Supercoilingof DNA
1.Topology
A. Right handed supercoiling= negative supercoiling(underwinding)
B. Left handed supercoiling= positive supercoiling

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C. Relaxed state is with no bends

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D. DNA must be constrained: plasmid DNA or by proteins

E. Unraveling the DNA at one position changes the superhelicity-

F. Topology only defined for continuous deformation -no strand breakage

 

 

 

Supercoilingof DNA
2. Numerical expression for degree of supercoiling
A. Equation Lk=Tw+Wr
B. L:linkingnumber, # of times that one DNA strand winds about the others strands, is always an integer
C. T: twist,# of revolutions about the duplex helix

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D. W: writhe, # of turns of the duplex axis about the superhelicalaxis
by definition the measure of the degree of supercoiling

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E. specific linking difference or superhelicaldensity=ΔLk/Lk0

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Supercoilingof DNA

 

1.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

E. Unraveling the DNA at one position changes the superhelicity-

http://s7/middle/53c3f40ag98c7ee4d4cb6&690超螺旋的折叠方式及比例（多图）" TITLE="DNA 超螺旋的折叠方式及比例（多图）" />

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F. Topology only defined for continuous deformation -no strand breakage

 

 

Supercoilingof DNA

 

3. DNA compaction requires special form of supercoiling

A. Interwound: supercoilingof DNA in solution

B. Toroidal-tight left handed turns, packing of DNA

both forms are interconvertible

 

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Supercoilingof DNA

 

4. Methods for measuring supercoiling-based on how compact the DNA is

A. Gel electrophoresis

i. 1 dimensional

ii. 2 dimensional

B. Density sedimentation

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Supercoilingof DNA

 

4. Topoisomerasesare required to relieve torsionalstrain

A. TopoisomerasesI :

breaks only one strand

B. TopoisomeraseII :

breaks both strands

 

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4. Topoisomerasesare required to relieve torsionalstrain

A. TopoisomerasesI -breaks only one strand

i. monomericprotein

ii. 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 catenates

iv. E. coli TopoI relaxes negatively supercoiledDNA

v. introduces a change of increments of 1 in writhe

 

 

4. Topoisomerasesare required to relieve torsionalstrain

B. TopoisomeraseII -breaks both strands

i. supercoilsDNA at the expense of ATP hydrolysis

ii. two subunits: (alpha)2 and (beta)2

iii. becomes covalently linked to the alpha subunit

iv. relaxes both negative and positively supercoiledDNA

v. introduces a change in increments of 2 in writhe.

 

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