RNA plays a central role in many aspects of biochemistry. To carry out these cellular functions, it is critical that RNAs maintain their complex secondary, tertiary and quaternary structures. Furthermore, it is becoming evident that RNAs readily interconvert between two or more stable (or pseudo-stable) structures as part of their normal biological function. These rearrangements can be involved in control of ribozyme activity, as in the case of docking, or translational control of an mRNA through formation of alternative structures in the 5'- or 3'-UTRs. This project revolves around understanding the thermodynamic basis for the structural changes observed in certain RNAs. One type of structural change we focus on is the process of cold denaturation, where RNAs unfold at low temperature. Of particular importance to these processes, is the change in heat capacity (deltaC-p) upon folding, a property previously believed to be negligible, but now shown to be significant in certain cases. The cold denaturation of the hammerhead ribozyme is the best studied to date and the focus of the first specific aim. The thermodynamics to cold denaturation will then be compared to denaturation induced by high temperature and chaotropic agents. The generality of cold denaturation will be probed as part of specific aim 2, as well as the relationship between cold denaturation and riboregulation processes involved in the cold shock response. A small non-coding RNA from E. coil called DsrA is involved in regulating this process. We are probing the structural changes of this RNA and how these structural changes affect the complexes it makes with proteins (Hfq) and other RNAs. The 3rd major goal of this proposal is to look at the underlying nature of deltaH and deltaC-p in nucleic acid folding and understand the thermodynamic contribution of metal hydration/dehydration reactions on the overall energetics of tertiary structure formation of RNAs.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
Project #
Application #
Study Section
Molecular and Cellular Biophysics Study Section (BBCA)
Program Officer
Lewis, Catherine D
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Indiana University Bloomington
Schools of Arts and Sciences
United States
Zip Code
Salim, Nilshad; Lamichhane, Rajan; Zhao, Rui et al. (2012) Thermodynamic and kinetic analysis of an RNA kissing interaction and its resolution into an extended duplex. Biophys J 102:1097-107
Feig, Andrew L (2009) Studying RNA-RNA and RNA-protein interactions by isothermal titration calorimetry. Methods Enzymol 468:409-22
Salim, Nilshad N; Feig, Andrew L (2009) Isothermal titration calorimetry of RNA. Methods 47:198-205
Feig, Andrew L (2007) Applications of isothermal titration calorimetry in RNA biochemistry and biophysics. Biopolymers 87:293-301
Mikulecky, Peter J; Feig, Andrew L (2006) Heat capacity changes associated with DNA duplex formation: salt- and sequence-dependent effects. Biochemistry 45:604-16
Mikulecky, Peter J; Feig, Andrew L (2006) Heat capacity changes associated with nucleic acid folding. Biopolymers 82:38-58
Mikulecky, Peter J; Feig, Andrew L (2004) Heat capacity changes in RNA folding: application of perturbation theory to hammerhead ribozyme cold denaturation. Nucleic Acids Res 32:3967-76
Mikulecky, Peter J; Takach, Jennifer C; Feig, Andrew L (2004) Entropy-driven folding of an RNA helical junction: an isothermal titration calorimetric analysis of the hammerhead ribozyme. Biochemistry 43:5870-81
Mikulecky, Peter J; Kaw, Meenakshi K; Brescia, Cristin C et al. (2004) Escherichia coli Hfq has distinct interaction surfaces for DsrA, rpoS and poly(A) RNAs. Nat Struct Mol Biol 11:1206-14
Takach, Jennifer C; Mikulecky, Peter J; Feig, Andrew L (2004) Salt-dependent heat capacity changes for RNA duplex formation. J Am Chem Soc 126:6530-1

Showing the most recent 10 out of 12 publications