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Absence of nuclease activity in commonly used oxygen-scavenging systems
BMC Research Notes volume 10, Article number: 606 (2017)
Oxygen scavenging systems are routinely used during single-molecule imaging experiments to improve fluorescent dye stability. Previous work has shown nuclease contamination in the commonly used oxygen scavenging systems. This study evaluates the potential for nuclease contamination in these oxygen scavenging systems.
Linear and plasmid DNA was incubated with two different oxygen scavenging systems (1) protocatechuic acid (PCA)-protocatechuate-3,4-dioxygenase (PCD) and (2) glucose-coupled glucose oxidase/catalase (GODCAT). No nucleic acid degradation was observed on single and double-stranded linear DNA and plasmid DNA, indicating the absence of nuclease contamination in these oxygen scavenging systems.
Previous work has suggested that contaminant nuclease enzymes could be affecting single-molecule studies . Using size-exclusion chromatography, this study reported the presence of nuclease contamination in the 40- and 100 kDa elution fractions of routinely used OSS system with protocatechuic acid (PCA)-protocatechuate-3,4-dioxygenase (PCD), with the 40 kDa fraction exhibiting the highest nuclease activity. Such contamination could compromise DNA integrity during a single-molecule experiment, leading to false or inaccurate data interpretation. Therefore, we decided to test if we can observe similar DNA degradation on linear single- and double-stranded DNA constructs as well as circular plasmid DNA in the presence of the commonly used OSS systems, (PCA)-(PCD) and glucose-coupled glucose oxidase/catalase (GODCAT).
Linear DNA substrates
Linear DNA sequences include the 92-mer strand, 5′-CCC TAC ATC CAT TCC TCG CGT TTT TT(Cy3-T) (T)65-3′, the single-stranded 66-mer, 5′-Cy3 ACC TCC TCA CCT TTC CTC TTT GCT TTC CCC TTT TCT ACA ATA CGG ATA CGG ACG GCT GCA TCT CTG-3′ and the 66-mer double-stranded DNA that contains a complementary 66-mer sequence annealed to the above mentioned 66-mer sequence with a 5′ biotin. DNA oligonucleotides were purchased from Eurofins Genomics.
Plasmid DNA substrates
Double-stranded circular pUC19 plasmid DNA (2686 bp) was tested for potential nuclease contamination. Plasmid DNA was purchased from Invitrogen.
Each reaction contained 0.01 nmol of Cy3 DNA, except for the double-stranded DNA reactions (Fig. 1a, lanes 7–8) that contained 0.01 nmol of Cy3 DNA and 0.01 nmol of the complementary DNA strand. Concentrations for each specified reaction are as follows, 60 nM protocatechuate-3,4-dioxygenase (PCD) (accounting for the 40% of PCD with stabilizer), 5 mM PCA, 35 units/mL glucose oxidase (GOD), 62,500 units/mL catalase (CAT) and 1% d-Glucose. GODCAT OSS includes glucose oxidase, catalase and d-Glucose while PCD OSS contains both PCD and PCA. For experiments with DNase1 (Turbo DNase Ambion, Life Technologies), reactions were performed at a final concentration of 0.4 U in 100 μL and stopped at 20 and 60 s. Reactions were tested in duplicate with the same buffer conditions as Senavirathne et al. . containing 50 mM Tris–HCl pH 7.5, 100 mM NaCl, 5 mM MgCl2 and 0.1 mM DTT at 22 °C for 40 min. Following each reaction, linear DNA was separated on a 15% polyacrylamide gel and plasmid DNA on a 1% agarose gel. SYBR gold was used for nucleic acid staining in addition to direct visualization with DNA containing Cy3. Gels were visualized on a FUJIFILM FLA-5100 instrument.
Results and discussion
Linear, single- and double-stranded, and plasmid DNA substrates were tested for nuclease contamination in oxygen scavenging systems that are routinely used during single-molecule imaging. The nuclease assay consisted of incubating the OSS with the respective DNA and running on a polyacrylamide, in the case of linear DNA, and an agarose gel in the case of plasmid DNA. Using standard protocols [2,3,4], we did not observe any DNA degradation on all DNA substrates tested under the same buffer conditions used by Senavirathne et al.  Fig. 1.
We have compared our reagent sources to those in the previous manuscript by Senavirathne et al. Most of the reagents come from the same source and lot number (Table 1), suggesting that potential contamination from the commercial source may not provide an answer for the degradation observed previously by Senavirathne et al.
Additionally, we have compared our experimental conditions to those in the manuscript by Senavirathne et al. (Table 2). While most concentrations used are similar, there are a few exceptions, which are outlined in Table 2. It is important to note that the largest amount of degradation observed by Senavirathne et al. was for the catalase enzyme. For this, we used a larger concentration of catalase in comparison to the previous study and still did not observe any nucleic acid degradation in our assays.
These findings are important to rule out the potential for nuclease contamination in the common oxygen scavenging systems used in single-molecule imaging . We feel it is of value to reassure the wider scientific community that we do not observe nucleic acid degradation with our samples and that alternative explanations may account for the previously reported DNA degradation . For example, while the most significant degradation observed in the previous work  was for the pBS SK (-) plasmid, in our hands we did not observe any degradation with the pUC19 plasmid DNA (Fig. 1b). This discrepancy could be due to a restriction enzyme contamination rather than a nuclease, in this instance the observed degradation would be sequence specific. If this is true, experiments involving plasmid DNA or sequences with restriction sites may require prior removal of any contaminant enzymes in the oxygen scavenging systems. Alternatively, the nuclease contamination could be an isolated set of data either from contamination introduced during the preparation of the enzyme-based oxygen scavenging samples or contamination directly from the commercial sources. However, the PCD and GOD enzymes tested by Senavirathne et al. and by us were from the same supplier with the same lot number (Table 1), suggesting that that commercial source may not provide a complete answer. Therefore, we encourage labs utilizing oxygen-scavenging systems to test for contaminants that might degrade DNA or RNA in their own experiments to mitigate any experimental artifacts.
Further DNA substrates should be tested with both oxygen scavenging systems (i.e. glucose oxidase/catalase and the PCA PCD system). It would also be good to test in a systematic way other nucleic acid substrates to asses if DNA sequence may be important.
oxygen scavenging system
glucose-coupled glucose oxidase/catalase
Senavirathne G, Liu J, Lopez MA Jr, Hanne J, Martin-Lopez J, Lee JB, Yoder KE, Fishel R. Widespread nuclease contamination in commonly used oxygen-scavenging systems. Nat Methods. 2015;12:901–2.
Lamichhane R, Solem A, Black W, Rueda D. Single-molecule FRET of protein–nucleic acid and protein–protein complexes: surface passivation and immobilization. Methods. 2010;52:192–200.
Senavirathne G, Bertram JG, Jaszczur M, Chaurasiya K, Pham P, Mak C, Goodman MF, Rueda D. Activation-induced deoxycytidine deaminase (AID) co-transcriptional scanning at single-molecule resolution. Nat Commun. 2015;6:10209.
Aitken CE, Marshall RA, Puglisi JD. An oxygen scavenging system for improvement of dye stability in single-molecule fluorescence experiments. Biophys J. 2008;94:1826–35.
HLG and DR designed the experiments. HLG performed the experiments and analyzed the data. PPD performed the experiments with DNase1 and helped analyze the data. HLG and DR wrote the correspondence. All authors read and approved the final manuscript.
We would like to thank Adam Cawte for helpful discussions and feedback.
The authors declare that they have no competing interests.
Availability of data and materials
All data are contained within the manuscript. Materials are available upon request.
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Ethics approval and consent to participate
This work was supported by the MRC London Institute of Medical Sciences (RCUK MC-A658-5TY10) and a start-up grant from Imperial College London. H.L.G. is a fellow of the Swiss National Science Foundation and the Marie Sklodowska-Curie Individual Fellowship.
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Gahlon, H.L., Poudevigne-Durance, P. & Rueda, D. Absence of nuclease activity in commonly used oxygen-scavenging systems. BMC Res Notes 10, 606 (2017). https://0-doi-org.brum.beds.ac.uk/10.1186/s13104-017-2929-6
- Single-molecule imaging
- Oxygen scavenging system
- Protocatechuic acid
- Glucose oxidase