Investigating the Feasability of a Sum Frequency/Second Harmonic Generation Experiment to Examine the Behavior of RNA on Ice

RNA world hypothesis proposes that life began with RNA instead of DNA. However, RNA hydrolyzes faster than it can reproduce in room temperature water. It has been found that RNA will not hydrolyze in super cooled water; this has led to the new hypothesis that RNA began life on the surface of ice. Spartan, molecular modeling software, and Gromacs, molecular dynamic simulations, were used to investigate whether or not RNA on ice could be studied with Sum Frequency Generation or Second Harmonic Generation (SFG and SHG). Both are surface sensitive spectroscopic techniques that would help investigate the orientation of RNA on ice. Using Spartan it was discovered that SHG is not a viable method to study RNA unless we attach a chromophore to the RNA. It was found that SFG is a viable method and the amines on the top of the bases will be deuterated and tracked on a vibrational spectrum. Future work will be done simulating vibrational spectra using Gromacs, preparing a procedure for cryo-SFG, and studying the rate that deuterated amines will exchange with surrounding water