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Related Concept Videos

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...
Homologous Recombination02:31

Homologous Recombination

The basic reaction of homologous recombination (HR) involves two chromatids that contain DNA sequences sharing a significant stretch of identity. One of these sequences uses a strand from another as a template to synthesize DNA in an enzyme-catalyzed reaction. The final product is a novel amalgamation of the two substrates. To ensure an accurate recombination of sequences, HR is restricted to the S and G2 phases of the cell cycle. At these stages, the DNA has been replicated already and the...
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...
Fixing Double-strand Breaks02:04

Fixing Double-strand Breaks

The double-stranded structure of DNA has two major advantages. First, it serves as a safe repository of genetic information where one strand serves as the back-up in case the other strand is damaged. Second, the double-helical structure can be wrapped around proteins called histones to form nucleosomes, which can then be tightly wound to form chromosomes. This way, DNA chains up to 2 inches long can be contained within microscopic structures in a cell. A double-stranded break not only damages...
Restarting Stalled Replication Forks02:37

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...
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...

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Related Experiment Video

Updated: Jun 20, 2026

Stable DNA Motifs, 1D and 2D Nanostructures Constructed from Small Circular DNA Molecules
09:32

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

Published on: April 12, 2019

DNA junction structure stabilized by molecular crowding conditions.

Daisuke Miyoshi1, Sanjukta Muhuri, Kenta Mimura

  • 1Faculty of Frontiers of Innovative Research in Science and Technology and Frontier Institute for Biomolecular Engineering Research, Konan University, Kobe 650-0047, Japan.

Nucleic Acids Symposium Series (2004)
|September 15, 2009
PubMed
Summary

Molecular crowding favors DNA three-way junctions (TWJs) by dehydrating the junction point. This cellular environment may promote TWJ formation over duplex structures.

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Area of Science:

  • Biochemistry
  • Molecular Biology
  • Structural Biology

Background:

  • DNA structures, such as duplexes and junctions, are influenced by their cellular environment.
  • Molecular crowding, a condition mimicking the cell interior, affects macromolecular behavior.
  • Understanding these effects is crucial for comprehending DNA structure formation in vivo.

Purpose of the Study:

  • To investigate the impact of molecular crowding on the structure and thermodynamics of DNA three-way junctions (TWJs).
  • To quantify the role of water molecules in TWJ formation under crowding conditions.

Main Methods:

  • Analysis of water molecule association with TWJs and their individual arms under molecular crowding.
  • Thermodynamic evaluation of TWJ structures in crowded environments.

Main Results:

  • A significant reduction in water molecules was observed at the TWJ junction point compared to the sum of individual arms, indicating dehydration.
  • Molecular crowding was found to be favorable for the junction point but unfavorable for the duplex structure.

Conclusions:

  • Cell-mimicking molecular crowding conditions, characterized by decreased water activity, favor the formation of DNA junction structures over duplexes.
  • These findings suggest that dehydration at the junction point plays a key role in promoting TWJ formation in crowded cellular environments.