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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. Type I...

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...

Single-Strand DNA Binding Proteins

Single-Strand DNA Binding Proteins

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...

Spin–Spin Coupling: Two-Bond Coupling (Geminal Coupling)

Spin–Spin Coupling: Two-Bond Coupling (Geminal Coupling)

Two NMR-active nuclei bonded to a central atom can be involved in geminal or two-bond coupling. Geminal coupling is commonly seen between diastereotopic protons in chiral molecules and unsymmetrical alkenes, among others.
The central atom need not be NMR-active because its electrons are affected by the electron polarization of the spin-active atoms. However, spin information is transmitted less effectively than in one-bond coupling, and 2J values are usually weaker than 1J values. The energy of...

Spin–Spin Coupling: One-Bond Coupling

Spin–Spin Coupling: One-Bond Coupling

Coupling interactions are strongest between NMR-active nuclei bonded to each other, where spin information can be transmitted directly through the pair of bonding electrons. While nuclei polarize their electrons to the opposite spins, the bonding electron pair has opposite spins. Configurations with antiparallel nuclear spins are expected to be lower in energy. When coupling makes antiparallel states more favorable, J is considered to have a positive value. The one-bond coupling constant, 1J,...

Spin–Spin Coupling: Three-Bond Coupling (Vicinal Coupling)

Spin–Spin Coupling: Three-Bond Coupling (Vicinal Coupling)

Vicinal or three-bond coupling is commonly observed between protons attached to adjacent carbons. Here, nuclear spin information is primarily transferred via electron spin interactions between adjacent C‑H bond orbitals. This generally favors the antiparallel arrangement of spins, so 3J values are usually positive.
The extent of coupling depends on the C‑C bond length, the two H‑C‑C angles, any electron-withdrawing substituents, and the dihedral angle between the involved orbitals. The...

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Related Experiment Video

Updated: Jun 22, 2026

Magnetic Tweezers for the Measurement of Twist and Torque

Magnetic Tweezers for the Measurement of Twist and Torque

Published on: May 19, 2014

Twist-stretch coupling and phase transition during DNA supercoiling.

Maxim Y Sheinin¹, Michelle D Wang

¹Department of Physics - LASSP, Cornell University, Ithaca, NY 14853, USA.

Physical Chemistry Chemical Physics : PCCP

|June 10, 2009

Summary

The extension maximum of supercoiled DNA does not signal a phase transition. Torque plateau detection and a new theory reveal DNA twist-stretch coupling and bending fluctuations influence DNA extension.

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Last Updated: Jun 22, 2026

Magnetic Tweezers for the Measurement of Twist and Torque

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Area of Science:

Biophysics
Molecular Biology
Polymer Physics

Background:

Supercoiling of DNA induces structural transitions.
Previous studies linked DNA extension maximum to B- to scP-DNA phase transition.

Purpose of the Study:

To investigate the relationship between DNA extension maximum and phase transitions.
To develop a more accurate model for DNA extension under supercoiling.
To determine the contribution of twist-stretch coupling and bending fluctuations.

Main Methods:

Utilized an angular optical trap to measure torque and extension of single DNA molecules.
Applied a theoretical model incorporating twist-stretch coupling and bending fluctuations.
Analyzed DNA extension curves under positive supercoiling.

Main Results:

The extension maximum does not coincide with the onset of the B- to scP-DNA phase transition.
A torque plateau, observed via angular optical trap, directly evidences the phase transition.
A new theory accurately explains DNA extension by including twist-stretch coupling and bending fluctuations.
The twist-stretch coupling modulus may be underestimated in previous studies.

Conclusions:

Torque detection is crucial for correctly identifying DNA phase transitions.
Twist-stretch coupling and bending fluctuations significantly impact DNA extension.
The developed theory offers a more accurate understanding of DNA mechanics under supercoiling.