Related Experiment Video
Updated: Feb 11, 2026
05:37
Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes
Published on: April 4, 2025
1.3K
Dynamic coupling between conformations and nucleotide states in DNA gyrase
Aakash Basu1,2,3, Matthew Hobson3,4, Paul Lebel1,2,5
1Department of Applied Physics, Stanford University, Stanford, CA, USA.
Nature Chemical Biology
|April 18, 2018
Summary
Bacterial gyrase uses ATP to wrap DNA, with ADP exchange driving the key remodeling step. ATP hydrolysis then facilitates DNA passage and enzyme resetting, linking gene expression to cellular energy.
Area of Science:
- Molecular biology
- Biochemistry
- Structural biology
Background:
- DNA gyrase is a crucial bacterial enzyme that regulates DNA topology through supercoiling.
- Understanding its mechanism requires mapping structural changes to the ATP nucleotide cycle.
Purpose of the Study:
- To elucidate the coupling mechanisms between DNA manipulation and ATP turnover in E. coli gyrase.
- To investigate the roles of ATP binding, hydrolysis, and product release in gyrase function.
Main Methods:
- Single-molecule tracking of DNA rotation and contraction.
- Analysis of gyrase activity under varied nucleotide conditions (ATP, ADP).
Main Results:
- ATP binding and ADP release are essential for the rate-limiting DNA wrapping transition.
- ATP hydrolysis accelerates DNA strand passage and enzyme resetting.
- Gyrase activity is modulated by nucleotide availability, suggesting a link to cellular energy levels.
Conclusions:
- Gyrase coordinates DNA rearrangements with its ATP-driven protein gate dynamics.
- The enzyme minimizes futile ATP hydrolysis cycles.
- Gyrase activity regulation may link gene expression to cellular metabolism.
Related Concept Videos
01:20Conformity
48.2K
Conformity is the change in a person’s behavior to go along with the group, even if that person does not agree with the group.
48.2K
01:08Nucleotide Excision Repair
40.9K
Overview
40.9K
01:38Nucleotide Excision Repair
5.3K
DNA Distortion and Damage
Cells are regularly exposed to mutagens—factors in the environment that can damage DNA and generate mutations. UV radiation is one of the most common mutagens and is estimated to introduce a significant number of changes in DNA. These include bends or kinks in the structure, which can block DNA replication or transcription. If these errors are not fixed, the damage can cause mutations, which in turn can result in cancer or disease depending on which sequences are...
Cells are regularly exposed to mutagens—factors in the environment that can damage DNA and generate mutations. UV radiation is one of the most common mutagens and is estimated to introduce a significant number of changes in DNA. These include bends or kinks in the structure, which can block DNA replication or transcription. If these errors are not fixed, the damage can cause mutations, which in turn can result in cancer or disease depending on which sequences are...
5.3K
00:55DNA Helicases
24.2K
DNA unwinding helicase enzymes are a type of motor protein. Motor proteins can translocate along filaments or polymers using energy generated from ATP hydrolysis. Helicases are involved in all the important cellular processes where DNA unwinding is required, such as DNA replication, repair, recombination, and transcription. They are present in all living organisms, but vary in their structure, function, and mechanism of action. For example, in prokaryotes, DnaB helicase binds and translocates...
24.2K
02:40DNA Replication
60.2K
DNA replication involves the separation of the two strands of the double helix, with each strand serving as a template from which the new complementary strand is copied. After replication, each double-stranded DNA includes one parental or “old” strand and one “new” strand. This is known as semiconservative replication. The resulting DNA molecules have the same sequence and are divided equally into the two daughter cells.
Replication in Prokaryotes
DNA replication...
Replication in Prokaryotes
DNA replication...
60.2K
02:20Conformations of Butane
18.3K
Unlike ethane and propane that have only two major conformations, butane has more than two conformers. The staggered form of butane in which the bulky methyl groups on the two carbons are placed on opposite sides, that is, at a dihedral angle of 180°, is the lowest energy, most stable form — called the anti conformer. This conformation is stabilized due to the absence of steric repulsion between the largely spaced out methyl groups. The other two staggered conformations are...
18.3K