# Serine integrase mechanisms and applications

> **NIH NIH R01** · UNIVERSITY OF PENNSYLVANIA · 2024 · $320,546

## Abstract

Serine integrases carry out recombination between short, specific DNA sequences commonly referred to as
attP and attB to integrate a viral genome into the chromosome of a host. The reaction does not require
accessory proteins, additional DNA elements, or other cofactors and is effectively irreversible in the absence of
a viral recombination directionality factor (RDF) protein. These features have led to the emergence of serine
integrases as important tools in genome engineering and synthetic biology applications. As bacteriophage
integrases, the serine integrases have a strong influence over microbial communities, including the human gut
microbiota, where the resident phage population is thought to influence human health. Serine integrases are
also responsible for the horizontal transfer of antibiotic resistance genes within bacterial communities. Despite
their importance in human health and their widespread use in biomedical research, our mechanistic
understanding of how serine integrases function is still primitive. To address the largest gaps in our
understanding of serine integrase structure and function, we will determine the first structure of an integrase-
attachment site structure, establish the structural basis for RDF function, and test the hypothesis that serine
integrase efficiency in mammalian cells is limited by the strength of attP and attB site association. Our
experimental approaches include a novel kinetic analysis of the integration reaction, structure determination of
reaction intermediates using X-ray diffraction, analytical ultracentrifugation, novel integration and excision
assays, and integration into chromosomal sites in human cells. Our functional model for serine integrase
regulation of site-specificity, directionality, and site-association using interactions between coiled-coil domains
is unprecedented among nucleic acid enzymes. These studies will provide an important framework for
engineering improved function in serine integrase applications and may lead directly to improved integrases for
targeted integration in mammalian cells.

## Key facts

- **NIH application ID:** 10760233
- **Project number:** 5R01GM108751-08
- **Recipient organization:** UNIVERSITY OF PENNSYLVANIA
- **Principal Investigator:** GREGORY D VAN DUYNE
- **Activity code:** R01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $320,546
- **Award type:** 5
- **Project period:** 2014-02-01 → 2025-01-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10760233

## Citation

> US National Institutes of Health, RePORTER application 10760233, Serine integrase mechanisms and applications (5R01GM108751-08). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10760233. Licensed CC0.

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