possible to reveal four distinct decay times ranging from 0.8 ps to 2-3 ns for all the three labeling positions. This suggests the existence of at least four different quenching conformations of 2-AP with its nearest neighbors, and underscores the structural heterogeneity of the loop region of ΔP(-)PBS. Sub-5-ps components are found and attributed to stacking interactions of 2-AP with the flanking guanine (G) side chains, consistent with the NMR structure of ΔP(-)PBS. The observation of a significant increase of their total amplitude when 2-AP is positioned close to the rigid 3'-half of the G-rich stem gives further support to this assignment. Only a minor portion of conformations involves slow nanosecond collisional quenching.
authors.affiliation: Institut de Physique et Chimie des Matériaux de Strasbourg, Université de Strasbourg- CNRS, 67034 Strasbourg, France.
authors.forename: Thomas
authors.initials: T
authors.lastname: Gelot
authors.forename: Patricia
authors.initials: P
authors.lastname: Tourón-Touceda
authors.forename: Olivier
authors.initials: O
authors.lastname: Crégut
authors.forename: Jérémie
authors.initials: J
authors.lastname: Léonard
authors.forename: Stefan
authors.initials: S
authors.lastname: Haacke
mesh_terms: D015075:2-Aminopurine / Q000737:chemistry*; D004279:DNA, Viral / Q000737:chemistry*; D005453:Fluorescence; D006147:Guanine / Q000737:chemistry*; D015497:HIV-1 / Q000737:chemistry*; D006801:Humans; D055029:Inverted Repeat Sequences; D007700:Kinetics; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry; D059629:Signal-To-Noise Ratio; D012996:Solutions; D013050:Spectrometry, Fluorescence; D013816:Thermodynamics; D013997:Time Factors
chemical_list: D004279:DNA, Viral; D009841:Oligonucleotides; D012996:Solutions; D015075:2-Aminopurine; D006147:Guanine