The biological functions of many RNAs depend on compact tertiary structures with irregular backbone conformations and close juxtapositions of phosphates. The resulting unfavorable electrostatic free energy is a major barrier to folding, and causes RNA tertiary structure to be much more sensitive to the ion and solvent environment than is secondary structure. The long term goal of these studies is to provide a systematic and quantitative picture of ion and solvent interactions stabilizing RNA tertiary structures, and relate the picture to the underlying electrostatic properties of RNA. A major aim of the proposed studies is to obtain accurate Mg 2+ - RNA binding isotherms for a set of RNA structures that illustrate the full range of potential Mg 2+ binding environments, including RNAs stabilized entirely by fully hydrated Mg 2+, RNAs in which Mg(H20)6[2]+ may be hydrogen bonded to pockets or channels in the RNA structure, RNAs with highly dehydrated ions bound atspecific sites, and RNAs that mimic the close packing of helices in large RNAs such as the ribosome. Mg 2+ binding to RNAs trapped in partially folded states (secondary structure only) will also be studied, to provide a picture of the net change in Mg 2+ binding during the folding reaction. Newly developed fluorescence-based methods for directly measuring free and RNA-bound Mg 2+ will be used in these studies. Other studies will look at the proposed phenomenon of """"""""electrostatic collapse"""""""" as a separate, Mg 2+- dependent transition in folding of large RNAs, at the selectivity of RNAs for monovatent ions, which may be a widespread feature of compact RNAs and reflect partial dehydration of monovalent ions bound close to the RNA surface, and at binding of small peptides or proteins that may serve as probes of ions and hydrating water stabilizing an RNA structure. Lastly, these results will be used as benchmarks for comparison with theoretical predictions of ion - RNA interactions, particularly a recently developed framework that uses the non-linear Poisson-Boltzmann equation to describe hydrated RNA-bound Mg 2+ and a Born model to compute the energetics of partially dehydrated ions at specific locations in the RNA. The ability to predict the Mg2+-dependent folding free energies of RNA tertiary conformations would be useful in a number of contexts.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM058545-08
Application #
7104406
Study Section
Molecular and Cellular Biophysics Study Section (BBCA)
Program Officer
Lewis, Catherine D
Project Start
1999-02-01
Project End
2007-07-31
Budget Start
2006-08-01
Budget End
2007-07-31
Support Year
8
Fiscal Year
2006
Total Cost
$230,175
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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