DNA TOPOLOGY. DNA supercoiling DNA topoisomerases. Topo II DNA preferences DNA knots. Topo II mechanics DNA relaxation in vivo INTRODUCTION TO
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1 DNA TOPOLOGY INTRODUCTION TO DNA supercoiling DNA topoisomerases Lecture 1 KEY EXPERIMENTS ON Topo II DNA preferences DNA knots Lecture 2 Topo II mechanics DNA relaxation in vivo Lecture 3
2 The Problem of Unwinding the Long Double Helix ( )
3 Discovery of Circular DNA and Supercoiled DNA Molecules ( Vinograd, 1960s ) Polyoma viral DNA sediments into 2 forms: form I compact & hard to denature form II less compact & denaturable Circular ( no free ends ) Linear ( free ends ) Electron Microscopy: Both forms are circular!
4 form I form II nick
5 Measure of DNA supercoiling : Linking Number (Lk) Lk = links between 2 closed curves in space: Dextro Lk = + 4 Lk o = Lk of relaxed DNA ( minimal torsional energy ) = N / h N = number of base pairs h = helical repeat : average bp / turn ( h ~ 10.5 at 0.2M NaCl, ph 7, 37 C ) When DNA is supercoiled ( has torsional energy ) : Lk = Lk - Lk 0 Specific Linking Difference or Supercoiling Density : = Lk / Lk 0
6 Lk 0 = Lower energy Lk in a given conditions Since N / h may not be an Integer Then, Lk m = Close Integer to LK o Lk 0 = 4 Lk m = Lk 0 = 3.5 Lk m = 3 o 4 Thermal fluctuation of DNA creates a normal distribution of Lk values Calculate the Free Energy of DNA Supercoiling G K ( Lk) 2 Calculate the Helical repeat of DNA in solution h 10.5 Agarose gel electrophoresis
7 Torsional energy ( Lk) generates topoisomers of different shape
8 DNA deformations driven by torsional energy ( Lk) Wr Tw ( Twist ) Strand turnnig around the DNA axis Tw Wr ( Writhe ) Deviations from planarity of the DNA axis Topology Geometry Lk = Tw + Wr James White (1969)
9 Interconversion between Tw and Wr Tw >>> Wr Being Lk constant : Tw = - Wr Tw <<< Wr GLOBAL Tw and Wr = Local Tw and Wr
10 TOPOLOGY Lk = Tw + Wr TOPOGRAPHY Strand Break & Passage TOPOISOMERASES DNA PHYSICS - Bending rigidity - Torsional rigidity - Efective diameter B-DNA TRANSITIONS - Cruciforms, Z-DNA, H-DNA DNA INTERACTIONS - Intercalators - Grove binders - Benders - Unwinders - Trackers -...
11 DNA behaves like a stiff rod : --> tendency to maximize base stacking --> mutual interphosphate repulsion -- Bend & twist rigidity -- Intrinsic bend / twist Sequence x Thermal motion -- Induced bend / twist
12 Bending Rigidity : Persistence length (P) is a measure of resistance to lateral bending For B-DNA, P ~ 50 nm (150 bp) Torsional Rigidity : The distance between two DNA sites to become insensitive to torsional phasing is ~ 2000 bp Effective DNA Diameter : Contributions of water ions to charge repulsion between duplexes
13 PHYSICAL DNA Lk = Tw + Wr Natural partition by torsional energy ~ 30% Tw ~ 70% Wr Solenoid vs Plectoneme folding
14 TOPOLOGY Lk = Tw + Wr GEOMETRY Strand Break & Passage TOPOISOMERASES DNA PHYSICS - Bending rigidity - Torsional rigidity - Efective diameter B-DNA TRANSITIONS - Cruciforms, Z-DNA, H-DNA DNA INTERACTIONS - Intercalators - Grove binders - Benders - Unwinding - Tracking -...
15 B-DNA TRANSITIONS generated by torsional energy ( < 0 ) Z-DNA Cruciform H-DNA Tw Tw Wr
16 TOPOLOGY Lk = Tw + Wr GEOMETRY Strand Break & Passage TOPOISOMERASES DNA PHYSICS - Bending rigidity - Torsional rigidity - Efective diameter B-DNA TRANSITIONS - Cruciforms, Z-DNA, H-DNA DNA INTERACTIONS - Intercalators - Grove binders - Benders - Unwinders - Trackers -...
17 Effect of DNA intercalators Intercalators reduce Tw, therefore increase Wr in closed-circular molecules
18 - + Wr < 0 Wr ~ 0 Wr > 0
19 Intercalators Tw Wr Grove binder Tw Wr
20 + intercalator R ( + ) ( - ) R JRB
21 B-DNA transitions revealed by 2D electrophoresis Altered migration in the FIRST dimension : Torsional energy drives a B-DNA transition Normal migration in the SECOND dimension : Intercalator stabilizes torsional energy & the transition reverts Z-DNA H-DNA Cruciform
22 TOPOLOGY Lk = Tw + Wr GEOMETRY Strand Break & Passage TOPOISOMERASES DNA PHYSICS - Bending rigidity - Torsional rigidity - Efective diameter B-DNA TRANSITIONS - Cruciforms, Z-DNA, H-DNA DNA INTERACTIONS - Intercalators - Grove binders - Benders - Unwinders - Trackers -...
23 NUCLEOSOMAL DNA TOPOLOGY and the Linking Number Paradox Nucleosome ~ 1.8 levo DNA turns ( Wr ~ -1.8 ) Each nucleosome estabilises Lk ~ 1.0 Then, DNA must be overtwisted ( Tw ~ ) such that average h ~ 10.0 However, DNAse I, Hydroxy radical AA/TT periodics X-tall structures h ~ 10.2
24 NUCLEOSOMAL DNA TOPOLOGY and the Linking Number Paradox Solutions : Geometry of linker regions h is not uniform and fluctuates Average Wr ~ -1.5 (-) (+) open
25 Dynamics of site juxtaposition in supercoiled DNA Huang, Schlick, and Vologodskii (2005) Supercoiling does not correspondingly increase the rate of juxtaposition between any sites
26 Random walks Strong interactions Bio - tunning Weak & Transient Interactions Directed walks
27 TOPOLOGY Lk = Tw + Wr GEOMETRY Strand Break & Passage TOPOISOMERASES DNA PHYSICS - Bending rigidity - Torsional rigidity - Efective diameter B-DNA TRANSITIONS - Cruciforms, Z-DNA, H-DNA DNA INTERACTIONS - Intercalators - Grove binders - Benders - Unwinders - Trackers -...
28
29 DNA TOPOISOMERASES 1. Break and rejoin DNA strands by means of a trans-estherification reaction, during which a covalent phospho-tyrosyl intermediate is form. 2. Allow the passage of another strand, or strands, of DNA across the transient break.
30 DNA TOPOISOMERASE FAMILIES Type-1A Type-1B Type-2
31 TOPOISOMERASES Type 1A Type 1B Type 2A Type 2B Gene (Protein) Gene (Protein) Gene (Protein) Gene (Protein) H. sapiens TOP3a TOP3b (Topoisomerase III ) (Topoisomerase III ) TOP1 (Topoisomerase I) TOP2a TOP2b (Topoisomerase II ) (Topoisomerase II ) D. melanogaster TOP3a TOP3b (Topoisomerase III ) (Topoisomerase III ) TOP1 (Topoisomerase I) TOP2 (Topoisomerase II) EUKARYA C. elegans TOP3a TOP3b (Topoisomerase III ) (Topoisomerase III ) TOP1 (Topoisomerase I) TOP2 (Topoisomerase II) S. pombe TOP3 (Topoisomerase III) TOP1 (Topoisomerase I) TOP2 (Topoisomerase II) S. cerevisiae TOP3 (Topoisomerase III) TOP1 (Topoisomerase I) TOP2 (Topoisomerase II) A. thaliana TOP3 (Topoisomerase III) TOP1 (Topoisomerase I) TOP2 (Topoisomerase II) E. coli TopA TopB (Topoisomerase I) (Topoisomerase III) GyrA + GyrB ParC + ParE (Gyrase) (Topoisomerase IV) BACTERIA TopA (Topoisomerase I) D. radiodurans TopIB (Topoisomerase I) GyrA + GyrB ParC + ParE (Gyrase) (Topoisomerase IV) H. pylori TopA TopB (Topoisomerase I) (Topoisomerase III) GyrA + GyrB (Gyrase) ARCHEA TopA (Topoisomerase I) TopRG (Gyrase Reverse) (( Topoisomerase V )) GyrA + GyrB (Gyrase like) TopVIA + TopVIB (Topoisomerase VI) VIRUS Phage T4 Poxvirus TOP1 (Topoisomerase I) Genes ( ) (Topoisomerase II)
32 Type-1B Topoisomerases Topoisomerase I (H. sapiens ) (S. cerevisiae) N Y C kda Topoisomerase I (vaccinia virus) N C 36 kda Tyrosin Recombinases Y
33 Type-1B Mechanism No ATP required Reactions
34 Type - 2 Topoisomerases Topoisomerase II (S. cerevisiae,..,..,..) N ATP (Top2) Y dim 170 kda x 2 C Topoisomerase IV (E. coli,..,..,.. ) N (ParE) (ParC) C Gyrase (E. coli,..,..) N (GyrB) (GyrA) C ATP Y
35 Type-2 Mechanism Reactions
36 GYRASE : A type - 2 topoisomerase that reduces Lk Reactions (+) (-)
37 Type-1A Topoisomerases Topoisomerase I (E. coli) N Y 97 kda C Topoisomerase III (E. coli) Topoisomerase III (S. cerevisiae) Reverse Gyrase (M. janaschii) H e l i c a s e Y
38 Mechanism Type 1A No ATP required Reactions ssdna
39 Reverse GYRASE : A type-1a topoisomerase that increases Lk Topoisomerase + Helicase (ATP)
40
41 in vivo ROLES OF TOPOISOMERASES
42 DNA transcription ( - ) ( + ) Topo I Topo IV E. Coli ~ ( chromatin? ) Gyrase
43 DNA transcription ( - ) ( + ) Topo I S. cerevisiae ~ ( chromatin ) Topo II
44
45 Fork Collision Catenates of sister duplexes
46 Topo IV Gyrase
47 Topo II Topo I
48
49 Relaxation of Supercoiled DNA in the Chromatin Context Figure adapted from Bancaud et al (2006)
50
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