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

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.