1. 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
E. Unraveling the DNA at one position changes the superhelicity -
F. Topology only defined for continuous deformation - no strand breakage

3. 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
E. Unraveling the DNA at one position changes the superhelicity -
F. Topology only defined for continuous deformation - no strand breakage

5. Supercoiling of DNA 2. Numerical expression for degree of supercoiling
A. Equation Lk=Tw+Wr
B. 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 supercoiling
E. specific linking difference or superhelical density=DLk/Lk0

8. Supercoiling of DNA 2. Numerical expression for degree of supercoiling
A. Equation Lk=Tw+Wr
B. 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 supercoiling
E. specific linking difference or superhelical density=DLk/Lk0

11. Supercoiling of DNA 2. Numerical expression for degree of supercoiling
A. Equation Lk=Tw+Wr
B. 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 supercoiling
E. specific linking difference or superhelical density=DLk/Lk0

15. 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
E. Unraveling the DNA at one position changes the superhelicity -
F. Topology only defined for continuous deformation - no strand breakage

19. 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

21. Supercoiling of 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

24. Supercoiling of DNA
4. Topoisomerases are required to relieve torsional strain
A. Topoisomerases I :
breaks only one strand
B. Topoisomerase II :
breaks both strands

27. Supercoiling of DNA
4. Topoisomerases are required to relieve torsional strain
A. Topoisomerases I - breaks only one strand
i. monomeric protein
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 Topo I relaxes negatively supercoiled DNA
v. introduces a change of increments of 1 in writhe

28. Supercoiling of DNA
4. Topoisomerases are required to relieve torsional strain
B. Topoisomerase II - breaks both strands
i. supercoils DNA 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 supercoiled DNA
v. introduces a change in increments of 2 in writhe.