tertiary structure: supercoiled dna figure 29-18schematic diagram of covalently closed circular...

Tertiary Structure: Supercoiled DNA

Figure 29-18 Schematic diagram of covalently closed circular duplex DNA

that has 26 double helical turns.

L = T + WL = Linkage Number

number of crossings in planar projection

T = Topological winding number-

(e.g, number of bp/ 10.5 for B-DNA)

W = Writhing number- number of turns the duplex axis makes around itselfAt the left W = 0 so L = T = 26

Proc Natl Acad Sci U S A. 1965 May; 53(5): 1104–1111. J Vinograd, J Lebowitz, R Radloff, R Watson, and P Laipis

<95% conversion

5% conversion>

of form I to II

polyomavirus DNA

by DNAse I

Proc Natl Acad Sci U S A. 1965 May; 53(5): 1104–1111. J Vinograd, J Lebowitz, R Radloff, R Watson, and P Laipis

Figure 4.18a: Closed covalent circle Figure 4.18b: Singly-nicked circle

Figure 4.20a: Linear double-stranded DNATropp: Adapted from Bert, J. M., et al. Biochemistry, Fifth Edition. W.H. Freeman and Company, 2002.

Figure 4.19: Simulated conformation of supercoiled DNA.

Tropp:

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http://mathworld.wolfram.com/Writhe.html

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Figure 4.20b: Relaxed circle

Tropp: Adapted from Bert, J. M., et al. Biochemistry, Fifth Edition. W.H. Freeman and Company, 2002.

Figure 4.20d: Unwound circle

Tropp: Adapted from Bert, J. M., et al. Biochemistry, Fifth Edition. W.H. Freeman and Company, 2002.

Figure 4.20e: Negative supercoil (right-handed)

Tropp: Adapted from Bert, J. M., et al. Biochemistry, Fifth Edition. W.H. Freeman and Company, 2002.

Figure 4.20c: Linear DNA unwound by two right-handed turns

Tropp: Adapted from Bert, J. M., et al. Biochemistry, Fifth Edition. W.H. Freeman and Company, 2002.

Figure 4.22b: An underwound covalent circle having only 32 turns of the helix.

Figure 4.22a: A nonsupercoiled or relaxed covalent circle having 36 turns

of the helix.

Figure 4.22c: The molecule in part (b) but with a writhing

number of 4 to eliminate the underwinding.

Tropp:

Figure 4.21b: Negative superhelix

Tropp: Adapted from Schvartzman, J. B., and Stasiak, A., EMBO Reports 5 (2004): 256-261.

Figure 4.21c: Positive superhelix

Bates & Maxwell, 2005

Bates & Maxwell, 2005

Bates & Maxwell, 2005

Bates & Maxwell, 2005

Bates & Maxwell, 2005

Bates & Maxwell, 2005

# Steven A. Wasserman and Nicholas R. Cozzarelli# Science, New Series, Vol. 232, No. 4753 (May 23, 1986), pp. 951-960

http://seemanlab4.chem.nyu.edu/rnatopo.html

Figure 4.23: Catalysis of transient breakage of DNA by DNA topoisomerases.

Tropp: Adapted from Wang, J. C., Nature Rev. Mol. Cell Biol. 3 (2002): 430-440.

Figure 4.24: Four types of topological coversions catalyzed by topoisomerase I

Tropp: Adapted from Kornberg, A., and Baker, T. A. DNA Replication, Second Edition. W.H. Freeman and Company, 1991.

Figure 4.25: Escherichia coli topoisomerase I, a type IA topoisomerase.

Tropp: Adapted from Champoux, J. J., Annu. Rev. Biochem. 70 (2001): 369-413.

Figure 4.26: Proposed mechanism of relaxation by E. coli topoisomerase I.

Tropp: Adapted from Champoux, J. J., Annu. Rev. Biochem. 70 (2001): 369-413.

Figure 4.26f: Proposed mechanism of relaxation by E. coli topoisomerase I.

TroppÑ Adapted from Champoux, J. J., Annu. Rev. Biochem. 70 (2001): 369-413.

Figure 4.27: Proposed mechanism for the catalytic cycle of DNA topoisomerase II.

TroppÑ Adapted from Larsen, A. K., et al., Pharmacol. Ther. 2 (2003): 167-181.

Bates & Maxwell, 2005

Bates & Maxwell, 2005

Bates & Maxwell, 2005