supercoiling
DESCRIPTION
supercoiling by MANIKANTAGITAM UNIVERSITYTRANSCRIPT
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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 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 DNA2. Numerical expression for degree of supercoiling
A. Equation Lk=Tw+WrB. L:linking number, # of times that one DNA strand winds about the others strands, is always an integerC. T: twist,# of revolutions about the duplex helixD. 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 superhelicaldensity=∆Lk/Lk0
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Supercoiling of DNA2. Numerical expression for degree of supercoiling
A. Equation Lk=Tw+WrB. L:linking number, # of times that one DNA strand winds about the others strands, is always an integerC. 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 superhelicaldensity=∆Lk/Lk0
![Page 9: Supercoiling](https://reader033.vdocuments.us/reader033/viewer/2022060110/5560e519d8b42a3d768b4ddc/html5/thumbnails/9.jpg)
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Supercoiling of DNA2. Numerical expression for degree of supercoiling
A. Equation Lk=Tw+WrB. L:linking number, # of times that one DNA strand winds about the others strands, is always an integerC. 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 superhelicaldensity=∆Lk/Lk0
![Page 12: Supercoiling](https://reader033.vdocuments.us/reader033/viewer/2022060110/5560e519d8b42a3d768b4ddc/html5/thumbnails/12.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](https://reader033.vdocuments.us/reader033/viewer/2022060110/5560e519d8b42a3d768b4ddc/html5/thumbnails/16.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 DNA4. 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 DNA4. 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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