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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 Isolation

DNA Isolation

DNA isolation protocols can be fast and straightforward or complex and time-consuming depending on the type and quality of DNA required for further processing. For example, plasmid DNA extraction is a bit more complicated than genomic DNA extraction because of the need for an appropriate lysis method to separate plasmid DNA from gDNA during isolation. However, for specific applications, such as long-range DNA sequencing that require a good yield of high- quality DNA samples, we need to follow...

DNA Isolation

DNA Isolation

DNA from cells is required for many biotechnology and research applications, such as molecular cloning. To remove and purify DNA from cells, researchers use various methods of DNA extraction. While the specifics of different protocols may vary, some general concepts underlie the process of DNA extraction.

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...

Restarting Stalled Replication Forks

Restarting Stalled Replication Forks

DNA replication is initiated at sites containing predefined DNA sequences known as origins of replication. DNA is unwound at these sites by the minichromosome maintenance (MCM) helicase and other factors such as Cdc45 and the associated GINS complex.The unwound single strands are protected by replication protein A (RPA) until DNA polymerase starts synthesizing DNA at the 5’ end of the strand in the same direction as the replication fork. To prevent the replication fork from falling apart, a...

Condensins

Condensins

Condensins are large protein complexes that use ATP to fuel the assembly of chromosomes during mitosis. They transform the tangled, shapeless mass of post-interphase DNA into individualized chromosomes by compacting, organizing, and segregating chromosomal DNA.
The plant and animal cells contain two types of condensin complexes—condensin I and condensin II. Both complexes have five subunits: two SMC (Structural Maintenance of Chromosomes) subunits, a kleisin subunit, and two HEAT-repeat...

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Related Experiment Video

Updated: Jun 18, 2026

Iterative Optimization of DNA Duplexes for Crystallization of SeqA-DNA Complexes

Iterative Optimization of DNA Duplexes for Crystallization of SeqA-DNA Complexes

Published on: November 1, 2012

Cyclodextrins in DNA decompaction.

Alfredo González-Pérez¹, Jonas Carlstedt, Rita S Dias

¹Physical Chemistry, Center for Chemistry and Chemical Engineering, Lund University, Lund, Sweden. alfredo@memphys.sdu.dk

Colloids and Surfaces. B, Biointerfaces

|November 10, 2009

Summary

Scientists decompacted T4DNA using cyclodextrins (CDs) by forming inclusion complexes with the surfactant cetyltrimethylammonium bromide (CTAB). This non-first-order transition from globules to coils was confirmed using various measurements.

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Last Updated: Jun 18, 2026

Iterative Optimization of DNA Duplexes for Crystallization of SeqA-DNA Complexes

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Published on: November 1, 2012

Single-Molecule Real-Time Visualization of DNA Unwinding by CMG Helicase

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CD Spectroscopy to Study DNA-Protein Interactions

CD Spectroscopy to Study DNA-Protein Interactions

Published on: February 10, 2022

Area of Science:

Biophysics
Polymer Science
Supramolecular Chemistry

Background:

DNA molecules can be compacted using cationic surfactants like cetyltrimethylammonium bromide (CTAB).
Understanding DNA structural transitions is crucial for molecular biology and nanotechnology applications.

Purpose of the Study:

To investigate the decompaction of CTAB-compacted T4DNA using alpha-cyclodextrin (α-CD) and beta-cyclodextrin (β-CD).
To characterize the transition process and determine the conditions for DNA decompaction.

Main Methods:

Utilized density and sound velocity measurements.
Employed steady-state fluorescence spectroscopy.
Generated phase maps for DNA-CTAB-CD systems.

Main Results:

Successfully achieved T4DNA decompaction by adding α-CD or β-CD to CTAB-compacted DNA.
Observed a non-first-order globule-to-coil transition.
Identified the approximate CD concentrations and CTAB concentration ranges for decompaction.
Detected evidence of DNA-CD interaction, though its nature remains unclear.

Conclusions:

Cyclodextrins effectively decompact CTAB-treated T4DNA through inclusion complex formation.
The globule-to-coil transition is a complex process influenced by cyclodextrin concentration.
Further research is needed to elucidate the precise nature of DNA-CD interactions and their role in decompaction.