This research will be done in Poland to provide materials to support NIH Grant GM22939. The ultimate goal of the parent grant is to characterize the forces directing RNA folding, and to use this knowledge to reliably predict RNA structure from sequence. One goal of the FIRCA grant is to develop a series of oligonucleotides that bind tightly and specifically enough to RNA to allow interrogation of RNA secondary structure by assaying binding of an RNA to an array of all possible 7-mers. It is possible that even shorter oligonucleotides may be sufficient. The results of this array assay will provide constraints for computer algorithms that predict structure from sequence. A second goal of the FIRCA grant is to develop model systems for studying the interactions that determine the stabilities of multibranch loops.

National Institute of Health (NIH)
Fogarty International Center (FIC)
Small Research Grants (R03)
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International and Cooperative Projects 1 Study Section (ICP)
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Katz, Flora N
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University of Rochester
Schools of Arts and Sciences
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Kierzek, Elzbieta; Kierzek, Ryszard; Moss, Walter N et al. (2008) Isoenergetic penta- and hexanucleotide microarray probing and chemical mapping provide a secondary structure model for an RNA element orchestrating R2 retrotransposon protein function. Nucleic Acids Res 36:1770-82
Yajima, Rieko; Proctor, David J; Kierzek, Ryszard et al. (2007) A conformationally restricted guanosine analog reveals the catalytic relevance of three structures of an RNA enzyme. Chem Biol 14:23-30
Chen, Gang; Kierzek, Ryszard; Yildirim, Ilyas et al. (2007) Stacking effects on local structure in RNA: changes in the structure of tandem GA pairs when flanking GC pairs are replaced by isoG-isoC pairs. J Phys Chem B 111:6718-27
Pasternak, Anna; Kierzek, Elzbieta; Pasternak, Karol et al. (2007) A chemical synthesis of LNA-2,6-diaminopurine riboside, and the influence of 2'-O-methyl-2,6-diaminopurine and LNA-2,6-diaminopurine ribosides on the thermodynamic properties of 2'-O-methyl RNA/RNA heteroduplexes. Nucleic Acids Res 35:4055-63
Kierzek, Elzbieta; Kierzek, Ryszard; Turner, Douglas H et al. (2006) Facilitating RNA structure prediction with microarrays. Biochemistry 45:581-93
Ma, Hairong; Proctor, David J; Kierzek, Elzbieta et al. (2006) Exploring the energy landscape of a small RNA hairpin. J Am Chem Soc 128:1523-30
Kierzek, Elzbieta; Mathews, David H; Ciesielska, Anna et al. (2006) Nearest neighbor parameters for Watson-Crick complementary heteroduplexes formed between 2'-O-methyl RNA and RNA oligonucleotides. Nucleic Acids Res 34:3609-14
Broda, Magdalena; Kierzek, Elzbieta; Gdaniec, Zofia et al. (2005) Thermodynamic stability of RNA structures formed by CNG trinucleotide repeats. Implication for prediction of RNA structure. Biochemistry 44:10873-82
Kierzek, Elzbieta; Ciesielska, Anna; Pasternak, Karol et al. (2005) The influence of locked nucleic acid residues on the thermodynamic properties of 2'-O-methyl RNA/RNA heteroduplexes. Nucleic Acids Res 33:5082-93
Proctor, David J; Ma, Hairong; Kierzek, Elzbieta et al. (2004) Folding thermodynamics and kinetics of YNMG RNA hairpins: specific incorporation of 8-bromoguanosine leads to stabilization by enhancement of the folding rate. Biochemistry 43:14004-14

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