Condensed phase vibrational dynamics study using femtosecond stimulated Raman and two-dimensional infrared spectroscopy.

 One of the most important photoactivated processes that directly affects human health is the absorption of UV light by the nucleic acids in DNA. Experimental studies of the molecular level photophysics and photochemistry of DNA have predominantly used electronic absorption and fluorescence. These experiments have established the ultrafast time-scale of excited state relaxation in the nucleic acid bases and several oligomers, but lack structural specificity. In the last decade, it has become possible to follow structural dynamics in photochemical reactions in greater detail by combining transient electronic absorption with ultrafast vibrational techniques, such as femtosecond stimulated Raman spectroscopy (FSRS) or femtosecond infrared absorption. Time-resolved Femtosecond Stimulated Raman Spectra of DNA nucleotide monomer, Guanosine-5’-monophosphate, during its relaxation from the electronic excited state will be presented in the first part of the talk.  The collection of the spectra was made possible by several technical advances in our lab: the development of a seeded stimulated Raman shifter to generate picosecond pulses at 343 nm, and the incorporation of a scanning multichannel detection methodology to eliminate detector fixed-pattern noise. 

2D-IR experiments, in combination with MD simulations, revealed the molecular level dynamics of the HIV-1 drug rilpivirine bound to clinically relevant mutations of the reverse transcriptase (HIV-1 RT), the details of which will be presented in the second part of the talk. HIV-1 RT is a DNA polymerase enzyme that enables the conversion of a single-stranded RNA into a double-stranded DNA in a process that is essential for viral replication. Rilpivirine is a conformationally flexible non-nucleoside reverse transcriptase inhibitor (NNRTI) designed to bind the wild type as well as the clinically relevant mutations of the HIV-1 RT. The inherent nitrile (-C≡N) vibrational modes of the inhibitor serve as excellent, narrow-band vibrational probes of biomolecular structure and dynamics due to their sensitivity to polarity, hydrogen bonding and the electric fields exerted by the protein environments. The results in summary indicated the presence of a dry environment for one of the nitriles and previously unnoticed accessibility of water molecules for the second nitrile in the ‘hydrophobic’ binding pocket of the reverse transcriptase.