The proposed research has three principal objectives: (I) a more quantitative understanding of the sequence-dependence and origins of nucleic acid helix rigidity; (ii)characterization of the conformational changes induced in DNA (or RNA) by three site- specific nucleic acid binding proteins; (iii) further development of two solution-based methods, namely, transient electric birefringence (TEB) and luminescence resonance energy transfer (LRET), for studying the long-range conformations of nucleic acids. Used in combination, these two methods should complement one another to reduce the experimental and theoretical uncertainties associated with either method alone. Each of the three protein-nucleic acid interactions is designed to examine a somewhat different issue: The TATA-box protein (TBP) is a critical component of the eukaryotic transcriptional machinery; its complex with DNA provides an excellent test system for examining large bends in solution, and for laying the groundwork for a more comprehensive study of the specific interactions that give rise to DNA bending. The basic region- leucine zipper protein (bZIP) family is extremely important in the process of tissue-specific transcriptional regulation; examination of the bZIP-DNA interaction will hopefully resolve the question of how much (or whether) those proteins bend their DNA targets. The third study will focus on the nature of the conformational change induced in a plant viral RNA genome (alfalfa mosaic virus) by site-specific binding of the viral coat protein. The RNA target is likely to possess a significant degree of flexibility prior to protein binding, thus providing a test of the TEB/LRET approach to assess flexibility.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
7R01GM035305-17
Application #
6402029
Study Section
Molecular and Cellular Biophysics Study Section (BBCA)
Program Officer
Lewis, Catherine D
Project Start
1985-07-01
Project End
2003-06-30
Budget Start
2000-12-01
Budget End
2001-06-30
Support Year
17
Fiscal Year
2000
Total Cost
$191,108
Indirect Cost
Name
University of California Davis
Department
Biochemistry
Type
Schools of Medicine
DUNS #
094878337
City
Davis
State
CA
Country
United States
Zip Code
95618
Mills, Janine B; Hagerman, Paul J (2004) Origin of the intrinsic rigidity of DNA. Nucleic Acids Res 32:4055-9
Frazer-Abel, Ashley A; Hagerman, Paul J (2004) Variation of the acceptor-anticodon interstem angles among mitochondrial and non-mitochondrial tRNAs. J Mol Biol 343:313-25
van Oppen, Madeleine J H; Catmull, Julian; McDonald, Brenda J et al. (2002) The mitochondrial genome of Acropora tenuis (Cnidaria; Scleractinia) contains a large group I intron and a candidate control region. J Mol Evol 55:1-13
Greco, C M; Hagerman, R J; Tassone, F et al. (2002) Neuronal intranuclear inclusions in a new cerebellar tremor/ataxia syndrome among fragile X carriers. Brain 125:1760-71
Tassone, F; Hagerman, R J; Taylor, A K et al. (2001) A majority of fragile X males with methylated, full mutation alleles have significant levels of FMR1 messenger RNA. J Med Genet 38:453-6
Stagg, S M; Frazer-Abel, A A; Hagerman, P J et al. (2001) Structural studies of the tRNA domain of tmRNA. J Mol Biol 309:727-35
Chiang, P W; Carpenter, L E; Hagerman, P J (2001) The 5'-untranslated region of the FMR1 message facilitates translation by internal ribosome entry. J Biol Chem 276:37916-21
Tassone, F; Hagerman, R J; Taylor, A K et al. (2000) Elevated levels of FMR1 mRNA in carrier males: a new mechanism of involvement in the fragile-X syndrome. Am J Hum Genet 66:15-Jun
Tassone, F; Hagerman, R J; Loesch, D Z et al. (2000) Fragile X males with unmethylated, full mutation trinucleotide repeat expansions have elevated levels of FMR1 messenger RNA. Am J Med Genet 94:232-6
Tassone, F; Hagerman, R J; Chamberlain, W D et al. (2000) Transcription of the FMR1 gene in individuals with fragile X syndrome. Am J Med Genet 97:195-203

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