supercoilingof dna - | siu school of medicinebbartholomew/-lectures/supercoiling 07.pdf ·...
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![Page 1: Supercoilingof DNA - | SIU School of Medicinebbartholomew/-lectures/Supercoiling 07.pdf · Supercoilingof DNA 2. Numerical expression for degree of supercoiling A. Equation Lk=Tw+Wr](https://reader033.vdocument.in/reader033/viewer/2022051523/5a768ed47f8b9a4b538d4f13/html5/thumbnails/1.jpg)
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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![Page 3: Supercoilingof DNA - | SIU School of Medicinebbartholomew/-lectures/Supercoiling 07.pdf · Supercoilingof DNA 2. Numerical expression for degree of supercoiling A. Equation Lk=Tw+Wr](https://reader033.vdocument.in/reader033/viewer/2022051523/5a768ed47f8b9a4b538d4f13/html5/thumbnails/3.jpg)
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
![Page 4: Supercoilingof DNA - | SIU School of Medicinebbartholomew/-lectures/Supercoiling 07.pdf · Supercoilingof DNA 2. Numerical expression for degree of supercoiling A. Equation Lk=Tw+Wr](https://reader033.vdocument.in/reader033/viewer/2022051523/5a768ed47f8b9a4b538d4f13/html5/thumbnails/4.jpg)
![Page 5: Supercoilingof DNA - | SIU School of Medicinebbartholomew/-lectures/Supercoiling 07.pdf · Supercoilingof DNA 2. Numerical expression for degree of supercoiling A. Equation Lk=Tw+Wr](https://reader033.vdocument.in/reader033/viewer/2022051523/5a768ed47f8b9a4b538d4f13/html5/thumbnails/5.jpg)
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 integer
C. 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=DLk/Lk0
![Page 6: Supercoilingof DNA - | SIU School of Medicinebbartholomew/-lectures/Supercoiling 07.pdf · Supercoilingof DNA 2. Numerical expression for degree of supercoiling A. Equation Lk=Tw+Wr](https://reader033.vdocument.in/reader033/viewer/2022051523/5a768ed47f8b9a4b538d4f13/html5/thumbnails/6.jpg)
![Page 7: Supercoilingof DNA - | SIU School of Medicinebbartholomew/-lectures/Supercoiling 07.pdf · Supercoilingof DNA 2. Numerical expression for degree of supercoiling A. Equation Lk=Tw+Wr](https://reader033.vdocument.in/reader033/viewer/2022051523/5a768ed47f8b9a4b538d4f13/html5/thumbnails/7.jpg)
![Page 8: Supercoilingof DNA - | SIU School of Medicinebbartholomew/-lectures/Supercoiling 07.pdf · Supercoilingof DNA 2. Numerical expression for degree of supercoiling A. Equation Lk=Tw+Wr](https://reader033.vdocument.in/reader033/viewer/2022051523/5a768ed47f8b9a4b538d4f13/html5/thumbnails/8.jpg)
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 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 superhelicaldensity=DLk/Lk0
![Page 9: Supercoilingof DNA - | SIU School of Medicinebbartholomew/-lectures/Supercoiling 07.pdf · Supercoilingof DNA 2. Numerical expression for degree of supercoiling A. Equation Lk=Tw+Wr](https://reader033.vdocument.in/reader033/viewer/2022051523/5a768ed47f8b9a4b538d4f13/html5/thumbnails/9.jpg)
![Page 10: Supercoilingof DNA - | SIU School of Medicinebbartholomew/-lectures/Supercoiling 07.pdf · Supercoilingof DNA 2. Numerical expression for degree of supercoiling A. Equation Lk=Tw+Wr](https://reader033.vdocument.in/reader033/viewer/2022051523/5a768ed47f8b9a4b538d4f13/html5/thumbnails/10.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 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 superhelicaldensity=DLk/Lk0
![Page 12: Supercoilingof DNA - | SIU School of Medicinebbartholomew/-lectures/Supercoiling 07.pdf · Supercoilingof DNA 2. Numerical expression for degree of supercoiling A. Equation Lk=Tw+Wr](https://reader033.vdocument.in/reader033/viewer/2022051523/5a768ed47f8b9a4b538d4f13/html5/thumbnails/12.jpg)
![Page 13: Supercoilingof DNA - | SIU School of Medicinebbartholomew/-lectures/Supercoiling 07.pdf · Supercoilingof DNA 2. Numerical expression for degree of supercoiling A. Equation Lk=Tw+Wr](https://reader033.vdocument.in/reader033/viewer/2022051523/5a768ed47f8b9a4b538d4f13/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: Supercoilingof DNA - | SIU School of Medicinebbartholomew/-lectures/Supercoiling 07.pdf · Supercoilingof DNA 2. Numerical expression for degree of supercoiling A. Equation Lk=Tw+Wr](https://reader033.vdocument.in/reader033/viewer/2022051523/5a768ed47f8b9a4b538d4f13/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 hydrolysisii. 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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