From Solvation Dynamics in DNA to the IR Spectroscopy of Local Structure

<p>Biochemical reactions on DNA induce changes in the double helical structure. In this context, the dynamics of polar structural elements in the vicinity of the reaction centre are essential. However, these dynamics could previously not be measured on a molecular scale. Infrared-spectroscopy can monitor fluctuations of polar groups. Yet, the wave length of the electro-magnetic field is too long to differentiate between individual base pairs.</p>
<p>Alternatively, we incorporate a molecular probe into the DNA and use it as a local spectrometer in the course of our project. By applying ultra-fast excitation-pulses to the probe, a high dipole moment is induced (IR-light source). The relaxation in the vicinity instigates a red-shift of the fluorescence (detector).
Our previous work has demonstrated the principle: a suitable fluorophore was designed and incorporated into a DNA double strand.</p>
<p>In the course of this project, we intend to<br>
(1) compare the polar solvation dynamics in DNA of the probes Hydroxy-Nitro-fluoren, Coumarin 102 and 2-Aminopurine,<br>
(2) determine the NMR structure of the DNA double strands containing the three probes, and<br>
(3) conduct Molecular Dynamics simulations of the polar fluctuations and solvation.</p>
<p>Our aim is to extract the local IR-spectrum of the duplex-DNA out of the solvation dynamics and to explain this spectrum with the NMR-derived structures. Primarily, our purpose is to demonstrate the principle as such, not necessarily the biophysical application.</p>