title: 2-Aminopurine fluorescence quenching and lifetimes: role of base stacking.
abstract: 2-Aminopurine (2AP) is a fluorescent analog of guanosine and adenosine and has been used to probe nucleic acid structure and dynamics. Its spectral features in nucleic acids have been interpreted phenomenologically, in the absence of a rigorous electronic description of the context-dependence of 2AP fluorescence. Now, by using time-dependent density functional theory, we describe the excited-state properties of 2AP in a B-form dinucleotide stacked with guanosine, adenosine, cytosine, or thymine. Calculations predict that 2AP fluorescence is quenched statically when stacked with purines, because of mixing of the molecular orbitals in the ground state. In contrast, quenching is predicted to be dynamic when 2AP is stacked with pyrimidines, because of formation of a low-lying dark excited state. The different quenching mechanisms will result in different experimentally measured fluorescence lifetimes and quantum yields.
authors: Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA.
authors: J M
authors: JM
authors: Jean
authors: K B
authors: KB
authors: Hall
mesh_terms: D015075:2-Aminopurine / Q000737:chemistry* / Q000378:metabolism; D000241:Adenosine / Q000031:analogs & derivatives; D000465:Algorithms; D020029:Base Pairing; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D005453:Fluorescence; D006151:Guanosine / Q000031:analogs & derivatives; D006860:Hydrogen Bonding; D007700:Kinetics; D008958:Models, Molecular; D011740:Pyrimidine Dimers / Q000737:chemistry* / Q000378:metabolism
chemical_list: D011740:Pyrimidine Dimers; D006151:Guanosine; D015075:2-Aminopurine; D004247:DNA; D000241:Adenosine