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BEGIN:VEVENT
DTSTAMP:20261026T000952Z
LAST-MODIFIED:20121116T203436Z
DTSTART:20110729T180000Z
DTEND:20110729T190000Z
UID:event818@bu.edu
URL:http://physics.bu.edu/internal/events/show/818
SUMMARY:Jianxun Lin - Ph.D Final Oral Examination
DESCRIPTION:\nPart of the PhD Final Oral Exams.\n\nTitle of Dissertation:&n
	bsp; Probing RNA Structure and RNA-Protein Interations Using Nanopore Force
	 Spectroscopy\n\n Examining Committee:  Amit Meller\, Kenneth Rothschi
	ld\, Ophelia Tsui\, Sidney Redner\, Robert Carey\n\n ABSTRACT\n Since the f
	irst demonstration of electrophoretically threading of single-stranded nucl
	eic acid through the alpha-Hemolysin (-HL) protein pore in 1996\, the us
	e of nanopores for the study of various biological systems has rapidly grow
	n\, leading to new and exciting applications in both biophysics and nano-bi
	otechnology. One of the most prominent applications of nanopore is a method
	 called ‘Nanopore Force Spectroscopy’ (NFS)\, which has enabled
	 studies of DNA structures and DNA-protein interactions\, at the single-mol
	ecule level. Much less work has been reported on RNA\, despite its vast bio
	logical relevance. The objective of this thesis is to further extend NFS to
	 probe the secondary structure of RNA and RNA-protein interactions\, with a
	n emphasis on revealing the dynamical properties of these bio-complexes for
	mation at the single molecule level.\n In this thesis I present three studi
	es related to specific processes involving RNA secondary structures and its
	 interaction with relevant protein. (1) The kinetics of polyadenylic acid (
	poly(A)) base stacking-unstacking\, which plays a role in the translational
	 control at the 3’ end of messenger RNA. The confinement of a RNA mol
	ecule inside a protein channel slows its kinetics by three orders of magnit
	ude as compared with bulk measurement of free poly(A) in solution. A phenom
	enological model describing our results is also described. (2) The unzippin
	g kinetics of double-stranded RNA molecules. Our study reveals clear differ
	ences between RNA and DNA duplexes with similar bulk thermodynamic properti
	es\, highlighting the nanopore ability to probe subtle differences in nucle
	ic acids’ free energy and their interactions with the pore. (3) Final
	ly\, the sensitivity of the nanopore system is used to examine the subtle i
	nteraction between poly(A) and the poly(A) binding protein (PABP)\, which i
	s part of the molecular pathway associated with translation initiation cont
	rol. For the first time the cooperative and non-cooperative binding modes o
	f multiple PABPs on the same poly(A) strand are directly observed at the si
	ngle molecule level. The decreased cooperative binding events of C-terminus
	 truncated PABP supports that C-terminus is the PABP-PABP interaction domai
	n\, in agreement with previous bulk biochemical studies.
LOCATION:SCI 352\, 590 Commonwealth Avenue\, 02215
STATUS:CONFIRMED
CLASS:PUBLIC
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