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

Conservative Site-specific Recombination and Phase Variation

Conservative Site-specific Recombination and Phase Variation

Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...

The Equilibrium Binding Constant and Binding Strength

The Equilibrium Binding Constant and Binding Strength

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:

The Equilibrium Binding Constant and Binding Strength

The Equilibrium Binding Constant and Binding Strength

Ligand Binding Sites

Ligand Binding Sites

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...

Conserved Binding Sites

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...

Conserved Binding Sites

Conserved Binding Sites

You might also read

Related Articles

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

Sort by

Same author

Formation of the intradimer disulfide bond in human calprotectin maintains metal-withholding function and tunes proteolytic susceptibility.

Chemical science·2026

Same author

25-Year revision, reoperation, and complication risk following 150,000 hallux valgus bunion operations in England.

Foot and ankle surgery : official journal of the European Society of Foot and Ankle Surgeons·2026

Same author

Characterization of Fluorinated Organic Chemicals in Pyrolysis Byproducts of Biosolids Using Complementary Analytical Approaches.

Environmental science & technology·2026

Same author

Resolving heterogeneity of targeted lipid nanoparticles through solution-based biophysical analyses.

bioRxiv : the preprint server for biology·2026

Same author

Vps35 p. D620N causes Lrrk2 kinase hyperactivity, chronic microglial activation and inflammation.

bioRxiv : the preprint server for biology·2026

Same author

Structures of nucleotide-bound Redondovirus Rep protein link conformation and function.

PLoS pathogens·2026

Search research articles

Related Experiment Video

Updated: Feb 5, 2026

Site-specific Bacterial Chromosome Engineering: ΦC31 Integrase Mediated Cassette Exchange (IMCE)

Site-specific Bacterial Chromosome Engineering: ΦC31 Integrase Mediated Cassette Exchange (IMCE)

Published on: March 16, 2012

Serine Integrase attP Binding and Specificity.

Huiguang Li¹, Robert Sharp¹, Karen Rutherford¹

¹Department of Biochemistry & Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.

Journal of Molecular Biology

|September 19, 2018

Summary

This summary is machine-generated.

Serine integrases are key for gene integration. This study reveals specific DNA-binding residues and shows that attachment sites can be engineered for improved efficiency in biotechnology applications.

Keywords:

attachment site integrase integration recombination specificity

More Related Videos

Detection and Removal of Nuclease Contamination During Purification of Recombinant Prototype Foamy Virus Integrase

Detection and Removal of Nuclease Contamination During Purification of Recombinant Prototype Foamy Virus Integrase

Published on: December 8, 2017

A Protocol for the Production of Integrase-deficient Lentiviral Vectors for CRISPR/Cas9-mediated Gene Knockout in Dividing Cells

A Protocol for the Production of Integrase-deficient Lentiviral Vectors for CRISPR/Cas9-mediated Gene Knockout in Dividing Cells

Published on: December 12, 2017

Related Experiment Videos

Last Updated: Feb 5, 2026

Site-specific Bacterial Chromosome Engineering: ΦC31 Integrase Mediated Cassette Exchange (IMCE)

Site-specific Bacterial Chromosome Engineering: ΦC31 Integrase Mediated Cassette Exchange (IMCE)

Published on: March 16, 2012

Detection and Removal of Nuclease Contamination During Purification of Recombinant Prototype Foamy Virus Integrase

Detection and Removal of Nuclease Contamination During Purification of Recombinant Prototype Foamy Virus Integrase

Published on: December 8, 2017

A Protocol for the Production of Integrase-deficient Lentiviral Vectors for CRISPR/Cas9-mediated Gene Knockout in Dividing Cells

A Protocol for the Production of Integrase-deficient Lentiviral Vectors for CRISPR/Cas9-mediated Gene Knockout in Dividing Cells

Published on: December 12, 2017

Area of Science:

Molecular Biology
Biochemistry
Structural Biology

Background:

Serine integrases facilitate site-specific DNA integration, crucial for gene therapy and synthetic biology.
Limited structural data exists for integrase-DNA interactions, hindering enzyme engineering.

Purpose of the Study:

To investigate the binding mechanisms of Listeria innocua serine integrase to its attP site.
To elucidate the structural basis of attP recognition by the integrase C-terminal domain (CTD).
To identify key residues for integrase binding and activity and explore attP site engineering.

Main Methods:

Quantitative binding assays to determine Int-attP affinity.
Saturation mutagenesis to identify critical residues in the attP site.
X-ray crystallography to obtain a high-resolution structure of the CTD•attP complex.

Main Results:

High-affinity binding of Int to attP (6.9 nM) was observed.
The Int CTD binds attP half-sites with only slightly lower affinity.
Mutagenesis identified only 6 essential residues for efficient binding and integration, with some substitutions improving the attP site.

Conclusions:

Serine integrase binding to attP involves energy expenditure to open an Int dimer.
The recombinase domain shows largely non-specific DNA binding.
AttP site engineering offers a route to enhance serine integrase efficiency for biotechnological uses.