Abstract

This Program Project proposal is focused on obtaining the deepest understanding possible of the folding of a single RNA, the Tetrahymena group I ribozyme. For this reason, a central Core responsible for the creation of common RNA reagents, the basic training of personnel, and the documentation and distribution of materials. The Molecular Biology, Chemistry and Biochemistry (MBCB) Project Core will consist of a molecular biology and chemistry laboratory with a technical staff skilled in the preparation of RNA and mutagenesis. The core is essential for the production of the large quantities of RNA required for some of the proposed biophysical experiments. The central production of RNA will also insure its consistency for all of the Component Projects. The core will also perform routine folding, stability and activity assays to provide basic characterizations of new constructs and to demonstrate that all products meet a level of quality and purity commensurate with demands of all the Component Projects.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Program Projects (P01)
Project #
1P01GM066275-01A1
Application #
6760487
Study Section
Special Emphasis Panel (ZRG1-PBC (02))
Project Start
2003-06-06
Project End
2008-05-31
Budget Start
Budget End
2004-05-31
Support Year
1
Fiscal Year
2003
Total Cost
$132,268
Indirect Cost

  Institution

Name
Stanford University
Department
Type
DUNS #
009214214
City
Stanford
State
CA
Country
United States
Zip Code
94305

  Publications

Merriman, Dawn K; Yuan, Jiayi; Shi, Honglue et al. (2018) Increasing the length of poly-pyrimidine bulges broadens RNA conformational ensembles with minimal impact on stacking energetics. RNA 24:1363-1376
Gracia, Brant; Al-Hashimi, Hashim M; Bisaria, Namita et al. (2018) Hidden Structural Modules in a Cooperative RNA Folding Transition. Cell Rep 22:3240-3250
Zettl, Thomas; Das, Rhiju; Harbury, Pehr A B et al. (2018) Recording and Analyzing Nucleic Acid Distance Distributions with X-Ray Scattering Interferometry (XSI). Curr Protoc Nucleic Acid Chem 73:e54
Ganser, Laura R; Lee, Janghyun; Rangadurai, Atul et al. (2018) High-performance virtual screening by targeting a high-resolution RNA dynamic ensemble. Nat Struct Mol Biol 25:425-434
Liu, Bei; Merriman, Dawn K; Choi, Seung H et al. (2018) A potentially abundant junctional RNA motif stabilized by m6A and Mg2. Nat Commun 9:2761
Denny, Sarah Knight; Bisaria, Namita; Yesselman, Joseph David et al. (2018) High-Throughput Investigation of Diverse Junction Elements in RNA Tertiary Folding. Cell 174:377-390.e20
Kimsey, Isaac J; Szymanski, Eric S; Zahurancik, Walter J et al. (2018) Dynamic basis for dG•dT misincorporation via tautomerization and ionization. Nature 554:195-201
Allred, Benjamin E; Gebala, Magdalena; Herschlag, Daniel (2017) Determination of Ion Atmosphere Effects on the Nucleic Acid Electrostatic Potential and Ligand Association Using AH+·C Wobble Formation in Double-Stranded DNA. J Am Chem Soc 139:7540-7548
Gilman, Benjamin; Tijerina, Pilar; Russell, Rick (2017) Distinct RNA-unwinding mechanisms of DEAD-box and DEAH-box RNA helicase proteins in remodeling structured RNAs and RNPs. Biochem Soc Trans 45:1313-1321
Shi, Xuesong; Walker, Peter; Harbury, Pehr B et al. (2017) Determination of the conformational ensemble of the TAR RNA by X-ray scattering interferometry. Nucleic Acids Res 45:e64

Showing the most recent 10 out of 126 publications