DichroCalc: DNA Dichroism Calculations

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In 1953, Crick and Watson deciphered the structure of DNA from the X-ray data of Franklin, Gosling and Wilkins, thereby laying the foundation of modern day molecular biology and molecular medicine. It is almost impossible to overstate the impact - scientific, medical and economic - that understanding the structure of DNA has had in the 20th and 21st centuries. In this proposal, we seek to provide a computational tool for relating the structure of DNA in SOLUTION to biophysical experiments that measure the interaction of DNA with polarized light. Such experiments can complement other approaches, using NMR or infrared spectroscopy. Probing the conformation of DNA as its binds other molecules provides valuable information on its interactions with other molecules and could be the first step in understanding a huge range of processes at the heart of molecular biology. Despite the clear importance of a fully quantitative theory relating structure to optical spectroscopy, such a theory has yet to be realized. Expertise developed at Nottingham over the past decade makes us almost uniquely well-placed to advance the theory necessary to calculate the optical spectroscopy of DNA accurately. This will involve quantum chemical calculations on Nottingham's 12-teraflop high performance computer (HPC). In addition, our web-server, DichroCalc, is the only one world-wide, where scientists can upload biological macromolecular structures and get back a calculated circular dichroism spectrum. Thus, we will be able to disseminate the results of research quite readily and make them accessible to the scientific research community in an-easy-to-use fashion.