Chapter III: DNA supercoiling

Supercoiling: coiling of the ds DNA helix upon itself (higher order coiling of the DNA helix). 3.1 3.2 3.3 3.4 Polyoma virus experiments Circular DNA; supercoiled DNA Biological consequences The concept of supercoiling: linking number and linking number difference Twist and writhe: Whites theorem

EM of supercoiled DNA D.Brutlag, Stanford University School of Medicine

3.5

Vinograd et al. (1965) PNAS USA 53: 1104-1111 March 16, 2010 Math 414-1 / 714-1 Lecture 13 1

3.2 DNA in nature is found in circular form (plasmids) or as structures topologically equivalent to circles

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Bates and Maxwel, DNA topology, 2005 Oxford University Press 2

3.3. Supercoiling naturally appears in many biological processes such as DNA replication

Bates and Maxwel, DNA topology, 2005 Oxford University Press March 16, 2010 Math 414-1 / 714-1 Lecture 13 3

Supercoiling is observed in chromosomes and is essential for cell viability

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Biological roles of supercoiling

DNA compaction Helps the opening of the double helix during DNA replication and transcription Site-specific recombination

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Supercoiling is a wellness sensor for the cell

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Supercoiling has broad implications in replication & transcription

Replicated domain Replicating domain

Prereplicated domain

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Who takes care of Supercoiling in the cell? Enzymes; type I and type II topoisomerases

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Figure courtesy of J. Roca

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Supercoiling in agarose gels

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3.4 How can we quantify supercoiling?

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How can we quantify supercoiling?

Intuitively: Supercoiling happens due to an excess of the number of times that the two DNA backbones coil around each other. Note to the students: the following slides are vague and should be complemented with your lecture notes
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Consider a linear fragment of DNA: N=Number of base-pairs of the fragment h=Number of base pairs/helical turn Lk0=N/h~ #helical turn Consider a planar circular molecule : Lkm= Closest integer to N/h

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How can we compute the linking number of any DNA molecule?

General definition of Linking Number

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+1

+1

-1 +1

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+1

+1 c1

-1 +1 c2

Lk=1/2( sign(ci))
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Supercoiling
Linking number difference: Lk=Lk- Lk0 Why Lk0 instead of Lkm?

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 Supercoiling density: = Lk/ Lk0 Example: In E. coli = -0.06

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Geometrical parameters
Twist: Measures the coiling of the two individual strands. Tw0=N/h for open circular not necessarily planar due to intrinsic curvature. Writhe: Describes how the helix axis coils in space. Wr0=due to intrinsic curvature
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Calugareanu-White-Fuller Theorem

Lk=Tw+Wr
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Computer simulations of DNA supercoiling: MD and Monte-Carlo

[Jian et al., 1998; Huang et al., 2001]

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Supercoiling is a wellness sensor for the cell

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Chapter IV: The mathematics of DNA supercoiling

Experimental evidence for supercoiling and basic definitions. Linking number, twist and writhe Whites theorem Modern experimental techniques to study supercoiling and applications

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