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Single-molecule studies of protein-D...

Blainey, Paul Clark.

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Single-molecule studies of protein-DNA interaction: Diffusive search and sequence-dependent motors.

Record Type:	Language materials, printed : Monograph/item
Title/Author:	Single-molecule studies of protein-DNA interaction: Diffusive search and sequence-dependent motors./
Author:	Blainey, Paul Clark.
Description:	191 p.
Notes:	Advisers: X. Sunney Xie; Gregory L. Verdine.
Contained By:	Dissertation Abstracts International68-05B.
Subject:	Biophysics, General. -
Online resource:	http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3264892
ISBN:	9780549035374

Single-molecule studies of protein-DNA interaction: Diffusive search and sequence-dependent motors.
Blainey, Paul Clark.

Single-molecule studies of protein-DNA interaction: Diffusive search and sequence-dependent motors. - 191 p.

Advisers: X. Sunney Xie; Gregory L. Verdine.

Thesis (Ph.D.)--Harvard University, 2007.

A new method for stretching many individual DNA molecules in parallel using hydrodynamic flow is developed and applied to problems in protein-DNA interaction. This new method, configured for precise measurement of the extension of long DNA template molecules, is used to investigate the sequence-dependent properties of DNA polymerase and exonuclease activities. Analysis of DNA digestion by individual bacteriophage lambda exonuclease molecules reveals sequence-dependent variations in the digestion rate controlled by a rapid base-melting equilibrium, while large-amplitude sequence-independent fluctuations of the digestion rate are attributed to slow conformational fluctuations of the enzyme/DNA complex. Conversely, the rate of DNA synthesis by the &phis;29 DNA polymerase is found to exhibit little dynamic fluctuation, but strong, reproducible variation due to the DNA template base sequence.

ISBN: 9780549035374Subjects--Topical Terms:

1019105
Biophysics, General.

Single-molecule studies of protein-DNA interaction: Diffusive search and sequence-dependent motors.
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020 $a 9780549035374
035 $a (UMI)AAI3264892
035 $a AAI3264892
040 $a UMI $c UMI
100 1 $a Blainey, Paul Clark. $3 1263288
245 1 0 $a Single-molecule studies of protein-DNA interaction: Diffusive search and sequence-dependent motors.
300 $a 191 p.
500 $a Advisers: X. Sunney Xie; Gregory L. Verdine.
500 $a Source: Dissertation Abstracts International, Volume: 68-05, Section: B, page: 3071.
502 $a Thesis (Ph.D.)--Harvard University, 2007.
520 $a A new method for stretching many individual DNA molecules in parallel using hydrodynamic flow is developed and applied to problems in protein-DNA interaction. This new method, configured for precise measurement of the extension of long DNA template molecules, is used to investigate the sequence-dependent properties of DNA polymerase and exonuclease activities. Analysis of DNA digestion by individual bacteriophage lambda exonuclease molecules reveals sequence-dependent variations in the digestion rate controlled by a rapid base-melting equilibrium, while large-amplitude sequence-independent fluctuations of the digestion rate are attributed to slow conformational fluctuations of the enzyme/DNA complex. Conversely, the rate of DNA synthesis by the &phis;29 DNA polymerase is found to exhibit little dynamic fluctuation, but strong, reproducible variation due to the DNA template base sequence.
520 $a Flow-stretched DNA molecules also serve as templates for tracking individual bound protein molecules using fluorescence microscopy. The search by DNA repair proteins for lesion sites in DNA is important to human disease and aging. Human and bacterial DNA glycosylases are found to slide almost barrierlessly along undamaged DNA, directly verifying a long-standing proposal that proteins find specific sites within DNA by sliding in contact with DNA. The rapid sliding observed in buffer and in viscous polymer solutions simulating the cellular environment indicate that lesion bases hidden within B-form DNA are located by a massively redundant search in which the enzymes selectively bind target bases under kinetic control.
520 $a The adenoviral proteinase (AVP) is prevented from prematurely processing substrates by binding to the packaged viral dsDNA genome. Single-molecule experiments show that this repression is relieved when AVP's catalytic cofactor, the eleven amino acid peptide pVIc, confers the sliding activity on AVP, allowing the proteinase to find and cleave precursor proteins to their mature forms. pVIc itself slides on DNA, defining a new minimal motif for sliding. Collectively, sliding data from several different proteins indicate that the proteins spin along the DNA helix as they search for targets. A new hydrodynamic theory based on a realistic physical model for helical sliding is described. The findings on sliding collated in this thesis, together with recent literature reports, suggest a more general role of one-dimensional diffusion along polymers in biology than is presently appreciated.
590 $a School code: 0084.
650 4 $a Biophysics, General. $3 1019105
650 4 $a Chemistry, Biochemistry. $3 1017722
650 4 $a Chemistry, Physical. $3 560527
690 $a 0487
690 $a 0494
690 $a 0786
710 2 $a Harvard University. $3 528741
773 0 $t Dissertation Abstracts International $g 68-05B.
790 $a 0084
790 1 0 $a Verdine, Gregory L., $e advisor
790 1 0 $a Xie, X. Sunney, $e advisor
791 $a Ph.D.
792 $a 2007
856 4 0 $u http://pqdd.sinica.edu.tw/twdaoapp/servlet/advanced?query=3264892