title: Fluorescence quenching over short range in a donor-DNA-acceptor system.
abstract: A new donor-DNA-acceptor system has been synthesized containing Nile red-modified 2'-deoxyuridine as charge donor and 6-N,N-dimethylaminopyrene-modified 2'-deoxyuridine as acceptor to investigate the charge transfer in DNA duplexes using fluorescence spectroscopy and time-resolved femtosecond pump-probe techniques. Fluorescence quenching experiments revealed that the quenching efficiency of Nile red depends on two components: 1) the presence of a charge acceptor and 2) the number of intervening CG and AT base pairs between donor and acceptor. Surprisingly, the quenching efficiency of two base pairs (73% for CG and the same for AT) is higher than that for one base pair (68% for CG and 37% for AT), while at a separation of three base pairs less than 10% quenching is observed. A comparison with the results of time-resolved measurements revealed a correlation between quenching efficiency and the first ultrafast time constant suggesting that quenching proceeds via a charge transfer from the donor to the acceptor. All transients are satisfactorily described with two decays: a rapid charge transfer with 600 fs (∼10(12) s(-1)) that depends strongly and in a non-linear fashion on the distance between donor and acceptor, and a slower time constant of a few picoseconds (∼10(11) s(-1)) with weak distance dependence. A third time constant on a nanosecond time scale represents the fluorescence lifetime of the donor molecule. According to these results and time-dependent density functional theory (TDDFT) calculations a combination of single-step superexchange and multistep hopping mechanisms can be proposed for this short-range charge transfer. Furthermore, significantly less quenching efficiency and slower charge transfer rates at very short distances indicate that the direct interaction between donor and acceptor leads to a local structural distortion of DNA duplexes which may provide some uncertainty in identifying the charge transfer rates in short-range systems.
authors.affiliation: Institute for Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Ehrenschwender
authors.forename: Yu
authors.initials: Y
authors.lastname: Liang
authors.forename: Andreas-Neil
authors.initials: AN
authors.lastname: Unterreiner
authors.forename: Hans-Achim
authors.initials: HA
authors.lastname: Wagenknecht
authors.forename: Thomas J A
authors.initials: TJ
authors.lastname: Wolf
mesh_terms: D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D004579:Electron Transport; D005456:Fluorescent Dyes / Q000737:chemistry*; D010078:Oxazines / Q000737:chemistry; D011789:Quantum Theory; D013050:Spectrometry, Fluorescence; D013696:Temperature; D014529:Uridine / Q000737:chemistry
chemical_list: D005456:Fluorescent Dyes; D010078:Oxazines; D004247:DNA; C044808:nile red; D014529:Uridine