supercoiling of dna
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Supercoiling of DNA. Topology A. Right handed supercoiling = negative supercoiling (underwinding) B. Left handed supercoiling = positive supercoiling C. Relaxed state is with no bends D. DNA must be constrained: plasmid DNA or by proteins - PowerPoint PPT PresentationTRANSCRIPT
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Supercoiling of DNA1. Topology
A. Right handed supercoiling = negative supercoiling (underwinding)B. Left handed supercoiling = positive supercoilingC. Relaxed state is with no bendsD. DNA must be constrained: plasmid DNA or by proteinsE. Unraveling the DNA at one position changes the superhelicity -F. Topology only defined for continuous deformation - no strand breakage
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Supercoiling of DNA1. Topology
A. Right handed supercoiling = negative supercoiling (underwinding)B. Left handed supercoiling = positive supercoilingC. Relaxed state is with no bends D. DNA must be constrained: plasmid DNA or by proteinsE. Unraveling the DNA at one position changes the superhelicity -F. Topology only defined for continuous deformation - no strand breakage
![Page 4: Supercoiling of DNA](https://reader035.vdocuments.site/reader035/viewer/2022062422/56813066550346895d9640ac/html5/thumbnails/4.jpg)
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Supercoiling of DNA
2. Numerical expression for degree of supercoilingA. Equation Lk=Tw+WrB. L:linking number, # of times that one DNA strand winds about the others strands, is always an integer C. T: twist,# of revolutions about the duplex helix D. W: writhe, # of turns of the duplex axis about the superhelical axis by definition the measure of the degree of supercoilingE. specific linking difference or superhelical density=Lk/Lk0
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![Page 8: Supercoiling of DNA](https://reader035.vdocuments.site/reader035/viewer/2022062422/56813066550346895d9640ac/html5/thumbnails/8.jpg)
Supercoiling of DNA
2. Numerical expression for degree of supercoilingA. Equation Lk=Tw+WrB. L:linking number, # of times that one DNA strand winds about the others strands, is always an integer C. T: twist,# of revolutions about the duplex helix D. W: writhe, # of turns of the duplex axis about the superhelical axis by definition the measure of the degree of supercoilingE. specific linking difference or superhelical density=Lk/Lk0
![Page 9: Supercoiling of DNA](https://reader035.vdocuments.site/reader035/viewer/2022062422/56813066550346895d9640ac/html5/thumbnails/9.jpg)
![Page 10: Supercoiling of DNA](https://reader035.vdocuments.site/reader035/viewer/2022062422/56813066550346895d9640ac/html5/thumbnails/10.jpg)
![Page 11: Supercoiling of DNA](https://reader035.vdocuments.site/reader035/viewer/2022062422/56813066550346895d9640ac/html5/thumbnails/11.jpg)
Supercoiling of DNA
2. Numerical expression for degree of supercoilingA. Equation Lk=Tw+WrB. L:linking number, # of times that one DNA strand winds about the others strands, is always an integer C. T: twist,# of revolutions about the duplex helix D. W: writhe, # of turns of the duplex axis about the superhelical axis by definition the measure of the degree of supercoilingE. specific linking difference or superhelical density=Lk/Lk0
![Page 12: Supercoiling of DNA](https://reader035.vdocuments.site/reader035/viewer/2022062422/56813066550346895d9640ac/html5/thumbnails/12.jpg)
![Page 13: Supercoiling of DNA](https://reader035.vdocuments.site/reader035/viewer/2022062422/56813066550346895d9640ac/html5/thumbnails/13.jpg)
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Supercoiling of DNA1. Topology
A. Right handed supercoiling = negative supercoiling (underwinding)B. Left handed supercoiling = positive supercoilingC. Relaxed state is with no bends D. DNA must be constrained: plasmid DNA or by proteinsE. Unraveling the DNA at one position changes the superhelicity -F. Topology only defined for continuous deformation - no strand breakage
![Page 16: Supercoiling of DNA](https://reader035.vdocuments.site/reader035/viewer/2022062422/56813066550346895d9640ac/html5/thumbnails/16.jpg)
![Page 17: Supercoiling of DNA](https://reader035.vdocuments.site/reader035/viewer/2022062422/56813066550346895d9640ac/html5/thumbnails/17.jpg)
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Supercoiling of DNA
3. DNA compaction requires special form of supercoiling
A. Interwound: supercoiling of DNA in solution
B. Toroidal- tight left handed turns, packing of DNA both forms are interconvertible
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Supercoiling of DNA
4. Methods for measuring supercoiling - based on how compact the DNA is
A. Gel electrophoresisi. 1 dimensional ii. 2 dimensional
B. Density sedimentation
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Supercoiling of DNA
4. Topoisomerases are required to relieve torsional strainA. Topoisomerases I :
breaks only one strand B. Topoisomerase II :
breaks both strands
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Supercoiling of DNA
4. Topoisomerases are required to relieve torsional strainA. Topoisomerases I - breaks only one strand
i. monomeric proteinii. after nicking DNA the 5'-PO4 is covalently linked
to enzyme (prokaryotes) or the 3' end is linked to the enzyme (eukaryotes)
iii. evidence is the formation of catenatesiv. E. coli Topo I relaxes negatively supercoiled DNAv. introduces a change of increments of 1 in writhe
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Supercoiling of DNA
4. Topoisomerases are required to relieve torsional strainB. Topoisomerase II - breaks both strands
i. supercoils DNA at the expense of ATP hydrolysis
ii. two subunits: (alpha)2 and (beta)2iii. becomes covalently linked to the alpha
subunitiv. relaxes both negative and positively
supercoiled DNAv. introduces a change in increments of 2
in writhe.
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