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

Ligand Binding and Linkage

Ligand Binding and Linkage

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...

You might also read

Related Articles

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

Sort by

Same author

RNALig: An ML-Driven Structure-Based Scoring Function for Estimating Binding Affinities of RNA-Ligand Complexes.

Chemphyschem : a European journal of chemical physics and physical chemistry·2026

Same author

Voices in Molecular Pharmaceutics: Meet Professor Pradeep Pant, Who Designs Precision DNA and RNA Aptamers to Target Disease-Related Proteins Using AI and Molecular Simulations to Fast-Track New Therapeutics.

Molecular pharmaceutics·2025

Same author

AIoptamer: Artificial Intelligence-Driven Aptamer Optimization Pipeline for Targeted Therapeutics in Healthcare.

Molecular pharmaceutics·2025

Same author

Identification of Potent Cell Penetrating, Nontoxic Peptides for Inhibiting MDM2-p53 Interactions: Characterization of Anticancer Peptides via Molecular Dynamics Simulations.

Journal of peptide science : an official publication of the European Peptide Society·2025

Same author

CHIMERA_NA: A Customizable Mutagenesis Tool for Structural Manipulations in Nucleic Acids and Their Complexes.

ACS omega·2024

Same author

Probing the Nucleic Acid Flexibility to Disarm the Viral Counter-Defense Machinery: Design and Characterization of Potent p19 Inhibitors.

The journal of physical chemistry. B·2023

Search research articles

Related Experiment Video

Updated: Apr 11, 2026

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

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

Published on: August 27, 2014

Design and Characterization of Neutral Linker-Based Bis-Intercalator via Computer Simulations: Balancing DNA Binding

¹Department of Biotechnology, School of Engineering and Applied Sciences, Bennett University, Greater Noida, UP, India.

Chemistry & Biodiversity

|July 9, 2024

Summary

Researchers designed a new bis-intercalator with a neutral linker, improving DNA binding and cell permeability. This modification reduces off-target effects, offering a promising strategy for developing novel DNA-targeting agents.

Keywords:

Binding affinity DNA binders Intercalators MM-PBSA Molecular dynamics simulations

More Related Videos

Creating Highly Specific Chemically Induced Protein Dimerization Systems by Stepwise Phage Selection of a Combinatorial Single-Domain Antibody Library

Creating Highly Specific Chemically Induced Protein Dimerization Systems by Stepwise Phage Selection of a Combinatorial Single-Domain Antibody Library

Published on: January 14, 2020

DNA-Tethered RNA Polymerase for Programmable In vitro Transcription and Molecular Computation

DNA-Tethered RNA Polymerase for Programmable In vitro Transcription and Molecular Computation

Published on: December 29, 2021

Related Experiment Videos

Last Updated: Apr 11, 2026

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

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

Published on: August 27, 2014

Creating Highly Specific Chemically Induced Protein Dimerization Systems by Stepwise Phage Selection of a Combinatorial Single-Domain Antibody Library

Creating Highly Specific Chemically Induced Protein Dimerization Systems by Stepwise Phage Selection of a Combinatorial Single-Domain Antibody Library

Published on: January 14, 2020

DNA-Tethered RNA Polymerase for Programmable In vitro Transcription and Molecular Computation

DNA-Tethered RNA Polymerase for Programmable In vitro Transcription and Molecular Computation

Published on: December 29, 2021

Area of Science:

Medicinal Chemistry
Biochemistry
Molecular Biology

Background:

Bis-intercalators are DNA-binding molecules with potential in cancer therapy.
Traditional bis-intercalators have high positive charges, limiting cellular uptake and causing off-target effects.

Purpose of the Study:

To design and evaluate a novel bis-intercalator with a neutral linker for improved DNA targeting and reduced side effects.
To investigate the DNA binding affinity and membrane permeability of the designed bis-intercalator.

Main Methods:

Utilized bis-intercalator TOTO, replacing its charged linker with a neutral peroxodisulphuric acid linker.
Employed molecular modeling and computer simulations (500 ns, 3 replicas) for analysis.
Assessed DNA binding using MM-PBSA and Delphi methods.

Main Results:

The designed bis-intercalator demonstrated enhanced DNA binding compared to the control.
Improved membrane translocation permeability was observed for the neutral-linker bis-intercalator.
Reduced overall charge is expected to decrease off-target binding.

Conclusions:

Bis-intercalators featuring peroxodisulphuric acid linkers show potential for effective DNA targeting.
This design offers a promising avenue for developing next-generation bis-intercalators with improved therapeutic profiles.