Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

4.1K
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...
4.1K
Labeling DNA Probes03:31

Labeling DNA Probes

7.8K
DNA probes are fragments of DNA labeled with a reporter tag to enable their detection or purification. The resulting labeled DNA probes can then hybridize to target nucleic acid sequences through complementary base-pairing, and may be used to recover or identify these regions.
Radioisotopes, fluorophores, or small molecule binding partners like biotin or digoxigenin, are the most widely used reporter tags for labeling DNA probes. These labels can be attached to the probe DNA molecule via...
7.8K
From DNA to Protein03:06

From DNA to Protein

20.9K
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...
20.9K
Single-Strand DNA Binding Proteins01:03

Single-Strand DNA Binding Proteins

12.9K
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...
12.9K
Regulated mRNA Transport02:22

Regulated mRNA Transport

5.7K
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...
5.7K
Covalently Linked Protein Regulators02:04

Covalently Linked Protein Regulators

8.2K
Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein....
8.2K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Multifaceted roles of PDS5B in RAD51-dependent homology-directed DNA repair and replication fork protection.

Nature communications·2026
Same author

Structural insight into how RAD51 paralog exchange regulates RAD51 filament formation.

Nature structural & molecular biology·2026
Same author

Author Correction: Structural insights into BCDX2 complex function in homologous recombination.

Nature·2026
Same author

Lineage-specific amino acids define functional attributes of the protomer-protomer interfaces for the Rad51 and Dmc1 recombinases.

The Journal of biological chemistry·2025
Same author

A hidden protamine PTM code in sperm generates heterogeneous chromatin states and finetunes reproductive fitness.

bioRxiv : the preprint server for biology·2025
Same author

An electrostatic repulsion model of centromere organisation.

bioRxiv : the preprint server for biology·2025

Related Experiment Video

Updated: May 6, 2026

DNA Sequence Recognition by DNA Primase Using High-Throughput Primase Profiling
08:04

DNA Sequence Recognition by DNA Primase Using High-Throughput Primase Profiling

Published on: October 8, 2019

8.0K

How do proteins locate specific targets in DNA?

Sy Redding1, Eric C Greene

  • 1Department of Chemistry, Columbia University, New York, NY 10032, United States.

Chemical Physics Letters
|November 5, 2013
PubMed
Summary

DNA-binding proteins like lac repressor and RNA polymerase use different strategies to find specific genome sites. Recent single-molecule studies reveal insights into their search mechanisms.

Area of Science:

  • Molecular Biology
  • Genetics
  • Biophysics

Background:

  • DNA-binding proteins are crucial for biological processes, requiring efficient genome site identification.
  • Advances in real-time single-molecule tracking microscopy have enabled detailed study of protein-DNA interactions.
  • Understanding protein search mechanisms is key to deciphering gene regulation and DNA-related functions.

Purpose of the Study:

  • To review how DNA-binding proteins, specifically lac repressor and RNA polymerase, locate target sites within the genome.
  • To highlight the influence of recent in vitro single-molecule studies on understanding these search mechanisms.
  • To compare and contrast the seemingly different search strategies employed by these two proteins.

Main Methods:

  • Review of existing literature focusing on in vitro single-molecule experiments.

More Related Videos

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
11:34

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Published on: August 9, 2019

5.8K
Visualizing Protein-DNA Interactions in Live Bacterial Cells Using Photoactivated Single-molecule Tracking
16:21

Visualizing Protein-DNA Interactions in Live Bacterial Cells Using Photoactivated Single-molecule Tracking

Published on: March 10, 2014

18.8K

Related Experiment Videos

Last Updated: May 6, 2026

DNA Sequence Recognition by DNA Primase Using High-Throughput Primase Profiling
08:04

DNA Sequence Recognition by DNA Primase Using High-Throughput Primase Profiling

Published on: October 8, 2019

8.0K
Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
11:34

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Published on: August 9, 2019

5.8K
Visualizing Protein-DNA Interactions in Live Bacterial Cells Using Photoactivated Single-molecule Tracking
16:21

Visualizing Protein-DNA Interactions in Live Bacterial Cells Using Photoactivated Single-molecule Tracking

Published on: March 10, 2014

18.8K
  • Analysis of microscopy-based technologies for real-time protein tracking.
  • Comparative analysis of lac repressor and RNA polymerase search mechanisms.

    • Main Results:

    • Lac repressor and RNA polymerase exhibit distinct yet effective strategies for target site recognition.
    • Single-molecule studies provide unprecedented resolution into the dynamics of protein-DNA searching.
    • The interplay between non-specific binding, sliding, and hopping is critical for efficient search.

    Conclusions:

    • Both lac repressor and RNA polymerase successfully navigate the genome to find specific binding sites.
    • Single-molecule biophysics has significantly advanced our understanding of protein-DNA search dynamics.
    • Further research using these advanced techniques will continue to illuminate fundamental biological processes.