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

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...
Nucleosome Remodeling02:54

Nucleosome Remodeling

Nucleosomes are the basic units of chromatin compaction. Each nucleosome consists of the DNA bound tightly around a histone core, which makes the DNA inaccessible to DNA binding proteins such as DNA polymerase and RNA polymerase. Hence, the fundamental problem is to ensure access to DNA when appropriate, despite the compact and protective chromatin structure.
Nucleosome remodeling complex
Eukaryotic cells have specialized enzymes called ATP-dependent nucleosome remodeling enzymes. These enzymes...
Cooperative Binding of Transcription Regulators02:13

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...
Protein Dynamics in Living Cells01:19

Protein Dynamics in Living Cells

Different fluorescence-based techniques are used to study the protein dynamics in living cells. These techniques include FRAP, FRET, and PET.
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...
Chromatin Position Affects Gene Expression02:35

Chromatin Position Affects Gene Expression

Chromatin is the massive complex of DNA and proteins packaged inside the nucleus. The complexity of chromatin folding and how it is packaged inside the nucleus greatly influences  access to genetic information. Generally, the nucleus' periphery is considered transcriptionally repressive, while the cell's interior is considered a transcriptionally active area. 
Topologically Associated Domains (TADs)
The 3-dimensional positioning of chromatin in the nucleus influences the timing and level of...

You might also read

Related Articles

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

Sort by
Same author

Condensin I but not Condensin II is crucial for mitotic chromosome mechanics.

Nature communications·2026
Same author

Mechanistic basis for relaxation of DNA supercoils by human topoisomerase IIIα-RMI1-RMI2.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same author

Resolving interface structure and local internal mechanics of mitotic chromosomes.

Nature communications·2025
Same author

DNA polymerase actively and sequentially displaces single-stranded DNA-binding proteins.

Nature communications·2025
Same author

Challenges in observing transcription-translation for bottom-up synthetic biology.

QRB discovery·2025
Same author

Force generation and resistance in human mitosis.

Biophysical reviews·2024
Same journal

Photocatalytic low-temperature defluorination of PTFE.

Nature protocols·2026
Same journal

Multimodal imaging and quantification of lanthanide chelate-labeled micro- and nanoplastics in plants.

Nature protocols·2026
Same journal

Facilitating structure-based drug discovery with an artificial intelligence-driven virtual screening platform.

Nature protocols·2026
Same journal

Yeast nuclei-mediated precise delivery of synthetic megabase-scale human DNA into mammalian embryos.

Nature protocols·2026
Same journal

Direct inoculation of bioreactor-controlled stirred suspension culture with cryopreserved human pluripotent stem cells.

Nature protocols·2026
Same journal

Whole-organ spatial transcriptional analysis at cellular resolution using TRISCO.

Nature protocols·2026
See all related articles
  1. Home
  3. Concurrent Positional Dynamics And Activity Mapping Of Dna-binding Proteins.
  1. Home
  3. Concurrent Positional Dynamics And Activity Mapping Of Dna-binding Proteins.

Related Experiment Video

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
09:17

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

Concurrent positional dynamics and activity mapping of DNA-binding proteins.

Longfu Xu1, Zhaowei Liu2, Colleen Caldwell2

  • 1Department of Physics and Astronomy and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands. longfuxu@berkeley.edu.

Nature Protocols
|June 9, 2026

View abstract on PubMed

Summary
This summary is machine-generated.

We developed a new method, concurrent positional dynamics and activity mapping (C-DAM), to simultaneously track DNA-binding enzyme position, dynamics, and activity. This technique provides high-resolution insights into protein-DNA interactions at the single-molecule level.

More Related Videos

DamID-seq: Genome-wide Mapping of Protein-DNA Interactions by High Throughput Sequencing of Adenine-methylated DNA Fragments
09:14

DamID-seq: Genome-wide Mapping of Protein-DNA Interactions by High Throughput Sequencing of Adenine-methylated DNA Fragments

Published on: January 27, 2016

CD Spectroscopy to Study DNA-Protein Interactions
06:48

CD Spectroscopy to Study DNA-Protein Interactions

Published on: February 10, 2022

Related Experiment Videos

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion
09:17

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

DamID-seq: Genome-wide Mapping of Protein-DNA Interactions by High Throughput Sequencing of Adenine-methylated DNA Fragments
09:14

DamID-seq: Genome-wide Mapping of Protein-DNA Interactions by High Throughput Sequencing of Adenine-methylated DNA Fragments

Published on: January 27, 2016

CD Spectroscopy to Study DNA-Protein Interactions
06:48

CD Spectroscopy to Study DNA-Protein Interactions

Published on: February 10, 2022

Area of Science:

  • Biophysics
  • Molecular Biology
  • Biochemistry

Background:

  • Single-molecule techniques offer insights into DNA-protein interactions.
  • Simultaneously tracking enzyme position, binding dynamics, and activity on DNA has been challenging.

Purpose of the Study:

  • To present a protocol for concurrent positional dynamics and activity mapping (C-DAM) of DNA-binding proteins.
  • To enable high-resolution correlation of enzyme activity with its precise location on DNA.

Main Methods:

  • Integration of optical tweezers and confocal fluorescence microscopy.
  • Optical tweezers track enzymes converting DNA, measuring mechanical changes for activity at nanometer/millisecond resolution.
  • Force-assisted imaging correlates mechanical data with fluorescence signals to pinpoint molecule location relative to activity.

Main Results:

  • C-DAM provides concurrent mapping of enzyme position, binding dynamics, and catalytic activity.
  • The method dissects distinct functional states, enzyme exchange events, and location-specific behaviors.
  • Correlating DNA and protein kymographs distinguishes binding modes (e.g., static ssDNA binding vs. dsDNA diffusion).

Conclusions:

  • C-DAM synergistically leverages mechanical and fluorescence data for direct, concurrent mapping.
  • The protocol is broadly adaptable for studying DNA-binding proteins and complexes.
  • Potential for future integration with techniques like Förster resonance energy transfer exists.