This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. Primary support for the subproject and the subproject's principal investigator may have been provided by other sources, including other NIH sources. The Total Cost listed for the subproject likely represents the estimated amount of Center infrastructure utilized by the subproject, not direct funding provided by the NCRR grant to the subproject or subproject staff. Studies of RNA are fundamental for the global genomics project. It plays a key role in translating genetic information stored in DNA and manifesting it via the ribosome machinery. The study of viral and bacterial RNA is an important component of RNA research and offers insights into disease control. There is a large, ongoing effort in RNA sequencing as well as efforts to obtain 3-D structures and their relation to RNA function. In our initial effort, we applied DQC ESR to measure end-to-end distances in A-form RNA. Three RNAs with 13, 16, and 26 base pairs were spin-labeled by 3-iodo-acetamido-proxyl attached to thiouridine. The 5'-5'distances were evaluated from DQC, yielding the distances between electron spins on 5-5'attached nitroxides of 40, 55, and 72?, respectively, which agrees well with the proposed structures. A short communication describing the application of double-quantum filtered refocused primary echo (DQF-RPE) to 26 b.p. RNA is in press in J. Am. Chem. Soc. The ongoing collaboration with S.Butcher, is poised to combine NOE and DQC constraints to improve structure refinement. This will include the study of a 30 kDa RNA homodimer with a helical packing motif known as the tetraloop receptor. This motif plays an important role in tertiary structure formation in many different ribozymes. The second RNA structure of interest is derived from HIV-1 stem-loop domain involved in translational frameshifting (Staple and Butcher, NAR 2003, pdb code 1PJY). This RNA structure is essential for viral replication, but occurs in the context of a larger (45 nucleotide) RNA of unknown structure. The uncertainty in the structure is the relationship between the two helices, which are separated by a 3 nucleotide purine """"""""hinge"""""""" region. The length of the molecule, based on molecular modeling, is approximately 71?. However, this distance is unknown and may be less than 71? if the hinge region causes a bend between the two helices, as expected.

Agency
National Institute of Health (NIH)
Institute
National Center for Research Resources (NCRR)
Type
Biotechnology Resource Grants (P41)
Project #
2P41RR016292-11
Application #
8363952
Study Section
Special Emphasis Panel (ZRG1-BCMB-K (40))
Project Start
2011-09-01
Project End
2012-08-31
Budget Start
2011-09-01
Budget End
2012-08-31
Support Year
11
Fiscal Year
2011
Total Cost
$1,412
Indirect Cost
Name
Cornell University
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
872612445
City
Ithaca
State
NY
Country
United States
Zip Code
14850
Jain, Rinku; Vanamee, Eva S; Dzikovski, Boris G et al. (2014) An iron-sulfur cluster in the polymerase domain of yeast DNA polymerase ?. J Mol Biol 426:301-8
Pratt, Ashley J; Shin, David S; Merz, Gregory E et al. (2014) Aggregation propensities of superoxide dismutase G93 hotspot mutants mirror ALS clinical phenotypes. Proc Natl Acad Sci U S A 111:E4568-76
Georgieva, Elka R; Borbat, Peter P; Ginter, Christopher et al. (2013) Conformational ensemble of the sodium-coupled aspartate transporter. Nat Struct Mol Biol 20:215-21
Airola, Michael V; Sukomon, Nattakan; Samanta, Dipanjan et al. (2013) HAMP domain conformers that propagate opposite signals in bacterial chemoreceptors. PLoS Biol 11:e1001479
Airola, Michael V; Huh, Doowon; Sukomon, Nattakan et al. (2013) Architecture of the soluble receptor Aer2 indicates an in-line mechanism for PAS and HAMP domain signaling. J Mol Biol 425:886-901
Sun, Yan; Zhang, Ziwei; Grigoryants, Vladimir M et al. (2012) The internal dynamics of mini c TAR DNA probed by electron paramagnetic resonance of nitroxide spin-labels at the lower stem, the loop, and the bulge. Biochemistry 51:8530-41
Smith, Andrew K; Freed, Jack H (2012) Dynamics and ordering of lipid spin-labels along the coexistence curve of two membrane phases: an ESR study. Chem Phys Lipids 165:348-61
Yu, Renyuan Pony; Darmon, Jonathan M; Hoyt, Jordan M et al. (2012) High-Activity Iron Catalysts for the Hydrogenation of Hindered, Unfunctionalized Alkenes. ACS Catal 2:1760-1764
Gaffney, Betty J; Bradshaw, Miles D; Frausto, Stephen D et al. (2012) Locating a lipid at the portal to the lipoxygenase active site. Biophys J 103:2134-44
Dzikovski, Boris; Tipikin, Dmitriy; Freed, Jack (2012) Conformational distributions and hydrogen bonding in gel and frozen lipid bilayers: a high frequency spin-label ESR study. J Phys Chem B 116:6694-706

Showing the most recent 10 out of 72 publications