| Abstract
| - Two-dimensional infrared spectroscopy was recently used to measure the vibrational couplings betweencarbonyl bonds located on DNA nucleobases (Krummel, A. T.; Mukherjee, P.; Zanni, M. T. J. Phys. Chem.B2003, 107, 9165 and Krummel, A. T.; Zanni, M. T. J. Phys. Chem. B2006, 110, 13991). Here, we extendthe coupling model derived from these 2D IR experiments to simulate the vibrational absorption and vibrationalcircular dichroism (VCD) spectra of three double-stranded DNA oligomers: poly(dG)−poly(dC), poly(dG−dC), and dGGCC. Using this model, we determine that the VCD spectrum of A-form poly(dG)−poly(dC) isdominated by interactions between stacked bases, whereas the coupling between base pairs and stacked basescarries equal importance in the VCD spectrum of B-form poly(dG−dC). We also simulate the absorption andVCD spectra of dGGCC, which is a combination of A- and B-form configurations. These simulations giveinsight into the structural interpretation of VCD and absorption spectroscopies that have long been used tomonitor DNA secondary structure and kinetics.
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