Double-strand specific DNases

Glycerol-free versions of
dsDNase and HL-dsDNase are now available

Overview

Double-strand specific DNases (dsDNases) are unique double-strand specific endonucleases. As they do not digest ssDNA or RNA, they can be used to specifically remove dsDNA in the presence of other nucleic acids. The enzymes are heat-labile, which makes them ideal for applications where the DNase have to be inactivated. There are two versions of this enzyme available, dsDNase and HL-dsDNase.

Kits

For ease of use, kits have been developed for some applications.

PCR Decontamination kit

Removes contaminating DNA in PCR master mixes, without reduction of PCR sensitivity.
This kit is useful if you struggle with:

  • Positive NTC’s in your PCR
  • qPCR background
  • Dirty PCR master mixes

Learn more →

Heat&Run gDNA removal kit

Allows rapid, effortless and complete removal of gDNA in RNA preps from any source.

  • Suited for high throughput experiments
  • HL-dsDNase can easily be inactivated
  • gDNA is removed, leaving RNA ready for reverse transcription in the same tube

Learn more →

Properties

Specificity towards double-stranded DNA

Nucleic acid specificity has been tested towards double- and single-stranded DNA and RNA oligonucleotides.

The specificity of dsDNase towards the substrate has been measured using 15-mer oligonucleotides with FAM at 5′ and DarkQuencher® 3′ (Eurogentec). The fluorescence is proportional to enzyme activity.

Assay conditions: 25 mM Tris pH 7.5, 5 mM MgCl2, and 2 μM oligonucleotide.

Relative activities

Substrate Relative activity
dsDNA 100%
ssDNA < 0.03%
dsRNA < 0.01 %
ssRNA < 0.01 %

From the data above we can conclude that the dsDNase is double-strand specific.

dsDNase

Heat inactivation

The dsDNase can be heat inactivated by heat treatment at 15 min at 65˚C, or 20 min at 60˚C. The enzyme requires 1 mM DTT and pH ≥ 8 for complete inactivation.

Specifications

  • Unit definition
    One Unit is defined as an increase in absorbance at 260 nm of 0.001 per minute, using 50 mg/ml high MW DNA in 50 mM Na-acetate pH 5.0 and 5 mM MgCl2.
  • Specific activity
    Ca. 400 000 Kunitz Units/mg.
  • Activity
    The dsDNase is highly active in a temperature range of 20-40°C. It needs at least 2.5 mM Mg for activity and has an optimal pH at 7.5.
  • Storage buffer
    20 mM Tris-HCl pH 7.5, 2 mM MgCl2, 10 mM NaCl, 0.01% (v/v) Triton X-100, 50% (v/v) glycerol.
  • Purity
    dsDNase is purified to apparent homogeneity.
  • Storage
    Minimum shelf life is 3 years at -20°C. Storage at 4°C is possible for at least 6 months. The enzyme also tolerates multiple freeze-thaw cycles.

HL-dsDNase

Heat inactivation

The HL-dsDNase can be heat inactivated by heat treatment at 5 min at 58˚C. The enzyme requires 1 mM DTT and pH ≥ 8 for complete inactivation.

Specifications

  • Unit definition
    One unit is defined as an increase in absorbance at 260 nm of 0.001 per minute, using 50 mg/ml of high MW DNA in 50 mM Na-acetate pH 5.0 and 5 mM MgCl2.
  • Specific activity
    Ca. 200 000 Kunitz Units/mg.
  • Activity
    The HL-dsDNase is highly active in a temperature range of 20-40°C. It needs at least 2.5 mM Mg for activity and has an optimal pH at 7.5.
  • Storage buffer
    20 mM Tris-HCl pH 7.5, 2 mM MgCl2, 10 mM NaCl, 0.01% (v/v) Triton X-100, 50% (v/v) glycerol.
  • Purity
    HL-dsDNase is purified to apparent homogeneity.
  • Storage
    Minimum shelf life is 2 years at -20°C. The enzyme also tolerates multiple freeze-thaw cycles.

Publications

Descriptive paper

  1. The Enzyme and the cDNA Sequence of a Thermolabile and Double-Strand Specific DNase from Northern Shrimps (Pandalus borealis).
    Nilsen I., et al. (2010)
    PLoS ONE. 5(4): e10295. doi:10.1371/journal.pone.0010295.

Papers showing use of dsDNase

  1. Seawater environmental DNA reflects seasonality of a coastal fish community
    Eva Egelyng Sigsgaard, Ida Broman Nielsen, Henrik Carl, Marcus Anders Krag, Steen Wilhelm Knudsen, Yingchun Xing, Tore Hejl Holm-Hansen, Peter Rask Møller, Philip Francis Thomsen
    Marine Biology, June 2017, 164:128
  2. A multiplexed amplicon approach for detecting gene fusions by next-generation sequencing
    Beadling, Carol et al.
    The Journal of Molecular Diagnostics , Volume 18 , Issue 2 , 165 – 175
  3. Microbial Typing by Machine Learned DNA Melt Signatures
    Andini, Nadya et al.
    Scientific Reports 7 (2017): 42097. PMC. Web. 15 Feb. 2017.
  4. Palm-Sized Device for Point-of-Care Ebola Detection
    Christian D. Ahrberg, Andreas Manz, and Pavel Neužil. April 11, 2016.
    Anal. Chem., Article ASAP. DOI: 10.1021/acs.analchem.6b00278
  5. A contamination assessment of the CI carbonaceous meteorite Orgueil using a DNA-directed approach.
    Aerts, J. W., Elsaesser, A., Röling, W. F. M. and Ehrenfreund, P. (2016)
    Meteoritics & Planetary Science. doi: 10.1111/maps.12629
  6. Analysis of Ancient DNA in Microbial EcologyOlivier Gorgé , E. Andrew Bennett, Diyendo Massilani, Julien Daligault, Melanie Pruvost, Eva-Maria Geigl , Thierry Grange Springer Protocol
    Microbial Environmental Genomics (MEG)
    Volume 1399 of the series Methods in Molecular Biology pp 289-315.
  7. The Influence of Tissue Procurement Procedures on RNA Integrity, Gene Expression, and Morphology in Porcine and Human Liver TissueKap Marcel, Sieuwerts Anieta M., Kubista Mikael, Oomen Monique, Arshad Shazia, and Riegman Peter. Biopreservation and Biobanking. June 2015, 13(3): 200-206. doi:10.1089/bio.2014.0076.
  8. Identification of a microscopically selected microorganism in milk samples
    N Bracke, et.al – Journal of Dairy Science, Volume 97, Issue 2, February 2014, Pages 609–615
  9. RNA quality matters (pdf)
    M Kubista, J Bjorkman, D Svec, R Sjoback – tataa.com
  10. Double-stranded DNA in exosomes: a novel biomarker in cancer detection
    Basant Kumar Thakur, Haiying Zhang, Annette Becker, Irina Matei, Yujie Huang, Bruno Costa-Silva, Yan Zheng, Ayuko Hoshino, Helene Brazier, Jenny Xiang, Caitlin Williams, Ruth Rodriguez-Barrueco, Jose M Silva, Weijia Zhang, Stephen Hearn, Olivier Elemento, Navid Paknejad, Katia Manova-Todorova, Karl Welte, Jacqueline Bromberg, Héctor Peinadoand David Lyden
    Cell Research (204) 24:766–769. doi:0.038/cr.204.44; published online 8 April 2014
  11. Association of markers of bacterial translocation with immune activation in decompensated cirrhosis
    C Mortensen, et al. – December 2014 – Volume 26 – Issue 12 – p 1360-1366
  12. Transcriptome Analysis Using the Ovation® Single Cell RNA-Seq System
    Expression analysis of mixed populations of cells masks the heterogeneity that exists within that population. Enabling a better understanding of these dynamics at the level of individual cell is vital to understanding the development of tissues and disease progression.
  13. Colonisation and interaction between S. epidermidis and S. aureus in the nose and throat of healthy adolescents
    E. G. A. Fredheim, T. Flægstad, F. Askarian, C. Klingenberg
    European Journal of Clinical Microbiology & Infectious Diseases August 2014
  14. Ancient DNA Analysis Reveals High Frequency of European Lactase Persistence Allele (T-13910) in Medieval Central Europe
    Annina Krüttli, Abigail Bouwman, Gülfirde Akgül, Philippe Della Casa, Frank Rühli, and Christina Warinner1* (2014)
    PLoS One. 2014; 9(1): e86251.doi: 10.1371/journal.pone.0086251
  15. Novel Sensitive Real-Time PCR for Quantification of Bacterial 16S rRNA Genes in Plasma of HIV-Infected Patients as a Marker for Microbial Translocation
    M. Kramski, A.J. Gaeguta, G.F. Lichtfuss, R. Rajasuriar, S.M. Crowe, M.A. French, S.R. Lewin, R.J. Center, and D. F. J. Purcell J Clin Microbiol. 2011 October; 49(10): 3691–3693.
  16. No difference in portal and hepatic venous bacterial DNA in patients with cirrhosis undergoing transjugular intrahepatic portosystemic shunt insertion.
    Christian Mortensen, Stine Karlsen, Henning Grønbæk, Dennis T. Nielsen, Susanne Frevert, Jens O. Clemmesen, Søren Møller, Jørgen S. Jensen, Flemming Bendtsen (2013)
    Liver Int. 2013; 33:1309–1315
  17. An Efficient Multistrategy DNA Decontamination Procedure of PCR Reagents for Hypersensitive PCR Applications.
    Champlot Sophie, Camille Berthelot, Mélanie Pruvost, E. Andrew Bennett, Thierry Grange, Eva-Maria Geigl (2010)
    PLoS ONE. 5(9): e13042. doi:10.1371/journal.pone.0013042.
  18. Genetic characterization of the ABO blood group in Neandertals.
    Lalueza-Fox C., et al. (2008)
    BMC Evolutionary Biolog. 8:342.
  19. The dietary histone deacetylase inhibitor sulforaphane induces human β-defensin-2 in intestinal epithelial cells.
    Schwab M., et al. (2008)
    Immunology. 125(2): 241–251.
  20. The Derived FOXP2 Variant of Modern Humans Was Shared with Neandertals.
    Krause J., et al. (2007)
    Current Biology. 17: 1–5.
  21. Quantification of reverse transcriptase in ALS and elimination of a novel retroviral candidate.
    McCormick A.L., et al. (2008)
    NEUROLOGY. 70: 278-283.
  22. Random DNA fragmentation allows detection of single-copy, single-exon alterations of copy number by oligonucleotide array CGH in clinical FFPE samples.
    Hostetter G., et al. (2009)
    Nucleic Acids Research Advance Access. 38(2): e9.
  23. Experimental Murine Endometriosis Induces DNA Methylation and Altered Gene Expression in Eutopic Endometrium1.
    Lee B., Du H., Taylor H.S. (2009)
    Biology of Reproduction. 80(1): 79-85.
  24. Bacterial communities of disease vectors sampled across time, space, and species.
    Jones R.T, et al. (2009)
    The ISME Journal. 4(2):223-31. doi:10.1038/ismej.2009.111.