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Local Dynamics
in DNA by Ultrafast Stokes-Shift Spectroscopy
Brauns, Eric1,
Madaras, Mihaela2, Coleman, Robert2,
Murphy, Catherine1 and Berg, Mark1
University of South Carolina, Columbia, South Carolina1
Ohio State University, Columbus, Ohio2
Abstract-
Any chemical process occurring in DNA is affected by how rapidly the
local environment reorganizes to accommodate the changing structure.
The local motions of bases, sugars, phosphates, etc. may affect processes
as diverse as electron transport and protein recognition of damaged
sequences. We have developed a method to measure these dynamics that
is analogous to solvation studies in simple liquids. A novel fluorescent
probe of the DNA interior has been developed for this technique. A coumarin-102
group is attached to a riboside and replaces a base pair in a synthetic
oligonucleotide. A dynamic Stokes shift of the fluorescence spectrum
is caused by local reorganization of the DNA near the probe and is measured
over the 25 ps - 50 ns time range. Dynamics are observed that are much
slower than either water dynamics or vibrational motion of the DNA.
Rather than having a single time constant, the DNA dynamics are spread
over a range of at least 4 orders-of-magnitude. The resulting decay
curves have an unusual logarithmic time dependence. These results suggest
that the relaxation of DNA is highly cooperative. Analysis suggests
that a still unresolved relaxation exists in the 100 fs - 25 ps time
range.
Keywords: DNA,
ultrafast, Stokes-shift, fluorescence
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