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Related Concept Videos

DNA Topoisomerases02:02

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...
The Nucleosome01:19

The Nucleosome

Human DNA is almost two meters long. However, it is compressed inside a tiny nucleus measuring only a few microns in diameter. To make this degree of compaction possible, DNA is organized into several sequential levels so that it can fit into such a tiny space. The most compact form of DNA is a chromosome that can be seen under a microscope in a dividing cell.
In a chromosome, DNA is wound twice around a protein complex called a histone octamer core, which consists of 8 histone proteins. This...
The Nucleosome02:33

The Nucleosome

DNA in a human cell is almost 2m long and it is packed inside a tiny nucleus that is only a few microns in diameter. The level of compaction of DNA inside the nucleus is astonishing. It is organized into several sequentially higher levels of compaction to fit into such a tiny space. The most compact form of DNA is a chromosome that can be seen under a microscope in a dividing cell.
DNA is wound twice around a protein complex called histone core, that consist of 8 histone proteins. This complex...
Nucleic Acid Structure01:25

Nucleic Acid Structure

The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA has a double-helix structure. The...
Single-Strand DNA Binding Proteins01:03

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...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...

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Related Experiment Video

Updated: May 16, 2026

Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

Orientational correlations in confined DNA.

E Werner1, F Persson, F Westerlund

  • 1Department of Physics, University of Gothenburg, Sweden.

Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics
|December 11, 2012
PubMed
Summary

We investigated how DNA orientational correlations change within nanochannels of varying diameters. Local correlations were found to dictate the DNA molecule's end-to-end distance, matching experimental findings.

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Last Updated: May 16, 2026

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Area of Science:

  • Biophysics
  • Polymer Physics
  • Nanotechnology

Background:

  • Understanding DNA behavior in confined environments is crucial for nanotechnology and biological applications.
  • Existing theories like Flory-de Gennes may not fully capture DNA conformations in certain nanochannel regimes.

Purpose of the Study:

  • To investigate the dependence of DNA orientational correlations on nanochannel diameter (D).
  • To develop a mean-field theory applicable to experimentally relevant DNA confinement scenarios.
  • To correlate local DNA correlations with the molecule's end-to-end distance as a function of channel diameter.

Main Methods:

  • Utilized Monte Carlo simulations to model DNA behavior.
  • Developed and applied a novel mean-field theory for DNA conformations.
  • Employed tapered nanochannels for high-resolution experimental measurements of DNA extension.

Main Results:

  • Established a quantitative link between local orientational correlations and DNA end-to-end distance.
  • Demonstrated that the DNA molecule's extension is dependent on the nanochannel diameter (D).
  • Achieved qualitative agreement between theoretical predictions and experimental observations.

Conclusions:

  • Local correlations are key determinants of DNA conformation in nanochannels.
  • The developed mean-field theory accurately describes DNA behavior beyond the applicability of Flory-de Gennes theory.
  • Experimental and theoretical findings confirm the influence of nanochannel diameter on confined DNA extension.