title: Probe Position-Dependent Counterion Dynamics in DNA: Comparison of Time-Resolved Stokes Shift of Groove-Bound to Base-Stacked Probes in the Presence of Different Monovalent Counterions.
abstract: Time-resolved fluorescence Stokes shifts (TRFSS) of 4',6-diamidino-2-phenylindole (DAPI) inside the minor groove of DNA are measured in the presence of three different monovalent counterions: sodium (Na(+)), rubidium (Rb(+)), and tetrabutylammonium (TBA(+)). Fluorescence up-conversion and time-correlated single photon counting are combined to obtain the time-resolved emission spectra (TRES) of DAPI in DNA from 100 fs to 10 ns. Time-resolved Stokes shift data suggest that groove-bound DAPI can not sense the counterion dynamics because the ions are displaced by DAPI far from the probe-site. However, when these results are compared to the earlier base-stacked coumarin data, the same ions are found to affect the nanosecond dynamics significantly. This suggests that the ions come close to the probe-site, such that they can affect the dynamics when measured by base-stacked coumarin. These results support previous molecular dynamics (MD) simulation data of groove-bound and base-stacked probes inside DNA.
authors: Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
authors: Sachin Dev
authors: SD
authors: Verma
authors: Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
authors: Nibedita
authors: N
authors: Pal
authors: Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
authors: Moirangthem Kiran
authors: MK
authors: Singh
authors: Spectroscopy Laboratory, School of Physical Sciences, Jawaharlal Nehru University, New Delhi 110067, India.
authors: Sobhan
authors: S
authors: Sen
keywords: DNA probes; TCSPC; fluorescence; solvation dynamics; time-resolved emission spectra; up-conversion