title: Probe position dependence of DNA dynamics: comparison of the time-resolved Stokes shift of groove-bound to base-stacked probes.
abstract: Time-resolved fluorescence Stokes shift dynamics of a fluorescent probe, 4',6-diamidino-2-phenylindole (DAPI), inside the minor groove of the DNA is measured over five decades in time spans from 100 fs to 10 ns. Two different techniques, fluorescence up-conversion and time correlated single photon counting, are combined to obtain the time-resolved emission spectra of DAPI in DNA over the entire five decades in time. Having the dynamics of groove-bound DAPI in DNA measured over such a broad time window, we are able to convincingly compare our data to earlier time-resolved fluorescence results of a base-stacked probe that replaces a DNA base pair. Results show that the dynamics measured with either the groove-bound or the base-stacked probe are similar in the time span of 100 fs to approximately 100 ps but differ substantially from approximately 100 ps to 10 ns. Our present data also help to reconcile the previously reported molecular dynamics simulation results and provide important clues that the groove-bound water molecules inside DNA are mainly responsible for the slow dynamics seen in native DNA.
authors.affiliation: Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
authors.forename: Nibedita
authors.initials: N
authors.lastname: Pal
authors.forename: Sachin Dev
authors.initials: SD
authors.lastname: Verma
authors.forename: Sobhan
authors.initials: S
authors.lastname: Sen
mesh_terms: D020029:Base Pairing; D001665:Binding Sites; D004247:DNA / Q000378:metabolism*; D005456:Fluorescent Dyes; D007211:Indoles; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D015335:Molecular Probes; D013997:Time Factors
chemical_list: D005456:Fluorescent Dyes; D007211:Indoles; D015335:Molecular Probes; C007293:DAPI; D004247:DNA