This award supports the research effort of Professor Andrei Tokmakoff aimed at developing the experimental method of two-dimensional infrared spectroscopy (2D IR) for the purposes of visualizing how DNA and proteins change their structure in real time. As important as these processes are in materials chemistry, biomedical research, and nanotechnology, few experiments are currently capable of studying how macromolecules change their structure during the course of chemical reactions and physical processes, since they occur on nanosecond to microsecond time-scales in solution. This work supports two graduate students as they learn about solution-phase chemical dynamics, macromolecular structure, and protein and DNA conformational changes. Additionally, this grant plays a role in supporting two continually expanding online textbooks, "Time-Dependent Quantum Mechanics and Spectroscopy" and "Concepts in Biophysical Chemistry".
The specific scientific objective of this grant is to continue the ongoing development of transient 2D IR spectroscopy. The current method uses a temperature-jump (T-jump) to initiate conformational changes of proteins and DNA, and tracks the resulting changes in molecular structure with 2D IR. First, T-jump transient 2D IR experiments are used to study the conformational dynamics of DNA oligonucleotides, including hybridization, bubbling, fraying, and base flipping. Second, as a complementary approach to T-jumps, nanosecond transient pH-jump methods based on photoacids are developed for transient 2D IR studies of protonation-triggered protein conformational changes. Finally, the research group is continuing their ongoing development of 2D IR to study conformational changes to membrane proteins and lipid bilayers.
