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dna-gyrase-faq | TopoGEN

Topoisomerase FAQ

Expert answers to topoisomerase enzyme, DNA gyrase, topo I/II assay, kDNA substrate, and drug screening questions for cancer and antibacterial research.

What is TopoGEN and what does the company specialize in?

TopoGEN, Inc. is a 20 year old biotechnology company specializing in DNA topoisomerases, DNA repair enzymes, genotoxicity assays, and mechanism-of-action studies related to cancer therapeutics, antibiotics, and genome stability research. The company provides purified enzymes, biochemical assay kits, cell-based assays, and contract research services to academic, pharmaceutical, and biotech laboratories worldwide.

What are TopoGEN’s best-selling products?

Some of the most widely used TopoGEN products include:

  • Human Topoisomerase I (human, bacterial)
  • Human Topoisomerase IIα,β
  • Bacterical DNA Gyrases (multiple species)
  • Kinetoplast DNA (kDNA) substrates (specific for type 2 enzymes)
  • Relaxed, supercoiled, linear plasmid DNA substrates
  • All DNA substrates validated and certified to work
  • DNA targets with high affinity topo binding sites
  • Topoisomerase assay & drug screening kits
  • Validate topo drugs: certified to work
  • Anti-topo antibodies: fully validated for specific applications (IF, IP, ICE, Westerns, etc)
  • Cell context assays for detecting covalent enzyme-DNA complexes (ICE Bio)
  • Technologies to interrogate topo-DNA damage/repair pathways
  • TDP1, TDP2 enzymes for drug discovery
  • Any topo pathway adjacent genes and gene products

These products are commonly used in anti-cancer drug discovery, antibiotic development, and DNA damage R&D.

What makes TopoGEN different from other enzyme suppliers?

TopoGEN focuses specifically on DNA topology, topoisomerases, and DNA repair biology. Unlike general reagent suppliers, the company combines:

  • Deep scientific expertise
  • Proprietary assay systems
  • Cell-based validation platforms
  • CRO services
  • Highly cited research products
  • Technical consultation from published experts in the topoisomerase field

TopoGEN also provides mechanism-of-action interpretation, not simply reagents.

What is an ICE assay and why is it important?

Developed by TopoGEN scientists, the ICE (In Vivo Complex of Enzyme) assay detects covalent topoisomerase-DNA cleavage complexes inside cells. Importantly, this technology validates whether an unknown drug will work in a patient context.  This is acutely valuable in all drug discovery campaigns.

TopoGEN is recognized for its expertise in ICE assay development and application in evaluating:

  • Topoisomerase poisons
  • DNA damage responses
  • Drug-induced genotoxicity
  • Cancer therapeutic mechanisms
Does TopoGEN offer contract research services (CRO)?

Yes. TopoGEN provides specialized CRO services focused on:

  • Topoisomerase mechanism-of-action studies
  • DNA intercalation testing
  • DNA unwinding assays
  • Cleavage complex detection
  • Enzyme inhibition studies
  • Cell-based validation assays
  • Genotoxicity screening
  • Cell context imaging of DNA repair
  • Cloning and expressing of virtually any topoisomerase from any biological source (TopOmniSource)

These services help clients distinguish catalytic inhibitors from interfacial poisons and validate drug activity in cellular systems.

What topoisomerase enzymes does TopoGEN provide?

TopoGEN supplies a broad portfolio of purified enzymes including:

  • Human Topoisomerase I
  • Human Topoisomerase II alpha
  • Human Topoisomerase II beta
  • Human Topoisomerase IIIA,B
  • E. coli DNA Gyrase
  • Bacterial Topoisomerase IV
  • Archaeal and microbial topoisomerases
  • Custom enzyme preparations from plant, animal or any viral source

The company also develops specialized substrates and assay systems optimized for these enzymes.

What are topoisomerases and why are they important in drug discovery?

Topoisomerases are essential enzymes that regulate DNA supercoiling, replication, transcription, and chromosome segregation. They are major therapeutic targets in:

  • Cancer therapy
  • Antibiotic development
  • Antifungal drug discovery
  • Antiparasitic research
  • Front line novel antivirals
  • Applications in veterinary medicine
  • Applications in agriculture

Many important FDA approved drugs target topoisomerases and the list is growing.

Does TopoGEN provide technical support and assay consultation?

Yes. TopoGEN is known for offering direct scientific support to customers. The company assists with:

  • Assay and HTS optimization
  • Hit to lead optimazation
  • Experimental design
  • Mechanism interpretation
  • Enzyme selection
  • Control recommendations
  • Troubleshooting difficult topoisomerase experiments

TopGEN’s scientific engagement  with both CRO clients and customers is a major differentiator for many researchers. All customers, all clients are treated as collaborators. We solve problems.

Who are TopoGEN’s competitors?

Companies operating in related markets include:
Thermo Fisher, Sigma, New England Biolabs. TopoGEN supplies these aggregators with products in many cases. Importantly, TopoGEN differentiates itself through its specialization in DNA topology, topoisomerase biology, DNA repair, mechanistic assays, and expert consultation.

Can TopoGEN help identify whether a compound is a topoisomerase poison or catalytic inhibitor?

Yes. This is one of TopoGEN’s core strengths.  We are experts at working out MOA (mechanism of action) details on unknowns using biochemical insight and cell-based validation systems. Specifically, the company can help determine whether a molecule acts as:

  • An interfacial poison (IFP)
  • A catalytic inhibitor (CIC)
  • A DNA intercalator
  • A DNA damaging agent
  • Displays the ability to act on living, intact cells.

This information is critical during early-stage drug discovery.

Does TopoGEN support antibiotic and antimicrobial drug discovery?

Yes. TopoGEN provides enzymes and assays targeting bacterial DNA gyrase and topoisomerase IV, which are major targets for antibacterial therapeutics.

The company also supports emerging research related to antifungal resistance and novel pathogen-targeted therapies.

What is kinetoplast DNA (kDNA) and why is it used in topoisomerase assays?

Kinetoplast DNA (kDNA) is a highly catenated DNA network isolated from trypanosomatid organisms. It is a highly specific substrate to detect and assay or any type 2 Topoisomerase.

TopoGEN is recognized internationally as a supplier of high-quality kDNA substrates for enzymology and drug screening applications.

Does TopoGEN work with universities and government-funded research programs?

Yes. TopoGEN collaborates with academic laboratories, SBIR/STTR programs, grant-funded initiatives, and translational research projects. The company has extensive experience supporting NIH-funded and university-based research. The Company has shared NIH grants with both commercial and academic labs over the years.

Why do researchers choose TopoGEN for topoisomerase research?

Researchers often choose TopoGEN because of the company’s:

  • Longstanding (25y)expertise in the field of DNA topology
  • Specialized enzyme portfolio
  • Proprietary assay technologies
  • Responsive technical support
  • High-quality biochemical reagents
  • Mechanistic drug discovery capabilities
  • Reputation in the topoisomerase research community

TopoGEN products and assays have been cited in thousands of scientific publications worldwide. 

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