The long-term goals of this proposal are to develop and demonstrate synthetic strategies necessary for the synthesis and utilization of specifically modified or labeled RNA fragments. Molecules that are site-specifically labeled with 15N and 13C can provide unique and model-independent insight into local RNA structure, including hydrogen bonding, protonation, hydration, protection from hydration and stacking. The utility of 15N specifically labeled nucleosides will be expanded by introducing 13C into the C8 position of both purines and the C2 position of adenine. The resulting coupling with 15N in only one of a pair of purines will allow otherwise similar NMR resonances to be distinguished. Furthermore, the 13C can provide independent information on base stacking. The procedures developed for RNA synthesis using specific 15N and 13C labels will be made more widely available by adapting them to the phosphoramidite method. Since many of the simpler RNA motifs like non-canonical base pairs, single bulges, and tetraloops have now been characterized by 15N NMR, the new NMR work will focus primarily on more complex systems, such as internal loops, large hairpin loops, pseudoknots, kissing loops, tetraloop receptors, ribozymes, and protein-RNA complexes. The use of 15N NMR to define metal ion binding to RNA, a crucial aspect of its structure and function, will be explored.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
2R01GM048802-05
Application #
2471304
Study Section
Bio-Organic and Natural Products Chemistry Study Section (BNP)
Project Start
1994-01-01
Project End
2002-05-31
Budget Start
1998-06-05
Budget End
1999-05-31
Support Year
5
Fiscal Year
1998
Total Cost
Indirect Cost
Name
Rutgers University
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
038633251
City
New Brunswick
State
NJ
Country
United States
Zip Code
08901
Shallop, Anthony J; Gaffney, Barbara L; Jones, Roger A (2004) Use of both direct and indirect 13C tags for probing nitrogen interactions in hairpin ribozyme models by 15N NMR. Nucleosides Nucleotides Nucleic Acids 23:273-80
Li, Tsai-Kun; Barbieri, Christopher M; Lin, Hsin-Chin et al. (2004) Drug targeting of HIV-1 RNA.DNA hybrid structures: thermodynamics of recognition and impact on reverse transcriptase-mediated ribonuclease H activity and viral replication. Biochemistry 43:9732-42
Shallop, Anthony J; Gaffney, Barbara L; Jones, Roger A (2003) Use of 13C as an indirect tag in 15N specifically labeled nucleosides. Syntheses of [8-13C-1,7,NH2-15N3]adenosine, -guanosine, and their deoxy analogues. J Org Chem 68:8657-61
Barbieri, Christopher M; Li, Tsai-Kun; Guo, Susan et al. (2003) Aminoglycoside complexation with a DNA.RNA hybrid duplex: the thermodynamics of recognition and inhibition of RNA processing enzymes. J Am Chem Soc 125:6469-77
Gu, Feng; Stillwell, W G; Wishnok, John S et al. (2002) Peroxynitrite-induced reactions of synthetic oligo 2'-deoxynucleotides and DNA containing guanine: formation and stability of a 5-guanidino-4-nitroimidazole lesion. Biochemistry 41:7508-18
Mukerji, Ishita; Williams, Alison P (2002) UV resonance Raman and circular dichroism studies of a DNA duplex containing an A(3)T(3) tract: evidence for a premelting transition and three-centered H-bonds. Biochemistry 41:69-77
Kuryavyi, V; Majumdar, A; Shallop, A et al. (2001) A double chain reversal loop and two diagonal loops define the architecture of a unimolecular DNA quadruplex containing a pair of stacked G(syn)-G(syn)-G(anti)-G(anti) tetrads flanked by a G-(T-T) Triad and a T-T-T triple. J Mol Biol 310:181-94
Veldhuyzen, W F; Shallop, A J; Jones, R A et al. (2001) Thermodynamic versus kinetic products of DNA alkylation as modeled by reaction of deoxyadenosine. J Am Chem Soc 123:11126-32
Kettani, A; Gorin, A; Majumdar, A et al. (2000) A dimeric DNA interface stabilized by stacked A.(G.G.G.G).A hexads and coordinated monovalent cations. J Mol Biol 297:627-44
Kuryavyi, V; Kettani, A; Wang, W et al. (2000) A diamond-shaped zipper-like DNA architecture containing triads sandwiched between mismatches and tetrads. J Mol Biol 295:455-69

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