This Program Project Grant brings together seven principal investigators committed to understanding the principles by which RNA molecules fold into their biologically active structures. The proposal comprises four Projects and a Resource Core, all bound together by a central hypothesis: RNA folding can be understood and eventually predicted from a reductionist perspective. RNA looked like a simple messenger in the early days of structural and molecular biology. The last two decades have demonstrated diverse biological, chemical, and physical roles of RNA, and yet our mechanistic understanding remains limited. Deep investigation of the physical behavior of RNA will enable a full description of gene expression and its control. In particular, a predictive and quantitative understanding will catalyz rational RNA engineering at the molecular and systems biology levels and ultimately facilitate rational therapeutic interventions that target or involve RNA. Our component projects build from simple to complex. Project 1 studies the ion atmosphere that surrounds simple helices and uses an integrated experimental-computational feedback loop to develop an understanding of electrostatics, the largest and most general force influencing the behavior and interactions of RNA. Project 2 focuses on helix-junction-helix motifs, the building blocks of RNA tertiary structure. We will develop and apply novel experimental and analytical approaches to fully describe the conformational ensemble for these elements. Project 3 determines the conformational ensembles of RNAs in their unfolded, folded, and intermediate states and defines the energetics of the transitions between these states. We will compare the behaviors of P4-P6 RNA and RNA/protein complexes to the behavior predicted from the properties of their elements, as delineated from Project 2. We thereby directly test the hypothesis that the energetics and behavior of complex RNAs can be understood from the 'sum of their parts', a hypothesis that if true, will lead to a general ability to predict RNA folding and energetics. Projct 4 builds on the reductionist framework developed in the other projects to now address RNA folding kinetics, testing quantitative predictions and developing novel systematic approaches to dissect the influence of co-transcription folding. Together, these studies will uncover basic properties and behaviors that define the physical, chemical, and biological behavior of RNA and catalyze a transformation from a descriptive to quantitative predictive understanding of RNA.

Public Health Relevance

HEALTH RELEVANCE: RNA is the central component in gene expression, transmitting information from DNA's stored genetic code. But RNA molecules are also dynamic and structured entities, and interactions with them are critical in development and in the regulation o all life forms. Thus, aberrant behavior of RNA can cause disease, and, conversely, the control of RNA-mediated processes in pathogens provides potential routes to new therapies.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Program Projects (P01)
Project #
5P01GM066275-07
Application #
8643241
Study Section
Special Emphasis Panel (ZRG1)
Program Officer
Preusch, Peter
Project Start
2003-06-06
Project End
2018-03-31
Budget Start
2014-04-01
Budget End
2015-03-31
Support Year
7
Fiscal Year
2014
Total Cost
Indirect Cost
Name
Stanford University
Department
Biochemistry
Type
Schools of Medicine
DUNS #
City
Stanford
State
CA
Country
United States
Zip Code
94304
Andrałojć, Witold; Ravera, Enrico; Salmon, Loïc et al. (2016) Inter-helical conformational preferences of HIV-1 TAR-RNA from maximum occurrence analysis of NMR data and molecular dynamics simulations. Phys Chem Chem Phys 18:5743-52
Shi, Xuesong; Huang, Lin; Lilley, David M J et al. (2016) The solution structural ensembles of RNA kink-turn motifs and their protein complexes. Nat Chem Biol 12:146-52
Gebala, Magdalena; Bonilla, Steve; Bisaria, Namita et al. (2016) Does Cation Size Affect Occupancy and Electrostatic Screening of the Nucleic Acid Ion Atmosphere? J Am Chem Soc 138:10925-34
Gracia, Brant; Xue, Yi; Bisaria, Namita et al. (2016) RNA Structural Modules Control the Rate and Pathway of RNA Folding and Assembly. J Mol Biol 428:3972-3985
Bisaria, Namita; Greenfeld, Max; Limouse, Charles et al. (2016) Kinetic and thermodynamic framework for P4-P6 RNA reveals tertiary motif modularity and modulation of the folding preferred pathway. Proc Natl Acad Sci U S A 113:E4956-65
Xue, Yi; Gracia, Brant; Herschlag, Daniel et al. (2016) Visualizing the formation of an RNA folding intermediate through a fast highly modular secondary structure switch. Nat Commun 7:ncomms11768
Schenk, Gundolf; Krajina, Brad; Spakowitz, Andrew et al. (2016) Potential for measurement of the distribution of DNA folds in complex environments using Correlated X-ray Scattering. Mod Phys Lett B 30:
Mustoe, Anthony M; Al-Hashimi, Hashim M; Brooks 3rd, Charles L (2016) Secondary structure encodes a cooperative tertiary folding funnel in the Azoarcus ribozyme. Nucleic Acids Res 44:402-12
Shi, Xuesong; Bonilla, Steve; Herschlag, Daniel et al. (2015) Quantifying Nucleic Acid Ensembles with X-ray Scattering Interferometry. Methods Enzymol 558:75-97
Greenfeld, Max; van de Meent, Jan-Willem; Pavlichin, Dmitri S et al. (2015) Single-molecule dataset (SMD): a generalized storage format for raw and processed single-molecule data. BMC Bioinformatics 16:3

Showing the most recent 10 out of 107 publications