Interpreting DNA vibrational circular dichroism spectra using a coupling model from two-dimensional infrared spectroscopy.

Amber T Krummel; Martin T Zanni

doi:10.1021/jp063227a

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Interpreting DNA vibrational circular dichroism spectra using a coupling model from two-dimensional infrared spectroscopy.

Amber T Krummel·Martin T Zanni

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Abstract

Two-dimensional infrared spectroscopy was recently used to measure the vibrational couplings between carbonyl bonds located on DNA nucleobases (Krummel, A. T.; Mukherjee, P.; Zanni, M. T. J. Phys. Chem. B 2003, 107, 9165 and Krummel, A. T.; Zanni, M. T. J. Phys. Chem. B 2006, 110, 13991). Here, we extend the coupling model derived from these 2D IR experiments to simulate the vibrational absorption and vibrational circular 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) is dominated by interactions between stacked bases, whereas the coupling between base pairs and stacked bases carries equal importance in the VCD spectrum of B-form poly(dG-dC). We also simulate the absorption and VCD spectra of dGGCC, which is a combination of A- and B-form configurations. These simulations give insight into the structural interpretation of VCD and absorption spectroscopies that have long been used to monitor DNA secondary structure and kinetics.

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Circular Dichroism Computer Simulation DNA Hydrogen Bonding Models, Molecular Nucleic Acid Conformation Spectrophotometry, Infrared Vibration Journal Article Research Support, U.S. Gov't, Non-P.H.S.

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Amber T Krummel, Martin T Zanni. 2006-12-07. Interpreting DNA vibrational circular dichroism spectra using a coupling model from two-dimensional infrared spectroscopy.. https://doi.org/10.1021/jp063227a

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