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

The Equilibrium Binding Constant and Binding Strength02:18

The Equilibrium Binding Constant and Binding Strength

15.1K
The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
15.1K
Ligand Binding Sites02:40

Ligand Binding Sites

15.1K
Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
15.1K
Single-Strand DNA Binding Proteins01:03

Single-Strand DNA Binding Proteins

16.7K
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...
16.7K
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

5.6K
Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...
5.6K
Factors Affecting Protein-Drug Binding: Drug Interactions01:23

Factors Affecting Protein-Drug Binding: Drug Interactions

611
Drug interactions are a critical aspect of pharmacology and can occur when two or more drugs compete for the same binding site. This competition can result in one drug displacing another, altering the effect of the displaced drug. Drug interactions are complex processes that rely heavily on how much of the displacer drug is present and how strongly it can bind to the same sites as the displaced drug.
Displacement interactions can have varying outcomes, ranging from toxicity to virtually...
611
Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

7.4K
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...
7.4K

You might also read

Related Articles

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

Sort by
Same author

Living sensors: Engineering plants to sense and report on their environments.

Current opinion in plant biology·2026
Same author

Metabolic engineering of Saccharomyces cerevisiae to enhance resistance toward microbial toxicity in agave extracts.

Bioresource technology·2026
Same author

Protein engineering of a genetically encoded biosensor for wastewater detection of profen NSAIDs.

bioRxiv : the preprint server for biology·2026
Same author

Computational design of dynamic biosensors for emerging synthetic opioids.

Nature communications·2026
Same author

Unusually broad-spectrum small-molecule sensing using a single protein scaffold.

Proceedings of the National Academy of Sciences of the United States of America·2025
Same author

Real-Time Flange Bolt Loosening Detection with Improved YOLOv8 and Robust Angle Estimation.

Sensors (Basel, Switzerland)·2025
Same journal

Mapping the 3D Chromosome Organization of a Biosynthetic Gene Cluster by Capture Hi-C (CHi-C).

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Mapping the 3D Chromosome Organization of Streptomyces by Hi-C.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

CUT&Tag Epigenomic Profiling of Biosynthetic Gene Clusters in Arabidopsis thaliana.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Rhizobium rhizogenes-Mediated Hairy Root Transformation Protocol for Lotus japonicus and Other Legumes.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Characterization of Bioactive Saponins from Sea Cucumbers.

Methods in molecular biology (Clifton, N.J.)·2026
Same journal

Methods for Functional Validation of Terpenoid Metabolic Clusters in Nicotiana benthamiana and Aspergillus oryzae.

Methods in molecular biology (Clifton, N.J.)·2026
See all related articles

Related Experiment Video

Updated: Feb 8, 2026

Combining Single-molecule Manipulation and Imaging for the Study of Protein-DNA Interactions
14:43

Combining Single-molecule Manipulation and Imaging for the Study of Protein-DNA Interactions

Published on: August 27, 2014

12.1K

Quantifying Small Molecule Binding Interactions with DNA Nanostructures.

Xuye Lang1, Yingning Gao1, Ian Wheeldon2

  • 1Chemical and Environmental Engineering, University of California Riverside, Riverside, CA, USA.

Methods in Molecular Biology (Clifton, N.J.)
|June 30, 2018
PubMed
Summary
This summary is machine-generated.

Quantifying small molecule binding to DNA nanostructures is crucial for biotechnology. This study presents methods like microscale thermophoresis and spectroscopy to measure these interactions, applicable to DNA DX tiles and various molecules.

Keywords:
DNA-sequence dependent bindingEnzyme–DNAMethylene blue displacement assayMicroscale thermophoresisProtein conjugation

More Related Videos

Gene-therapy Inspired Polycation Coating for Protection of DNA Origami Nanostructures
08:30

Gene-therapy Inspired Polycation Coating for Protection of DNA Origami Nanostructures

Published on: January 19, 2019

9.7K
Visualization of Surface-tethered Large DNA Molecules with a Fluorescent Protein DNA Binding Peptide
08:51

Visualization of Surface-tethered Large DNA Molecules with a Fluorescent Protein DNA Binding Peptide

Published on: June 23, 2016

11.3K

Related Experiment Videos

Last Updated: Feb 8, 2026

Combining Single-molecule Manipulation and Imaging for the Study of Protein-DNA Interactions
14:43

Combining Single-molecule Manipulation and Imaging for the Study of Protein-DNA Interactions

Published on: August 27, 2014

12.1K
Gene-therapy Inspired Polycation Coating for Protection of DNA Origami Nanostructures
08:30

Gene-therapy Inspired Polycation Coating for Protection of DNA Origami Nanostructures

Published on: January 19, 2019

9.7K
Visualization of Surface-tethered Large DNA Molecules with a Fluorescent Protein DNA Binding Peptide
08:51

Visualization of Surface-tethered Large DNA Molecules with a Fluorescent Protein DNA Binding Peptide

Published on: June 23, 2016

11.3K

Area of Science:

  • Biotechnology and Material Science
  • Nanotechnology
  • Molecular Biology

Background:

  • DNA nanostructures offer controllable, molecule-level features for diverse applications.
  • Characterizing interactions between DNA nanostructures and small molecules is essential for their technological development.
  • Quantifying binding affinity is critical for understanding and optimizing these systems.

Purpose of the Study:

  • To describe and quantify ligand binding interactions between DNA nanostructures and small molecules.
  • To provide a comprehensive set of experimental and in silico protocols for binding affinity analysis.
  • To demonstrate the broad applicability of these methods using specific examples.

Main Methods:

  • Microscale thermophoresis (MST) for real-time binding measurements.
  • Ligand competition assays to determine binding constants.
  • Circular dichroism (CD) spectroscopy to analyze structural changes upon binding.
  • AutoDock simulations for in silico prediction of binding modes.

Main Results:

  • Detailed protocols for quantifying binding affinity between DNA nanostructures and small molecules.
  • Demonstration of methods using DNA DX tiles and organophosphates (including model chemical nerve agents).
  • Validation of experimental results through complementary techniques and computational analysis.

Conclusions:

  • The presented protocols provide a robust framework for characterizing small molecule binding to DNA nanostructures.
  • These methods are broadly applicable beyond the specific examples, facilitating the development of new DNA-based technologies.
  • Accurate quantification of binding affinity is key to advancing DNA nanostructures in biotechnology and material science.