With the support of a CAREER award from the Chemistry of Life Processes at the National Science Foundation, Professor Maumita Mandal of Carnegie Mellon University will lead a research program that will focus on understanding the dynamics of structural rearrangements in riboswitches and other regulatory RNAs in single-molecules by combining the fluorescence and force spectroscopy using high resolution optical tweezers. This advanced technique opens new opportunities to visually monitor pathways of allosteric switching in RNA molecules in real time that are key to the regulatory activities. Riboswitches exhibit a myriad of secondary and tertiary structures and the ligands they bind to regulate gene expression. These allosteric rearrangements are central to perform the required biological functions in these structures as in riboswitches; a mechanism that may be far more widespread in other RNA-based systems too. Although the structure of ligand binding and mechanism of riboswitch action is fairly comprehensible, it is the allosteric modulation between distant domains that is yet to be understood mainly because the RNA secondary structures are less well defined under low ionic conditions which make them difficult to study by biochemical means. While theoretical descriptions of this behavior abound, experimental approaches to test the theories are challenging using biochemical toolkit alone, and different approaches often lead to complicated interpretations of the molecular events. The results of this research will be important in unraveling how RNA structural domains play a regulatory role in bringing components together both spatially and temporally to form a functional complex in the presence of small molecules. Additionally, the role of molecular motors such as RNA polymerases that utilize this information during transcription will be also investigated.
The research proposed here by Professor Mandal is highly interdisciplinary that incorporates elements of physics, biophysics, chemistry and biomedical engineering with a goal of addressing the fundamental gene regulatory problem in biology. An important objective of the proposed activity is to create a two semester curriculum in physical chemistry directed towards biology, chemistry, physics and engineering students, wherein the students are exposed to the emerging areas of single-molecule research in upper division undergraduate courses, while focusing on the meaningful conceptual learning in the classroom settings. The curriculum developed by the investigator at Carnegie Mellon University is in its first year that brings together undergraduates from different disciplines with an aim to create an excitement and generating an understanding of the physical chemistry and its usefulness and applicability of the material in interdisciplinary research.