Alternative splicing is the primary mechanism for generation of multiple protein isoforms. Regulation of alternative splicing often requires proteins specific to a cell type or developmental stage, but this very diversity has prevented definition of a molecular mechanism of the process. The functional biochemical and biophysical properties of one protein in the splicing of two neuronal pre-mRNAs offers the opportunity to describe a mechanism. Our goal is to understand the mechanism of exon exclusion of the c-src N1 exon and the GABAA receptor ?2 neuron exon by the polypyrimidine tract binding protein (PTB). PTB is known to be necessary and sufficient for exon exclusion of the N1 exon of c-src pre-mRNA in non-neural cells, and is required for exclusion of the neuron exon of the GABAA receptor ?2 pre-mRNA in non-neural cells. PTB binds near the 3'splice sites of these RNA, but how its binding effectively sequesters the splice site is obscure. Equally obscure is the mechanism by which this repression is relieved by other proteins.
Specific Aim 1 is devoted to the characterization of PTB complexes formed on the rat GABA pre-mRNA intron/exon.
Specific Aim 2 details interactions of PTB with mouse c-src N1 pre-mRNA exon and flanking introns. We use gel mobility shift assays, nitrocellulose filter binding, enzymatic footprinting, fluorescence anisotropy, and NMR to determine binding affinity, stoichiometry, the RNA sites bound by PTB, and the domains of PTB in contact with the RNA, and fluorescence fluctuation spectroscopy to observe the exchange of fluorescently labeled PTB molecules. Our data have led to the testable hypothesis that the two halves of PTB have specialized RNA binding sites. The two N-terminal domains recognize polypyrimidine tracts in structured RNAs, while the two C-terminal domains bind unstructured RNAs;these RNA sites could be on the same or different RNAs. PTB association/dissociation from complexes will be measured in the presence of nPTB, a reported antagonist, to characterize its mechanism of repression relief.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Macromolecular Structure and Function C Study Section (MSFC)
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Preusch, Peter C
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Washington University
Schools of Medicine
Saint Louis
United States
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Melnykov, Artem V; Nayak, Rajesh K; Hall, Kathleen B et al. (2015) Effect of loop composition on the stability and folding kinetics of RNA hairpins with large loops. Biochemistry 54:1886-96
Nayak, Rajesh K; Van Orden, Alan (2013) Counterion and polythymidine loop-length-dependent folding and thermodynamic stability of DNA hairpins reveal the unusual counterion-dependent stability of tetraloop hairpins. J Phys Chem B 117:13956-66
Nayak, Rajesh K; Peersen, Olve B; Hall, Kathleen B et al. (2012) Millisecond time-scale folding and unfolding of DNA hairpins using rapid-mixing stopped-flow kinetics. J Am Chem Soc 134:2453-6
Hall, Kathleen B (2012) Spectroscopic probes of RNA structure and dynamics. Methods Mol Biol 875:67-84
Liu, Feng; Maynard, Caroline; Scott, Gregory et al. (2010) A natural missing link between activated and downhill protein folding scenarios. Phys Chem Chem Phys 12:3542-9
Maynard, Caroline M; Hall, Kathleen B (2010) Interactions between PTB RRMs induce slow motions and increase RNA binding affinity. J Mol Biol 397:260-77
Clerte, Caroline; Hall, Kathleen B (2009) The domains of polypyrimidine tract binding protein have distinct RNA structural preferences. Biochemistry 48:2063-74
Hall, Kathleen B (2009) 2-aminopurine as a probe of RNA conformational transitions. Methods Enzymol 469:269-85
Melnykov, Artem V; Hall, Kathleen B (2009) Revival of high-order fluorescence correlation analysis: generalized theory and biochemical applications. J Phys Chem B 113:15629-38