1. Lehninger Principles of Biochemistry 6th Ed
24.2 DNA supercoling
Most cellular DNA is underwound
DNA Underwinding is defined by topological linking number
Topoisomerase catalyze changes in the linking number of DNA
DNA compaction requires a special form of supercoiling
Lehninger Principles of Biochemistry 6th Ed

2. Lehninger Principles of Biochemistry 6th Ed
Summary 24.2 DNA Supercioling
DNA Supercoiling
>Most cellular DNA are supercoiled. Underwinding decreases the total number of helical turns in the DNA relative to the released, B form. To maintain an underwound state, DNA must be either a closed circle or bound to protein. Underwinding is quantified by a topological parameter called linking number, Lk
>Underwinding is measured in terms of specific linking difference. σ (also called superhelical density), which is (Lk-Lk0/Lk0). For cellular DNAs, σ is typically to -0.07, which means that approximately 5% to 7% of the helical turns in the DNA have been removed. DNA underwinding facilitate strand separation by enzymes of DNA metabolism
>DNAs that differ only in linking number are called topoisomers. Enzymes that underwind and/or relax DNA, the topoisomerase catalyze changes in liking number. The two classes of topoisomerase type I and type II, change Lk in increments of 1 or 2, respectively, per catalytic event.
Lehninger Principles of Biochemistry 6th Ed

3. Lehninger Principles of Biochemistry 6th Ed
24.2 DNA Supercoiling
“Supercoil”= coiling of a coil,
1.DNA compaction involved some form of supercoiling
2.Less predictable is that replication and transcription of DNA (require a separation of DNA strands) also affect and are affected by supercoiling. Fig 24-12
Most cellular DNA is underwound
Plasmids and small circular DNAs with no breaks in either strand, they are referred to as closed circular DNAs (closely to the B-form structure)
purified closed-circular DNA is rarely relaxed, regardless of its biological origin. Furthermore, DNAs derived from a given cellular source have a characteristic degree of supercoiling. DNA structure is therefore strained in a manner that is regulated by the cell to induce the supercoiling
Lehninger Principles of Biochemistry 6th Ed

4. Lehninger Principles of Biochemistry 6th Ed
Every cell actively underwinds its DNA with the aid of enzymatic processes.
Cells maintain DNA in an underwound state
1) to facilitate its compaction by coiling.
2) also important to enzymes of DNA metabolism that must bring about strand separation as part of their function.
-The underwound state can be maintained only if the Dna is a closed circle or if it is bound and stabilized by proteins so that the strands are not free to rotate about each other.
-In a closed-circular DNA molecule, however, the number of helical turns cannot be changed without at least transiently breaking one of the DNA strands.
-Thus, the number of helical turns in a DNA molecule provides a “precise description of supercoiling”
Lehninger Principles of Biochemistry 6th Ed

5. DNA Underwinding is defined by topological linking number
FIGURE Linking number, Lk. Here, as usual, each blue ribbon represents one strand of a double-stranded DNA molecule. For the molecule in (a), Lk = 1. For the molecule in (b), Lk = 6. One of the strands in (b) is kept untwisted for illustrative purposes, to define the border of an imaginary surface (shaded blue). The number of times the twisting strand penetrates this surface provides a rigorous definition of linking number
Specific linking difference (σ) or superhelical density
= measure of the no of turns removed relative to the no present in relaxed DNA
σ = ΔLk/Lk0 =-2/200
σ = -0.01
=> 1% of the helical turns present in the DNA (in its B forms) have been removed.
The degree of underwinding in cellular DNAs generally falls in the range of 5-7%; that is σ = ~ -0.07
The supercoiling induced by underwinding is therefor defined as negative supercoiling

6. Lehninger Principles of Biochemistry 6th Ed
Topoisomerase catalyze changes in the linking number of DNA
-DNA supercoiling is a precisely regulated process that influences many aspects of DNA metabolism. Every cell has enzymes with the sole function of underwinding and/or relaxing DNA.
-The enzymes that increase or decrease the extent of DNA underwinding are topoisomerase; the property of DNA that they change is the linking number.
These enzymes play an especially important role in processes such as replication and packaging.(figure visualization of topoisomers)
->Type I topoisomerase act by transiently breaking one of the two DNA strands, passing the unbroken strand through the break and rejoins the broken ends; they change Lk in increments of 1
Type II topoisomerases break both DNA strands and change Lk in increments of 2
-> The degree of supercoiling of bacterial DNA is maintained by regulation of the net activity of topoisomerease I and II
-Topoisomerases play a critical role in every aspect of DNA metabolism.
As a consequence, they are important drug targets for the treatment of bacterial infections and cancer (Box 24-1)
Lehninger Principles of Biochemistry 6th Ed

7. Lehninger Principles of Biochemistry 6th Ed
BOX 24-1
Curing Disease by inhibiting Topoisomerases
The topological state of cellular DNA is intimately connected with its function. Without topoisomerases, cells CANNOT replicate or package their DNA, or express their genes- and they die. Inhibitors of topoisomerases have therefore become important pharmaceutical agents, targeted at infectious agents and malignant cells
Bacterial topoisomerase inhibitor: coumarins and quinolone antibiotics
Human topoisomerase inhibitor: topoisomerase is higher in malignant cells
1) type I topo- inhibitor =>camptothecin, irinotecan, topotecan
2) type II=>doxorubicin, etoposide, ellipticine
increase the levels of DNA damage in the targeted, rapidly growing tumor cells. However, noncancerous tissues can also be affected, leading to a more general toxicity and unpleasant side effects
Lehninger Principles of Biochemistry 6th Ed

8. Lehninger Principles of Biochemistry 6th Ed
Summary 24.2 DNA Supercioling
DNA Supercoiling
>Most cellular DNA are supercoiled. Underwinding decreases the total number of helical turns in the DNA relative to the released, B form. To maintain an underwound state, DNA must be either a closed circle or bound to protein. Underwinding is quantified by a topological parameter called linking number, Lk
>Underwinding is measured in terms of specific linking difference. σ (also called superhelical density), which is (Lk-Lk0/Lk0). For cellular DNAs, σ is typically to -0.07, which means that approximately 5% to 7% of the helical turns in the DNA have been removed. DNA underwinding facilitate strand separation by enzymes of DNA metabolism
>DNAs that differ only in linking number are called topoisomers. Enzymes that underwind and/or relax DNA, the topoisomerase catalyze changes in liking number. The two classes of topoisomerase type I and type II, change Lk in increments of 1 or 2, respectively, per catalytic event.
Lehninger Principles of Biochemistry 6th Ed