In contrast with the earliest models suggesting that it functioned only as messenger, RNA is now known to participate in a myriad of essential biological processes, ranging from gene expression through protein manufacturing. Short double-stranded RNAs participate in selective degradation of messenger RNA transcripts (RNA interference);folded RNAs can catalyze reactions, or switch genes on and off;in conjunction with numerous proteins, RNAs fold into large molecular machines, like the protein-manufacturing ribosome. Furthermore, because small RNAs can be designed to selectivity bind specific targets, these molecules have enormous potential as therapeutics. These widely varying roles are enabled by RNA's structural versatility. We propose to test new hypotheses about the roles of ions and RNA architecture in RNA self-assembly or folding. We will use time resolved small angle x-ray scattering to report the time-dependent formation of global structures, time-resolved hydroxyl radical footprinting to report the formation of individual contacts within the folding molecule, and time-resolved fluorescence methods to report specific intramolecular distances during folding. To enhance experimental studies, we propose to develop efficient atomically detailed simulations of the kinetics and thermodynamics of RNA folding. Initially, these coupled tools will be applied to further quantify the important role of ions in RNA folding. We will also study folding of different classes of RNA enzymes or ribozymes to explore the role of RNA architecture in folding. Our long term goal is to understand the factors involved in RNA folding. Such knowledge is essential for the efficient development and application of RNA-based therapeutics.

Public Health Relevance

RNA molecules can "fold" into biologically active structures that carry out a wide variety of functions. The numerous roles assumed by RNA highlight its usefulness and its great potential as a therapeutic molecule or a target for other therapeutics. These studies will enable us to better understand how RNA structures assemble, thus will teach us how to more efficiently design RNAs for application in medicine or biotechnology.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM085062-04
Application #
8324271
Study Section
Macromolecular Structure and Function B Study Section (MSFB)
Program Officer
Preusch, Peter C
Project Start
2009-09-01
Project End
2014-08-31
Budget Start
2012-09-01
Budget End
2014-08-31
Support Year
4
Fiscal Year
2012
Total Cost
$323,862
Indirect Cost
$92,840
Name
Cornell University
Department
Engineering (All Types)
Type
Schools of Engineering
DUNS #
872612445
City
Ithaca
State
NY
Country
United States
Zip Code
14850
Chen, Yujie; Tokuda, Joshua M; Topping, Traci et al. (2014) Revealing transient structures of nucleosomes as DNA unwinds. Nucleic Acids Res 42:8767-76
Meisburger, Steve P; Warkentin, Matthew; Chen, Huimin et al. (2013) Breaking the radiation damage limit with Cryo-SAXS. Biophys J 104:227-36
Meisburger, Steve P; Sutton, Julie L; Chen, Huimin et al. (2013) Polyelectrolyte properties of single stranded DNA measured using SAXS and single-molecule FRET: Beyond the wormlike chain model. Biopolymers 99:1032-45
Pabit, Suzette A; Sutton, Julie L; Chen, Huimin et al. (2013) Role of ion valence in the submillisecond collapse and folding of a small RNA domain. Biochemistry 52:1539-46
Chen, Huimin; Meisburger, Steve P; Pabit, Suzette A et al. (2012) Ionic strength-dependent persistence lengths of single-stranded RNA and DNA. Proc Natl Acad Sci U S A 109:799-804
Kirmizialtin, Serdal; Pabit, Suzette A; Meisburger, Steve P et al. (2012) RNA and its ionic cloud: solution scattering experiments and atomically detailed simulations. Biophys J 102:819-28
Kirmizialtin, Serdal; Silalahi, Alexander R J; Elber, Ron et al. (2012) The ionic atmosphere around A-RNA: Poisson-Boltzmann and molecular dynamics simulations. Biophys J 102:829-38
Li, Li; Pabit, Suzette A; Meisburger, Steve P et al. (2011) Double-stranded RNA resists condensation. Phys Rev Lett 106:108101
Blose, Joshua M; Pabit, Suzette A; Meisburger, Steve P et al. (2011) Effects of a protecting osmolyte on the ion atmosphere surrounding DNA duplexes. Biochemistry 50:8540-7
Pollack, Lois (2011) SAXS studies of ion-nucleic acid interactions. Annu Rev Biophys 40:225-42

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