Biology Reference
In-Depth Information
Dynamics of Lesion Processing
by Bacterial Nucleotide
Excision Repair Proteins
Neil M. Kad
*
and Bennett
Van Houten
{
*Department of Biological Sciences,
University of Essex, Colchester, Essex,
United Kingdom
{
Hillman Cancer Center, Department of
Pharmacology and Chemical Biology,
University of Pittsburgh School of Medicine
& University of Pittsburgh Cancer Institute,
University of Pittsburgh, Pittsburgh,
Pennsylvania, USA
I. Structural Insights of Bacterial Nucleotide Excision Repair . . . . . . . . . . . . . . . . . . . . . . .
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A. Overview of the Process . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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B. Dynamics of the UvrA
2
B
2
-DNA Complex . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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C. Kinetic Proofreading as Part of a Dynamic DNA Damage Recognition
Process: Role of ATP . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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II. So Few DNA Repair Proteins, So Much DNA: Defining the Big Problem . . . .
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A. Challenge of Repair Inside a Bacterial Cell. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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B. Potential Modes of Damage Site Location . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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C. Necessary Experimental Components to Observe Single Molecules
in Action . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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III. Damage Searching by UvrA
2
and UvrA
2
B
2
............................................
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IV. Future Directions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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A. Observing Protein Nanomachines at Work. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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B. Overcoming the Brownian Motion Barrier. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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Single-molecule approaches permit an unrivalled view of how complex
systems operate and have recently been used to understand DNA-protein
interactions. These tools have enabled advances in a particularly challenging
problem, the search for damaged sites on DNA. DNA repair proteins are
present at the level of just a few hundred copies in bacterial cells to just a
few thousand in human cells, and they scan the entire genome in search of their
specific substrates. How do these proteins achieve this herculean task when
their targets may differ from undamaged DNA by only a single hydrogen bond?
Here we examine, using single-molecule approaches, how the prokaryotic
nucleotide excision repair system balances the necessity for speed against
specificity. We discuss issues at a theoretical, biological, and technical level
and finally pose questions for future research.
