This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Accurate details in RNA structures are important for understanding RNA function, but the backbone conformation is difficult to determine and most existing RNA structures show serious steric clashes. In cell signaling, small RNA molecules such as riboswitches often interact with ligands to trigger changes of basic cellular activities such as gene expressions, where these RNA-ligand interactions often involve specific backbone interactions and the details of RNA backbones are essential for understanding the interaction mechanisms. In our previous work, we have developed a program called RNABC (RNA Backbone Correction) that searches for alternative clash-free conformations with acceptable geometry in a dinucleotide. The results from RNABC are acceptable but it still has a long way to become a mature tool. We plan to use various geometric techniques to improve RNABC in both solvability and speed, analyze RNA both theoretical model and experimental data and derive geometric rules to better understand RNA geometry, and develop 3D interactive program for crystallographers and other researchers to refine RNA structures.
The specific aims are: 1. Improving solvability and efficiency of current RNABC (RNA Backbone Correction) program, which provides clash-free alternative conformations for RNA dinucleotide backbone, and expanding RNABC to provide clash-free alternative conformations for multi-nucleotides. 2. Analyzing distributions of RNA backbone dihedral angles and RNA backbone conformations in theoretical space-filling model and experimental crystallographic data and deriving geometric rules to help understand RNA structures and incorporate into RNABC. 3. Developing 3D interactive program based on RNABC as a graphical user interface for nucleic acid crystallographers and other researchers to refine RNA structures.

Agency
National Institute of Health (NIH)
Institute
National Center for Research Resources (NCRR)
Type
Exploratory Grants (P20)
Project #
2P20RR016454-09
Application #
7959943
Study Section
Special Emphasis Panel (ZRR1-RI-4 (01))
Project Start
2009-04-01
Project End
2010-03-31
Budget Start
2009-04-01
Budget End
2010-03-31
Support Year
9
Fiscal Year
2009
Total Cost
$67,181
Indirect Cost
Name
University of Idaho
Department
Biology
Type
Schools of Arts and Sciences
DUNS #
075746271
City
Moscow
State
ID
Country
United States
Zip Code
83844
Tawara, Ken; Bolin, Celeste; Koncinsky, Jordan et al. (2018) OSM potentiates preintravasation events, increases CTC counts, and promotes breast cancer metastasis to the lung. Breast Cancer Res 20:53
Boursier, Michelle E; Moore, Joseph D; Heitman, Katherine M et al. (2018) Structure-Function Analyses of the N-Butanoyl l-Homoserine Lactone Quorum-Sensing Signal Define Features Critical to Activity in RhlR. ACS Chem Biol 13:2655-2662
Culbertson, Vaughn L; Rahman, Shaikh E; Bosen, Grayson C et al. (2018) Implications of Off-Target Serotoninergic Drug Activity: An Analysis of Serotonin Syndrome Reports Using a Systematic Bioinformatics Approach. Pharmacotherapy 38:888-898
Gunderson, Mark P; Nguyen, Brandon T; Cervantes Reyes, Juan C et al. (2018) Response of phase I and II detoxification enzymes, glutathione, metallothionein and acetylcholine esterase to mercury and dimethoate in signal crayfish (Pacifastacus leniusculus). Chemosphere 208:749-756
Ruffley, Megan; Smith, Megan L; EspĂ­ndola, AnahĂ­ et al. (2018) Combining allele frequency and tree-based approaches improves phylogeographic inference from natural history collections. Mol Ecol 27:1012-1024
Nhu Lam, Mila; Dudekula, Dastagiri; Durham, Bri et al. (2018) Insights into ?-ketoacyl-chain recognition for ?-ketoacyl-ACP utilizing AHL synthases. Chem Commun (Camb) 54:8838-8841
McGinn, Timothy E; Mitchell, Diana M; Meighan, Peter C et al. (2018) Restoration of Dendritic Complexity, Functional Connectivity, and Diversity of Regenerated Retinal Bipolar Neurons in Adult Zebrafish. J Neurosci 38:120-136
LaFoya, Bryce; Munroe, Jordan A; Pu, Xinzhu et al. (2018) Src kinase phosphorylates Notch1 to inhibit MAML binding. Sci Rep 8:15515
Sun, Chi; Galicia, Carlos; Stenkamp, Deborah L (2018) Transcripts within rod photoreceptors of the Zebrafish retina. BMC Genomics 19:127
Karmakar, Saswata; Guenther, Dale C; Gibbons, Bradley C et al. (2017) Recognition of mixed-sequence DNA using double-stranded probes with interstrand zipper arrangements of O2'-triphenylene- and coronene-functionalized RNA monomers. Org Biomol Chem 15:9362-9371

Showing the most recent 10 out of 476 publications