FREE ENERGY PROFILES OF SINGLE STRANDED DNA

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This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Recent single molecule experiments on single stranded DNA have shown that the form the DNA takes is dependent on its method of formation. Our collaborator Mara Prentiss has shown that slow thermal melting creates ?short? single strands that have a base separation of 0.54 nm while unzipping creates a ?long? form with base separation of 0.7-0.8 nm. We propose to study these experiments by using molecular dynamics to calculate free energy profiles of single stranded DNA as a function of base pair separation. This may require multiple free energy profiles as we study the effects of temperature and initial conditions on the extension. In addition we would like to take this opportunity to explore the Teragrid resources for future requests for allocations.