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DNA Topoisomerases02:02

DNA Topoisomerases

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Topoisomerases are enzymes that relax overwound DNA molecules during various cell processes, including DNA replication and transcription. These enzymes regulate positive and negative DNA supercoiling without changing the nucleotide sequence. DNA overwinding in a clockwise direction results in positively supercoiled DNA, whereas underwinding in a counterclockwise direction produces negatively supercoiled DNA.
Types and Mechanism of action
Topoisomerases are divided into two main types. ...
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Replication in Prokaryotes01:32

Replication in Prokaryotes

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DNA replication has three main steps: initiation, elongation, and termination. Replication in prokaryotes begins when initiator proteins bind to the single origin of replication (ori) on the cell's circular chromosome. Replication then proceeds around the entire circle of the chromosome in each direction from the two replication forks, resulting in two DNA molecules.
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Replication is coordinated and carried out by a host of specialized...
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Replication in Prokaryotes02:35

Replication in Prokaryotes

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Overview
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Single-Strand DNA Binding Proteins01:03

Single-Strand DNA Binding Proteins

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For successful DNA replication, the unwinding of double-stranded DNA must be accompanied by stabilization and protection of the separated single strands of the DNA. This crucial task is performed by single-strand DNA-binding (SSB) proteins. They bind to the DNA in a sequence-independent manner, which means that the nitrogenous bases of the DNA need not be present in a specific order for binding of SSB proteins to it. The binding of SSB proteins straightens single-stranded DNA (ssDNA) and makes...
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The DNA Replication Fork01:02

The DNA Replication Fork

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An organism’s genome needs to be duplicated in an efficient and error-free manner for its growth and survival. The replication fork is a Y-shaped active region where two strands of DNA are separated and replicated continuously. The coupling of DNA unzipping and complementary strand synthesis is a characteristic feature of a replication fork.   Organisms with small circular DNA, such as E. coli, often have a single origin of replication; therefore, they have only two replication...
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Mismatch Repair01:20

Mismatch Repair

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Organisms are capable of detecting and fixing nucleotide mismatches that occur during DNA replication. This sophisticated process requires identifying the new strand and replacing the erroneous bases with correct nucleotides. Mismatch repair is coordinated by many proteins in both prokaryotes and eukaryotes.
The Mutator Protein Family Plays a Key Role in DNA Mismatch Repair
The human genome has more than 3 billion base pairs of DNA per cell. Prior to cell division, that vast amount of genetic...
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Updated: Mar 13, 2026

Inducing a Site Specific Replication Blockage in E. coli Using a Fluorescent Repressor Operator System
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Inducing a Site Specific Replication Blockage in E. coli Using a Fluorescent Repressor Operator System

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Supercoiling Effects on Short-Range DNA Looping in E. coli.

Lauren S Mogil1,2, Nicole A Becker1, L James Maher1

  • 1Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First St. SW, Rochester, Minnesota 55905, United States of America.

Plos One
|October 27, 2016
PubMed
Summary

Negative supercoiling in Escherichia coli DNA promotes gene repression by facilitating small DNA-protein loops. This study investigated DNA looping in different bacterial strains to understand superhelicity

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Area of Science:

  • Molecular Biology
  • Genetics
  • Biophysics

Background:

  • DNA-protein loops are crucial for gene regulation.
  • The Escherichia coli lactose (lac) operon serves as a model system for studying DNA looping.
  • Bacterial DNA superhelicity, influenced by gyrase and topoisomerase, affects DNA structure and function.

Purpose of the Study:

  • To test the hypothesis that negative superhelical strain facilitates the formation of short-range repression loops in E. coli.
  • To quantitatively measure DNA looping under varying supercoiling conditions.
  • To investigate the role of superhelicity in the regulation of the lac operon.

Main Methods:

  • Quantitative measurement of DNA looping in three E. coli strains with differing supercoiling levels: wild type, gyrase mutant (gyrB226), and topoisomerase mutant (ΔtopA10).
  • Assaying repression of the endogenous lac operon.
  • Assessing repression of ten reporter constructs with DNA loop sizes ranging from 70-85 base pairs.

Main Results:

  • Data indicate that negative supercoiling facilitates gene repression by small DNA-protein loops in living bacteria.
  • Differences in DNA looping were observed across the tested E. coli strains, correlating with supercoiling levels.
  • Reporter construct repression varied, supporting the role of loop size and supercoiling in regulatory efficiency.

Conclusions:

  • Negative supercoiling is a significant factor in promoting gene repression mediated by short DNA-protein loops.
  • The findings support the hypothesis that bacterial superhelicity plays a direct role in gene regulation.
  • This study provides quantitative evidence for the interplay between DNA topology and gene expression in E. coli.