dna topology
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DNA TOPOLOGY. De Witt Sumners Department of Mathematics Florida State University Tallahassee, FL [email protected]. Pedagogical School: Knots & Links: From Theory to Application. Pedagogical School: Knots & Links: From Theory to Application. De Witt Sumners: Florida State University - PowerPoint PPT PresentationTRANSCRIPT
DNA TOPOLOGY
De Witt Sumners
Department of Mathematics
Florida State University
Tallahassee, FL
Pedagogical School: Knots & Links: From Theory to Application
Pedagogical School: Knots & Links: From Theory to Application
De Witt Sumners: Florida State University
Lectures on DNA Topology: Schedule
• Introduction to DNA Topology
Monday 09/05/11 10:40-12:40
• The Tangle Model for DNA Site-Specific Recombination
Thursday 12/05/11 10:40-12:40
• Random Knotting and Macromolecular Structure Friday 13/05/11 8:30-10:30
DNA Site-Specific Recombination
• Topological Enzymology
• Rational tangles and 4-plats
• The Tangle Model
• Analysis of Tn3 Resolvase Experiments
• Open tangle problem
Site-Specific RecombinationSite-Specific Recombination
RecombinaseRecombinase
Biology of Recombination
• Integration and excision of viral genome into and out of host genome
• DNA inversion--regulate gene expression
• Segregation of DNA progeny at cell division
• Plasmid copy number regulation
Topological Enzymology
Mathematics: Deduce enzyme binding and mechanism from
observed products
GEL ELECTROPHORESIS
Rec A Coating Enhances EM
RecA Coated DNA
DNA Trefoil Knot
Dean et al. J. Biol. Chem. 260(1985), 4795Dean et al. J. Biol. Chem. 260(1985), 4795
DNA (2,13) TORUS KNOT
Spengler et al. Cell 42(1985), 325Spengler et al. Cell 42(1985), 325
T4 TWIST KNOTS
Wasserman & Cozzarelli, J. Biol. Chem. Wasserman & Cozzarelli, J. Biol. Chem. 3030(1991), 20567 (1991), 20567
GIN KNOTS
Kanaar et al. CELL Kanaar et al. CELL 6262(1990), 553(1990), 553
SITE-SPECIFIC RECOMBINATION
Enzyme Bound to DNA
DIRECT vs INVERTED REPEATS
RESOLVASE SYNAPTIC COMPLEX
DNA 2-STRING TANGLES
2-STRING TANGLES
3 KINDS OF TANGLES
A A tangle tangle is a configuration of a pair of strands in a 3-ball. We consider all is a configuration of a pair of strands in a 3-ball. We consider alltangles to have the SAME boundary. There are 3 kinds of tangles:tangles to have the SAME boundary. There are 3 kinds of tangles:
RATIONAL TANGLES
RATIONAL TANGLE CLASSIFICATION
q/p = a2k + 1/(a2k-1 + 1(a 2k-2 +1/…)…)
Two tangles are equivalent iff q/p = q’/p’
J. Conway, Proc. Conf. Oxford 1967, Pergamon (1970), 329
TANGLE OPERATIONS
RATIONAL TANGLES AND 4-PLATS
4-PLATS (2-BRIDGE KNOTS AND LINKS)
4-PLATS
4-PLAT CLASSIFICATION
4-plat is b() where = 1/(c1+1/(c2+1/…)…)
b(b(’’as unoriented knots and links) iff ’and ’ (mod )
Schubert Math. Z. (1956)
TANGLE EQUATIONS
SOLVING TANGLE EQUATIONS
SOLVING TANGLE EQUATIONS
RECOMBINATION TANGLES
SUBSTRATE EQUATION
PRODUCT EQUATION
TANGLE MODEL SCHEMATIC
ITERATED RECOMBINATION
• DISTRIBUTIVE: multiple recombination events in multiple binding encounters between DNA circle and enzyme
• PROCESSIVE: multiple recombination events in a single binding encounter between DNA circle and enzyme
DISTRIBUTIVE RECOMBINATION
PROCESSIVE RECOMBINATION
RESOLVASE PRODUCTS
RESOLVASE MAJOR PRODUCT
• MAJOR PRODUCT is Hopf link [2], which does not react with Tn3
• Therefore, ANY iterated recombination must begin with 2 rounds of processive recombination
RESOLVASE MINOR PRODUCTS
• Figure 8 knot [1,1,2] (2 rounds of processive recombination)
• Whitehead link [1,1,1,1,1] (either 1 or 3 rounds of recombination)
• Composite link ( [2] # [1,1,2]--not the result of processive recombination, because assumption of tangle addition for iterated recombination implies prime products (Montesinos knots and links) for processive recombination
1st and 2nd ROUND PRODUC TS
RESOLVASE SYNAPTIC COMPLEX
Of = 0
THEOREM 1
PROOF OF THEOREM 1
• Analyze 2-fold branched cyclic cover T* of tangle T--T is rational iff T* = S1 x D2
• Use Cyclic Surgery Theorem to show T* is a Seifert Fiber Space (SFS)
• Use results of Dehn surgery on SFS to show T* is a solid torus--hence T is a rational tangle
• Use rational tangle calculus to solve tangle equations posed by resolvase experiments
Proof that Tangles are Rational
2 biological arguments
• DNA tangles are small, and have few crossings—so are rational by default
• DNA is on the outside of protein 3-ball, and any tangle on the surface of a 3-ball is rational
Proof that Tangles are Rational
THE MATHEMATICAL ARGUMENT
•The substrate (unknot) and the 1st round product (Hopf link) contain no local knots, so Ob, P and R are either prime or rational.
• If tangle A is prime, then ∂A* (a torus) is incompressible in A. If both A and B are prime tangles, then (AUB)* contains an incompressible torus, and cannot be a lens space.
Proof that Tangles are Rational
THE MATHEMATICAL ARGUMENT
N(Ob+P) = [1] so N(Ob+P)* = [1]* = S3
If Ob is prime, the P is rational, and Ob* is a knot complement in S3. One can similarly argue that R and (R+R) are rational; then looking at the 2-fold branched cyclic covers of the 1st 2 product equations, we have:
Proof that Tangles are RationalN(Ob+R) = [2] so N(Ob+R)* = [2]* = L(2,1)
N(Ob+R+R) = [2,1,1] so N(Ob+R+R)* = [2,1,1]* = L(5,3)
Cyclic surgery theorem says that since Dehn surgery on a knot complement produces two lens spaces whose fundamental group orders differ by more than one, then Ob* is a Seifert Fiber Space. Dehn surgery on a SFS cannot produce L(2,1) unless Ob* is a solid torus, hence Ob is a rational tangle.
N(Ob+R+R) = [] so N(Ob+R)* = [2]* = L(5,3)
3rd ROUND PRODUCT
THEOREM 2
4th ROUND PRODUCT
THEOREM 3
UTILITY OF TANGLE MODEL
• Precise mathematical language for recombination-allows hypothesis testing
• Calculates ALL alternative mechanisms for processive recombination
• Model can be used with incomplete experimental evidence (NO EM)--crossing # of products, questionable relationship between product and round of recombination
REFERENCES
JMB COVER
XER RECOMBINATION
Tangle analysis produces 3 solutions
Vazquez et al, J. Mol. Bio. 346 (2005), 493-504
TANGLES ARE PROJECTION DEPENDENT
P R
3 XER SOLUTIONS ARE SAME TANGLE, PROJECTED DIFFERENTY
UNSOLVED TANGLE PROBLEM
• Let A be a rational tangle; how many other rational tangles can be obtained from A by choosing another projection?
Thank You
•National Science Foundation
•Burroughs Wellcome Fund