Kinetoplast DNA (kDNA)

• High-quality kinetoplast DNA (kDNA) purified from Crithidia fasciculata for decatenation and topoisomerase assays
• Ideal substrate for Topo II and Topo IV activity studies, offering fast, clear results compared with relaxation assays
• Enables rapid visual detection of decatenation – minicircles separate cleanly from non-decatenated DNA on gels
• Prepared using the Shapiro et al. (1999) method for structural integrity and reproducibility
• Supplied at 100 ng/µl in 10 mM Tris-HCl (pH 8.0), 1 mM EDTA for stability and ease of use
• Compatible with high-resolution and single-molecule studies of DNA topology
• Referenced in He et al. (2023) and Ramakrishnan et al. (2024) for advanced mechanistic research
• Validated for use in topoisomerase inhibitor screening and enzyme mechanism analysis
• Supplied ready-to-use for Topo II decatenation assays and other DNA topology applications
• Store at 4°C for long-term stability and consistent performance

Kinetoplast DNA (kDNA) is a highly catenated network of circular DNA molecules purified from Crithidia fasciculata. It provides an excellent substrate for decatenation assays using DNA topoisomerase II (Topo II) or topoisomerase IV (Topo IV). Because the decatenated minicircles can be rapidly resolved from non-decatenated material during gel electrophoresis, kDNA assays offer a faster and more visually distinct readout than relaxation reactions.

Our kDNA is prepared following the established method of Shapiro et al. (1999) and is supplied at a concentration of 100 ng/µl in 10 mM Tris-HCl (pH 8.0) and 1 mM EDTA. Each batch is carefully purified to ensure structural integrity, reproducibility and high performance in enzymatic assays. The preparation is suitable for both research and teaching applications requiring well-defined kinetoplast substrates.

Product features

• Purified kinetoplast DNA from Crithidia fasciculata
• Supplied at 100 ng/µl in Tris-EDTA buffer
• Highly catenated DNA structure, ideal for decatenation assays
• Compatible with topoisomerase II and topoisomerase IV enzymes
• Enables rapid detection of decatenation activity through clear gel separation
• Validated for use in high-resolution and single-molecule studies

Applications

• Decatenation assays for Topo II and Topo IV activity
• Screening and characterisation of topoisomerase inhibitors
• Single-molecule and high-resolution studies of DNA topology
• Training and teaching in molecular enzymology

Recent publications, including He et al. (2023) and Ramakrishnan et al. (2024), have demonstrated the suitability of our kDNA for advanced biophysical and enzymatic analyses.

Storage and stability

Store kinetoplast DNA at 4°C. The preparation is stable under these conditions and retains its performance over extended use.

Our kDNA substrate offers a reliable, well-characterised tool for studying DNA topology and enzyme mechanisms in both academic and pharmaceutical research settings.

FAQs About Kinetoplast DNA (kDNA)

What is kinetoplast DNA (kDNA)?
Kinetoplast DNA, or kDNA, is a unique network of catenated circular DNA molecules found in the mitochondria of trypanosomatid protozoa such as Crithidia fasciculata. It forms a complex structure of interlocked minicircles and maxicircles, making it an ideal substrate for studying DNA topology and enzyme mechanisms.

How is kDNA produced?
Our kDNA is purified from Crithidia fasciculata using the method described by Shapiro et al. (1999). Each batch is prepared under controlled conditions to ensure consistent catenation, purity and performance in decatenation assays.

What is the concentration and buffer composition?
kDNA is supplied at a concentration of 100 ng/µl in 10 mM Tris-HCl (pH 8.0) and 1 mM EDTA. This buffer provides stable conditions for long-term storage and reliable assay performance.

What are the main applications of kDNA?
Typical applications include:

• Decatenation assays with DNA topoisomerase II and topoisomerase IV
• Screening and characterisation of topoisomerase inhibitors
• High-resolution and single-molecule studies of DNA topology
• Teaching and demonstration of enzyme mechanisms in molecular biology

Why is kDNA used for decatenation assays?
kDNA provides a clear and rapid readout of decatenation activity. When incubated with topoisomerase II or IV, the decatenated minicircles migrate distinctly on an agarose gel, while the remaining catenated network stays in the well. This allows quicker and easier visualisation of results compared with relaxation assays.

How should kinetoplast DNA be stored?
Store kDNA at 4°C. The preparation is stable under these conditions and retains full activity for extended use.

Has kDNA been used in published studies?
Yes. Our kDNA has been used in high-resolution and single-molecule studies, including He et al. (2023) and Ramakrishnan et al. (2024), demonstrating its quality and suitability for advanced research.

References

1. Shapiro, T.A., Klein, V.A. and Englund, P.T. (1999) Isolation of kinetoplast DNA, in DNA Topoisomerase Protocols Vol.I (Bjornsti, M-A and Osheroff, N., eds.). Humana Press Inc., N. Jersey, pp. 61-68
2. He, P., Katan, A. J., Tubiana, L., Dekker, C., & Michieletto, D. (2023). Single-Molecule Structure and Topology of Kinetoplast DNA Networks. Physical Review X, 13(2), 1-13. Article 021010. https://doi.org/10.1103/PhysRevX.13.021010
3. Ramakrishnan, S., Chen, Z., Gutierrez Fosado, Y. A., Tubiana, L., Vanderlinden, W., Savill, N. J., Schnaufer, A., & Michieletto, D. (2024). Single-molecule morphology of topologically digested olympic networks. PRX Life.