The biological function of RNA is intimately related to its three-dimensional structure. A tertiary RNA structure forms through a network of interactive modules. Independently stable tertiary structures can be linked together in a RNA enzyme to improve substrate binding and catalysis. The long-term objective of this proposal is to design stable tertiary RNA structures that can be incorporated as an essential part of an enzyme. The ribozyme consists of two domains that are independently stable.
The first aim i s to study how one of the two domains is stabilized by small, modular structures. This domain is proposed to contain two tertiary structural modules, one involved in function and the other involved in stability. Two naturally occurring modules of different sequences will be exchanged to demonstrate this two- module concept. The quantitative effect of altering the relative orientation and flexibility of the functional and stability module will be determined. A collection of the stability modules will be generated by in vitro section and the relative thermodynamic contribution of the selected modules will be determined in anticipation of the rational design.
The second aim i s to study how this ribozyme uses its two-domain composition to carry out catalysis. A new model of catalysis by this ribozyme will be tested in which both domains undergo a conformation change to increase the fraction of an obligatory ribozyme-substrate complex along the reaction pathway. The junction region of these domains will be modified to correlate the formation of this obligatory ribozyme-substrate complex to the conformation adjustment of these domains. Spectroscopic detection of the changes in the domain-domain orientation will be attempted by fluorescence resonance energy transfer.
The third aim i s to generate """"""""custom-made"""""""" ribozymes that recognize and cleave RNA structures or even RNA-protein complexes of choice. This goal will be accomplished by a combination of rational design and in vitro section and is made possible through our extensive knowledge on binding and catalysis of this ribozyme. These results will reveal how to stabilize a complex RNA structure, how to employ multiple domains to improve RNA catalysis and how to isolate ribozymes that can cleave any RNA structure or an RNA-protein complex.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
3R01GM052993-07S1
Application #
6468834
Study Section
Biochemistry Study Section (BIO)
Program Officer
Jones, Warren
Project Start
1995-08-04
Project End
2003-07-31
Budget Start
2001-08-01
Budget End
2002-07-31
Support Year
7
Fiscal Year
2001
Total Cost
$42,875
Indirect Cost
Name
University of Chicago
Department
Biochemistry
Type
Schools of Medicine
DUNS #
225410919
City
Chicago
State
IL
Country
United States
Zip Code
60637
Barrera, Alessandra; Fang, Xingwang; Jacob, Jaby et al. (2002) Dimeric and monomeric Bacillus subtilis RNase P holoenzyme in the absence and presence of pre-tRNA substrates. Biochemistry 41:12986-94
Qin, H; Sosnick, T R; Pan, T (2001) Modular construction of a tertiary RNA structure: the specificity domain of the Bacillus subtilis RNase P RNA. Biochemistry 40:11202-10
Loria, A; Pan, T (2001) Modular construction for function of a ribonucleoprotein enzyme: the catalytic domain of Bacillus subtilis RNase P complexed with B. subtilis RNase P protein. Nucleic Acids Res 29:1892-7
Fang, X W; Yang, X J; Littrell, K et al. (2001) The Bacillus subtilis RNase P holoenzyme contains two RNase P RNA and two RNase P protein subunits. RNA 7:233-41
Loria, A; Pan, T (2000) The 3' substrate determinants for the catalytic efficiency of the Bacillus subtilis RNase P holoenzyme suggest autolytic processing of the RNase P RNA in vivo. RNA 6:1413-22
Pan, T (2000) Probing RNA structure and function, by circular permutation. Methods Enzymol 317:313-30
Mobley, E M; Pan, T (1999) Design and isolation of ribozyme-substrate pairs using RNase P-based ribozymes containing altered substrate binding sites. Nucleic Acids Res 27:4298-304
Loria, A; Pan, T (1999) The cleavage step of ribonuclease P catalysis is determined by ribozyme-substrate interactions both distal and proximal to the cleavage site. Biochemistry 38:8612-20
Loria, A; Pan, T (1998) Recognition of the 5' leader and the acceptor stem of a pre-tRNA substrate by the ribozyme from Bacillus subtilis RNase P. Biochemistry 37:10126-33
Odell, L; Huang, V; Jakacka, M et al. (1998) Interaction of structural modules in substrate binding by the ribozyme from Bacillus subtilis RNase P. Nucleic Acids Res 26:3717-23

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