Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

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...

Cooperative Binding of Transcription Regulators

Cooperative Binding of Transcription Regulators

Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome. Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form dimers that...

Karyotyping

Karyotyping

Labeling DNA Probes

Labeling DNA Probes

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...

DNA Microarrays

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

DNA Packaging

DNA Packaging

You might also read

Related Articles

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

Sort by

Same author

Compaction and swelling of single stretched DNAs driven by molecular crowding.

Physical review. E·2026

Same author

GapR is a nucleoid-associated protein that stiffens and overtwists DNA to promote transcription and replication.

bioRxiv : the preprint server for biology·2026

Same author

Compaction and swelling of single stretched DNAs driven by molecular crowding.

bioRxiv : the preprint server for biology·2025

Same author

Molecular crowding suppresses mechanical stress-driven DNA strand separation.

Biophysical journal·2025

Same author

Cell cycle and age-related modulations of mouse chromosome stiffness.

eLife·2025

Same author

Independence of centromeric and pericentromeric chromatin stability on CCAN components.

Molecular biology of the cell·2025

Search research articles

Related Experiment Video

Updated: May 28, 2026

Counting Proteins in Single Cells with Addressable Droplet Microarrays

Counting Proteins in Single Cells with Addressable Droplet Microarrays

Published on: July 6, 2018

Counting proteins bound to a single DNA molecule.

John S Graham¹, Reid C Johnson, John F Marko

¹Northwestern University, Department of Molecular Biosciences, 2205 Tech Drive, Hogan 2-100, Evanston, IL 60208-3500, United States. john-graham@northwestern.edu

Biochemical and Biophysical Research Communications

|October 25, 2011

Summary

Researchers developed a simple fluorescence microscopy method to count GFP-conjugated proteins on DNA. This technique aids in understanding protein-DNA interactions and genome regulation.

More Related Videos

Proteome-wide Quantification of Labeling Homogeneity at the Single Molecule Level

Proteome-wide Quantification of Labeling Homogeneity at the Single Molecule Level

Published on: April 19, 2019

A Quantitative Assay to Study Protein:DNA Interactions, Discover Transcriptional Regulators of Gene Expression, and Identify Novel Anti-tumor Agents

A Quantitative Assay to Study Protein:DNA Interactions, Discover Transcriptional Regulators of Gene Expression, and Identify Novel Anti-tumor Agents

Published on: August 31, 2013

Related Experiment Videos

Last Updated: May 28, 2026

Counting Proteins in Single Cells with Addressable Droplet Microarrays

Counting Proteins in Single Cells with Addressable Droplet Microarrays

Published on: July 6, 2018

Proteome-wide Quantification of Labeling Homogeneity at the Single Molecule Level

Proteome-wide Quantification of Labeling Homogeneity at the Single Molecule Level

Published on: April 19, 2019

A Quantitative Assay to Study Protein:DNA Interactions, Discover Transcriptional Regulators of Gene Expression, and Identify Novel Anti-tumor Agents

A Quantitative Assay to Study Protein:DNA Interactions, Discover Transcriptional Regulators of Gene Expression, and Identify Novel Anti-tumor Agents

Published on: August 31, 2013

Area of Science:

Molecular Biology
Genomics
Biophysics

Background:

Chromosomes utilize DNA and proteins for structural organization and gene regulation.
Quantifying protein binding to specific genomic regions is crucial for understanding these functions.

Purpose of the Study:

To develop a straightforward method for counting GFP-conjugated proteins bound to individual DNA molecules.
To enable precise quantification of protein-DNA interactions using fluorescence microscopy.

Main Methods:

Utilized wide-field fluorescence microscopy for protein counting.
Calibrated measurements using a commercially available fluorescence standard.
Demonstrated the method with the E. coli nucleoid-associated protein Fis.

Main Results:

Successfully established a method to quantify GFP-conjugated proteins on single DNA molecules.
Provided a reliable technique for measuring protein-DNA binding events.
Validated the method's efficacy with a specific bacterial protein.

Conclusions:

The developed method offers a simple and effective way to count proteins bound to DNA.
This technique is valuable for studying genome architecture and transcriptional regulation.
Facilitates quantitative analysis of protein-DNA interactions in various biological contexts.