Chapter 24, Problem 8P

(a)

Summary Introduction

To determine: The Lk of a 5000 bp circular duplex DNA molecule with a nick in one strand.

Introduction:

Linking number (Lk) is a topological characteristic of a DNA molecule. It determines the numbers of helical turns within a closed-circular DNA molecule without any supercoiling. It does not vary whether the DNA is deformed or bent. It causes both DNA strands to remain intact.

(b)

Summary Introduction

To determine: The Lk of a $5,000\text{ bp}$ circular DNA duplex molecule when the nick is sealed (relaxed).

Introduction:

Linking number does not vary, as long as both strands of DNA molecule remain intact. It defines the number of times in which each strand is underwinds around each other. During the relaxed form, the linkage number (Lk) is equal to the number of turns found in the DNA double helix.

(c)

Summary Introduction

To determine: The way through which Lk of a 5’000 bp circular DNA duplex when it is in relaxed form, would be affected by the action of a single molecule of E. coli topoisomerase I.

Introduction:

Topoisomers are formed when two forms of a given circular DNA molecule differ only in a topological characteristic. Topoisomerase enzymes can increase or reduce the numbers of DNA underwinding. They can also influence the topological characteristics.

(d)

Summary Introduction

To determine: The Lk of a 5,000 bp circular DNA duplex molecule after eight enzymatic turnovers by a single molecule of DNA gyrase in the presence of ATP.

Introduction:

DNA topoisomerase causes the reduction in topological stress that is formed during the strand separation within the DNA by helicases.

(e)

Summary Introduction

To determine: Lk of a 5000 bp circular DNA duplex molecule be after four enzymatic turnovers by a single molecule of bacterial type I topoisomerase.

Introduction:

Type I topoisomerase break one strand of double helical DNA molecule. The unbroken strand is further transferred to the single stranded breaks, and resealed.

(f)

Summary Introduction

To determine: The Lk of a 5000 bp circular DNA duplex molecule be after binding of one nucleosome core.

Introduction:

When a protein complex is associated for forming a nucleosome, the linking number does not change because the strand of DNA does not break and rejoin.