Folding of RNA molecules into specific tertiary structures is important for a large number of cellular processes relating to gene expression. For instance, protein synthesis requires transfer RNA and ribosomal RNAs to adopt functional structures, and processing of transfer and messenger RNAs depend on ribozymes or RNA-protein complexes which must also fold properly. The very high negative charge carried by RNA molecules limits their folding possibilities and causes the stabilities of folded RNAs to be very sensitive to the concentrations of Mg2+ and other ions present in solution. The long term goal of these studies is to provide a systematic and quantitative picture of ion and solvent interactions that stabilize RNA tertiary structures, and to relate the picture to the underlying electrostatic properties of RNA. A quantitative description of Mg2+ - RNA interactions that considers diffuse (hydrated) and chelated ions has been successful in accounting for the stabilities of some RNAs. To explore the limitations of this model, in future work close attention will be paid to RNAs with Mg2+ or monovalent ions in unusual environments, and the characteristics of the partially structured RNAs from which native structures fold will be studied. Other work will examine the effects of osmolytes, naturally occurring compounds accumulated by cells to high concentrations to maintain osmolarity, on RNA stability. Besides their relevance to the folding of RNAs in vivo, osmolytes may also be useful tools for characterizing the kinds of structures present in a RNA. Lastly, unusual effects of ions on the heat capacity of folded RNAs will be explored because of the potential implications for RNA hydration. Health relevance of the proposed work: Many cellular RNAs are directly involved in the synthesis of proteins, and other RNA structures regulate the levels of proteins in cells. Some of these RNAs are targets for natural antibiotics. Drugs which stabilize or alter specific critical RNA structures could have wide therapeutical applications. An understanding of the forces that stabilize RNA structures could aid in selection of drug targets and the design of new drugs. ? ? ?

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM058545-10
Application #
7478026
Study Section
Macromolecular Structure and Function B Study Section (MSFB)
Program Officer
Preusch, Peter C
Project Start
1999-02-01
Project End
2011-07-31
Budget Start
2008-08-01
Budget End
2009-07-31
Support Year
10
Fiscal Year
2008
Total Cost
$256,741
Indirect Cost
Name
Johns Hopkins University
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
001910777
City
Baltimore
State
MD
Country
United States
Zip Code
21218
Draper, David E (2013) Folding of RNA tertiary structure: Linkages between backbone phosphates, ions, and water. Biopolymers 99:1105-13
Li, Biao; Kimmel, Marek (2013) Factors influencing ascertainment bias of microsatellite allele sizes: impact on estimates of mutation rates. Genetics 195:563-72
Trachman 3rd, Robert J; Draper, David E (2013) Comparison of interactions of diamine and Mg²? with RNA tertiary structures: similar versus differential effects on the stabilities of diverse RNA folds. Biochemistry 52:5911-9
Lambert, Dominic; Draper, David E (2012) Denaturation of RNA secondary and tertiary structure by urea: simple unfolded state models and free energy parameters account for measured m-values. Biochemistry 51:9014-26
Leipply, Desirae; Draper, David E (2011) Evidence for a thermodynamically distinct Mg2+ ion associated with formation of an RNA tertiary structure. J Am Chem Soc 133:13397-405
Leipply, Desirae; Draper, David E (2011) Effects of Mg2+ on the free energy landscape for folding a purine riboswitch RNA. Biochemistry 50:2790-9
Lambert, Dominic; Leipply, Desirae; Draper, David E (2010) The osmolyte TMAO stabilizes native RNA tertiary structures in the absence of Mg2+: evidence for a large barrier to folding from phosphate dehydration. J Mol Biol 404:138-57
Leipply, Desirae; Draper, David E (2010) Dependence of RNA tertiary structural stability on Mg2+ concentration: interpretation of the Hill equation and coefficient. Biochemistry 49:1843-53
Chen, Alan A; Draper, David E; Pappu, Rohit V (2009) Molecular simulation studies of monovalent counterion-mediated interactions in a model RNA kissing loop. J Mol Biol 390:805-19
Lambert, Dominic; Leipply, Desirae; Shiman, Ross et al. (2009) The influence of monovalent cation size on the stability of RNA tertiary structures. J Mol Biol 390:791-804

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