The long term objectives are as follows: (1) Use cro repressor as a model system for learning how proteins recognize DNA sequences. First we want to determine how cro recognizes its operator. This will be achieved by site specific mutagenesis of cro and selected nucleoside analog substitutions into cro operator. We also want to learn how to change cro at defined positions so that it now recognizes new DNA sequences. Achievement of this goal will aid us in understanding cro repressor-operator interactions and generally how proteins recognize DNA. Finally, how this protein interacts in a nonspecific binding mode with both operator and nonoperator DNA will be studied. (2) Investigate the lac repressor- operator interaction. Recently we discovered that lac repressor binds with high affinity to three sequence divergent operators. Using base analogs, we went to probe the mechanism whereby this protein binds with high affinity to several sequences. (3) Investigate whether repressors and operators can be used diagnostically or therapeutically. The possible diagnostic use will depend upon redesigning cro to recognize nonoperator sequences. Success would encourage us to test a sandwich assay for detecting DNA sequences using mutant cro repressors and cro antibodies. Therapeutic uses for gene control sequences will be explored with a model system, the lac operator. We will attempt to generate a nuclease resistant operator and use it in E. coli to derepress chromosomal lac expression. (4) Determine how regions of E. coli promoters contribute to formation of closed and open complexes. The goal is to measure the kinetics of forming open and closed complexes with promoters that are either covalently crosslinked or lacking defined functional groups. These experiments should identify functional groups involved in initial recognition and in forming an open complex. (5) Investigate components of RNA splicing. First we want to purify and functionally characterize a factor we have isolated from HeLa cell nuclear extracts that is required to reconstitute an active hnRNA splicing complex. We also will purify the debranching enzyme from HeLa cells and characterize its enzymatic activity. Currently we are using a synthetic branched tetranucleotide for these experiments. These studies will be extended to other branch structures having different sequences as well as base and phosphorus analogs. Finally, we plan to examine the catalytic activity of small ribozymes by synthetically introducing various analogs and measuring ribozyme activity.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM021120-17
Application #
3270265
Study Section
Microbial Physiology and Genetics Subcommittee 2 (MBC)
Project Start
1977-12-01
Project End
1993-06-30
Budget Start
1991-07-01
Budget End
1992-06-30
Support Year
17
Fiscal Year
1991
Total Cost
Indirect Cost
Name
University of Colorado at Boulder
Department
Type
Schools of Arts and Sciences
DUNS #
City
Boulder
State
CO
Country
United States
Zip Code
80309
Cummins, L; Graff, D; Beaton, G et al. (1996) Biochemical and physicochemical properties of phosphorodithioate DNA. Biochemistry 35:8734-41
Tonkinson, J L; Guvakova, M; Khaled, Z et al. (1994) Cellular pharmacology and protein binding of phosphoromonothioate and phosphorodithioate oligodeoxynucleotides: a comparative study. Antisense Res Dev 4:269-78
Wiesler, W T; Marshall, W S; Caruthers, M H (1993) Synthesis and purification of phosphorodithioate DNA. Methods Mol Biol 20:191-206
Marshall, W S; Caruthers, M H (1993) Phosphorodithioate DNA as a potential therapeutic drug. Science 259:1564-70
Caruthers, M H; Beaton, G; Wu, J V et al. (1992) Chemical synthesis of deoxyoligonucleotides and deoxyoligonucleotide analogs. Methods Enzymol 211:3-20
Marshall, W S; Beaton, G; Stein, C A et al. (1992) Inhibition of human immunodeficiency virus activity by phosphorodithioate oligodeoxycytidine. Proc Natl Acad Sci U S A 89:6265-9
Caruthers, M H; Beaton, G; Cummins, L et al. (1991) Synthesis and biological studies with dithioate DNA. Nucleic Acids Symp Ser :91-4
Delannoy, P; Caruthers, M H (1991) Detection and characterization of a factor which rescues spliceosome assembly from a heat-inactivated HeLa cell nuclear extract. Mol Cell Biol 11:3425-31
Hubbard, A J; Bracco, L P; Eisenbeis, S J et al. (1990) Role of the Cro repressor carboxy-terminal domain and flexible dimer linkage in operator and nonspecific DNA binding. Biochemistry 29:9241-9
Caruthers, M H; Brill, W K; Grandas, A et al. (1989) Synthesis of oligodeoxynucleoside phosphorodithioates. Nucleic Acids Symp Ser :119-20

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