Related Experiment Video
Updated: Aug 5, 2026
16:24
Analyzing and Building Nucleic Acid Structures with 3DNA
Published on: April 26, 2013
One- and three-dimensional pathways for proteins to reach specific DNA sites
N P Stanford1, M D Szczelkun, J F Marko
1Department of Biochemistry, School of Medical Sciences, University of Bristol, University Walk, Bristol BS8 1TD, UK.
The EMBO Journal
|December 2, 2000
Summary
DNA-binding proteins like Eco:RV endonuclease use three-dimensional search strategies, not just one-dimensional diffusion, to find target DNA sites. This involves multiple dissociation and re-associations, suggesting a different mechanism than previously assumed.
Area of Science:
- Molecular Biology
- Biophysics
Background:
- Proteins interacting with specific DNA sites locate targets via random binding and translocation.
- Possible translocation mechanisms include one-dimensional diffusion or three-dimensional movement through dissociation/re-association.
Purpose of the Study:
- To differentiate between one-dimensional and three-dimensional search mechanisms for DNA-binding proteins.
- To investigate the translocation pathway of the Eco:RV endonuclease.
Main Methods:
- Studied Eco:RV endonuclease reactions on DNA substrates with two Eco:RV sites.
- Varied the distance between the two DNA recognition sites.
- Analyzed the effect of inter-site spacing on processive cleavage.
Main Results:
- Processive cleavage of both sites decreased as the distance between DNA sites increased.
- The observed decrease in processivity did not align with predictions for one-dimensional diffusion.
- Results support a three-dimensional search mechanism involving dissociation and re-association.
Conclusions:
- Eco:RV endonuclease utilizes a three-dimensional search pathway, moving between sites via dissociation and re-association.
- This three-dimensional mechanism, including local DNA scanning after re-association, may be prevalent for DNA-binding proteins.
- Challenges the prevailing view that DNA-binding proteins primarily use one-dimensional pathways.
More Related Videos
Related Concept Videos
01:25The Central Dogma
Overview
03:06From DNA to Protein
The flow of genetic information in cells from DNA to mRNA to protein is described by the central dogma, which states that genes specify the sequence of mRNAs, which in turn specify the sequence of amino acids making up all proteins. The decoding of one molecule to another is performed by specific proteins and RNAs. Because the information stored in DNA is so central to cellular function, it makes intuitive sense that the cell would make mRNA copies of this information for protein synthesis...
01:49Conserved 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...
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...
02:05DNA as a Genetic Template
Two structural features of the DNA molecule provide a basis for the mechanisms of heredity: the four nucleotide bases and its double-stranded nature. The Watson-Crick model of double-helical DNA structure, proposed in 1952, drew heavily upon the X-ray crystallography work of researchers Rosalind Franklin and Maurice Wilkins. Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine for their work in 1962. Franklin was, controversially, excluded from the prize for...
02:22Regulated mRNA Transport
In eukaryotes, transcription and translation are compartmentalized; an mRNA is first synthesized in the nucleus and then selectively transported to the cytoplasm for protein synthesis. Before transport, a pre-mRNA undergoes several steps of post-transcriptional modifications including splicing, 5' capping, and the addition of a poly-adenine tail. Various proteins bind to the pre-mRNA during these modifications. The mRNA transport takes place with the help of multiple proteins playing specific...
01:20The Central Dogma
The central dogma explains the flow of genetic information from DNA nucleotides to the amino acid sequence of proteins.
RNA is the Missing Link Between DNA and Proteins
In the early 1900s, scientists discovered that DNA stores all the information needed for cellular functions and that proteins perform most of these functions. However, the mechanisms of converting genetic information into functional proteins remained unknown for many years. Initially, it was believed that a single gene is...
RNA is the Missing Link Between DNA and Proteins
In the early 1900s, scientists discovered that DNA stores all the information needed for cellular functions and that proteins perform most of these functions. However, the mechanisms of converting genetic information into functional proteins remained unknown for many years. Initially, it was believed that a single gene is...