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Biochemistry 441 Lecture 3 Ted Young Feb. 11, 2000

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Biochemistry 441 Lecture 3 Ted Young Feb. 11, 2000

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    3. Biochemistry 441 Lecture 5 Ted Young January 12, 2011 Topics for today: DNA tertiary structure and DNA topoisomerases

    4. 4 Comparison of open and supercoiled DNA molecules by electron microscopy

    5. 5 DNA topology The same double-stranded DNA molecule can have different conformations

    6. 6 Different topoisomers of circular DNA can be separated by electrophoresis

    7. 7 Detecting different DNA topoisomers by intercalation of dye molecules

    8. 8 L, T, and W characterize superhelical DNA L= linking number = number of times one strand wraps around the other. It is an integer for a closed circular DNA. T = twists/turns in the DNA (=number of bp/10.4); positive for right-handed DNA W = writhes =number of turns of the helix around the superhelical axis

    9. 9 Naturally occurring superhelical DNA is underwound

    10. 10 Topoisomerases change the linking number of superhelical DNA

    11. 11 Model of DNA topo I (Ec N-terminus)

    12. 12 Type I topoisomerases (nicking-closing enzymes)

    13. 13 Topo I-step 1

    14. 14 Topo I-step 2

    15. 15 Topo I-step 3

    16. 16 Structure of the Topo II DNA binding and cleavage core bound to DNA Berger et al 2007 Nature 450 1201 PDB 3ILW

    17. 17 Change in topoII conformation upon DNA binding

    18. 18 DNA bending by topo II

    19. 19 Mg++ at the active site

    20. 20 Two-gate model for DNA transport in type IIA topoisomerases

    21. 21 Prokaryotic Topoisomerase II is a DNA gyrase In the presence of ATP DNA gyrase can create supercoils; it can relax supercoils in the absence of ATP

    22. 22 Summary DNA exists in different topological forms in vivo and in vitro DNA topoisomerases catalyze the interconversion of DNA forms Negative superhelicity (underwinding) helps proteins bind DNA by favoring unwinding of the helix.

    23. 23 Proposed mechanism of topo II

    24. 24 The DNA substrate bound by the enzyme in this study

    25. 25 Overview of the DNA sequence

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