Integrase-On-Demand (IOD): simplifying site-specific DNA integration across diverse microbes

As part of the Intrinsic Control for Genome and Transcriptome Editing in Communities (InCoGenTEC) team, Sandia researchers and academic partners developed a new method called Integrase-On-Demand (IOD), which makes it easier to insert large stretches of DNA into the chromosomes of a wide variety of bacteria, even those that are difficult to genetically engineer.

Integrases are specialized enzymes that splice DNA at matching “attachment” sites, but most bacteria lack the exact sites recognized by the integrases commonly used in the lab.

IOD software searches through a list of integrases, mined from diverse microbes, to find unused attachment sites in a target microbe’s own genome. The team demonstrated, in two strains of Pseudomonas and in a fast-growing cyanobacterium (Synechococcus elongatus), that their predicted integrase–attachment site pairs can efficiently insert DNA into specific target sites in the genome.

By eliminating the need to first introduce synthetic attachment sites, IOD enables one-step, reliable integration of large genetic circuits into non-model and even hard-to-culture bacteria. From a national security standpoint, this capability can accelerate the development of microbial platforms to produce useful products or carry out specific tasks – for on-demand biomanufacturing of medicines or materials, field-deployable biosensors, and rapid prototype strains for biodefense; at the same time, it underscores the importance of careful oversight to prevent misuse in engineering harmful pathogens.

<em>Pictorial representation of the IOD method.</em>
Pictorial representation of the IOD method.
<em>Pictorial representation of the IOD method.</em>
Pictorial representation of the IOD method.
<em>Pictorial representation of the IOD method.</em>
Pictorial representation of the IOD method.

Sandia researchers linked to work

  • McClain, H.M.
  • Lowrey, L.C.
  • Quinto, L.B.
  • Torrance, E.L.
  • Mageeney, C.M.

Sponsored by

U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research; Sandia National Laboratories Laboratory Directed Research and Development; U.S. Department of Energy, Office of Science, Office of Workforce Development for Teachers and Scientists; and Phage Pathways

Associated Publications

McClain, H.M., Lowrey, L.C., Quinto, L.B., Torrance, E.L., GaglianoT.R., Isaacs, F.J., Schoeniger, J.S., Williams, K.P., and Mageeney, C.M., (2026). “Integrase-On-Demand: bioprospecting integrases for targeted genomic insertion of genetic cargo,” Nucleic Acids Research, 54: 4. https://academic.oup.com/nar/article/54/4/gkag106/8468451


August 24, 2026