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DNA Topoisomerases

DNA Topoisomerases

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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Molecular Shape and Polarity

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Polarity of the Cytoskeleton

The intrinsic polarity of cells can be primarily attributed to two factors- i) the asymmetric accumulation of mobile components such are regulatory molecules and subcellular components across the cell and ii) the orientation of polar cytoskeletal filaments that make up the cytoskeletal networks, specifically microfilaments, and microtubules arranged along the axis of polarity. Interactions between the cytoskeletal filaments are crucial for the establishment and maintenance of the polar nature...

DNA Helicases

DNA Helicases

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...

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Related Experiment Video

Updated: Sep 9, 2025

Stable DNA Motifs, 1D and 2D Nanostructures Constructed from Small Circular DNA Molecules

Stable DNA Motifs, 1D and 2D Nanostructures Constructed from Small Circular DNA Molecules

Published on: April 12, 2019

Visualizing Poloidal Orientation in DNA Minicircles.

Tony Lemos¹, Harold D Kim¹

¹School of Physics, Georgia Institute of Technology, Atlanta, GA 30332-0430, USA.

Biorxiv : the Preprint Server for Biology

|September 2, 2025

Summary

This summary is machine-generated.

Researchers experimentally confirmed DNA minicircles adopt specific inside-out orientations, known as poloidal orientation. This finding, visualized using atomic force microscopy, validates theoretical predictions of DNA minicircle dynamics.

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Last Updated: Sep 9, 2025

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Visualization of miniSOG Tagged DNA Repair Proteins in Combination with Electron Spectroscopic Imaging ESI

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Published on: September 24, 2015

Area of Science:

Molecular Biology
Biophysics
Structural Biology

Background:

DNA minicircles form from short double-stranded DNA (dsDNA) ligated end-to-end.
Theoretical models predict sequence-dependent, nonuniform bending energetics cause DNA minicircles to adopt a preferred poloidal orientation.
Experimental evidence for this predicted DNA minicircle orientation has been lacking.

Purpose of the Study:

To experimentally visualize and confirm the poloidal orientation of DNA minicircles.
To provide empirical evidence supporting theoretical predictions of DNA minicircle structure.
To investigate sequence-specific DNA minicircle conformations.

Main Methods:

Development of a single-molecule approach using atomic force microscopy (AFM).
Construction of DNA minicircles with a single biotin marker at varying positions.
Imaging biotin-bound NeutrAvidin relative to the DNA minicircle to determine orientation.
Utilizing coarse-grained simulations to model and compare with experimental results.

Main Results:

Distinct poloidal orientations were observed for two different DNA sequences, evidenced by phase shifts in NeutrAvidin positions.
AFM results were consistent with coarse-grained simulations, which showed narrowly distributed poloidal orientations.
Experimental data confirmed the predicted sequence-dependent preferred orientations of DNA minicircles.

Conclusions:

The study provides the first experimental confirmation of preferred poloidal orientations in DNA minicircles.
Findings offer valuable insights into the intrinsic dynamics and conformational preferences of circular DNA.
This work bridges the gap between theoretical predictions and experimental observation in DNA structural biology.