New spectroscopic tools are being developed exploiting ultrafast transient absorption that report on energy delocalization between the bases of duplex DNA.  While there is keen recent interest in exploring femtosecond phenomena associated with DNA,^1-3 optical signatures for how energy flows have not been reported in native DNA and this is expected to be sensitive to the pair-wise electronic couplings between bases.  As such, DNA oligomer systems serve as structurally defined architectures of chromophores where electronic couplings can be systematically probed. 

A 30 fs linearly-polarized UV pulse excites a random base on a strand of DNA.  Information on the excited state evolution of the oligomer is tracked in two ways.  In the first experiment, the dispersed polarized transient absorption from 300 – 700 nm is recorded.  At times <100fs a stimulated emission signal is observed that is characteristic of single base emission.  At later times, a time-evolving excited state absorption spectrum is observed that probes how the electronic excitation evolves and is trapped prior to deactivation.  We have recorded data on (dA)₂₀,(dT)₂₀ and double-stranded (dA)_20•(dT)₂₀.  Extensive accompanying work on electronic relaxation in isolated DNA bases in solution has also been carried out.  The second experiment instead captures the dynamic bleach depolarization using a second polarized probe pulse of the same wavelength as the initial excitation. If there is migration of the excited state to other bases on the helix, depolarization below an anisotropy value of 0.4 should be observed due to a rotation of the transition dipole direction (Given the 10^-13 s depolarization timescale, this is not motion of the bases or the DNA chain). Representative depolarization signals are shown in the Figure. Isolated nucleotides and single-stranded poly(A) show no depolarization, whereas signals from two duplexes are different in two respects: (i) they both reach a lower terminal anisotropy (~0.2) and (ii) the decay rate is sensitive to sequence.  Careful characterization is performed of the DNA oligomers before and after exposure to verify the rate of permanent photodamage and the monodispersity of the oligomer chain lengths. 

The observation of evolution of localization in the excited system is also highly relevant to mechanisms of photodamage in natural DNA.  However, it is not clear whether the different depolarization rates for example are due to structural differences or the different GC/AT compositions, or a more complex combination of the two.  We are currently testing this characteristic by comparing DNAs with the same GC/AT composition, and same order of bases, but with different polarity sequences that are believed to have markedly different conformations.

The experimental work on this project has included the participation of a SUMR undergraduate scholar from Virginia State University.  A collaboration with Eric Bittner (U. Houston) has been initiated to provide a theoretical construct for understanding the competing energy and charge transfer dynamics in excited oligonucleotides.

References:

1.  D. Markovitsi, A. Sharonov, D. Onidas, and T. Gustavsson, ChemPhysChem 4, 303-07 (2003).

2.  C. E. Crespo-Hernandez, B. Cohen, and B. Kohler, Nature 436, 1141-44 (2005).

3.  B. Bouvier, T. Gustavsson, D. Markovitsi, and P. Millie, Chem. Phys. 275, 75-92 (2002).