1. Oligonucleotide library design and preparation
2. Bacterial culture
3. Supernatant preparation
4. Nuclease Activity Assay
5. Screening Rounds’ Selection Criteria (Figure 1)
Figure 1 shows the work flow of this methodology, which is divided into two screening rounds. In the first round of screening, we used 5 DNA probes (DNA, DNA Poly A, DNA Poly T, DNA Poly C and DNA Poly G) and also 5 RNA probes (RNA, RNA Poly A, RNA Poly U RNA Poly C and RNA Poly G). The raw data of this screening round can be found in Supplementary Table 1. In the second round, chemically modified probes were synthesized by replacing the RNA sequence with chemically modified nucleosides (All 2'-Fluoro and All 2'-OMethyl) or by the combination of RNA and purines or pyrimidines chemically modified (RNA Pyr-2'F, RNA Pyr-2'OMe, RNA Pur-2'F and RNA Pur-2'OMe). The raw data of this screening round can be found in Supplementary Table 2. A detailed description of the sequences can be found in Table 1. The results obtained from the first screening round are shown in Figure 2, where Salmonella culture supernatants report a clear preference for RNA probes over DNA probes. In contrast, E. coli and culture media controls show very limited capability to degrade RNA probes. In addition, we have calculated the fold difference (FD) between the rate coefficients of Salmonella and E.coli (Supplementary Table 3 and Supplementary Table 4) in order to identify the best performing probes. The calculations were performed as described in the protocol section.
These results suggest the presence of an RNase type of activity derived from Salmonella. Based on the identification of RNA as the preferred nucleic acid type for Salmonella nucleases, we have designed a new library using chemically modified nucleotides to be used in the second round of screening aimed at increasing the specificity of the probes. Figure 3 shows the kinetic profiles of the probes containing chemically modified nucleotides. Interestingly, RNA Pyr-2'OMe and RNA Pur-2'OMe show the best performing kinetic behavior when compared with RNA Pyr-2'F and RNA Pur-2'F, respectively.
These results suggest that Salmonella has an important RNase activity that can be used for selecting probes capable of specifically recognizing this bacteria. Moreover, we observed that 2'-OMe chemically modified nucleosides are more suitable for the type of RNAses secreted by Salmonella. With this in mind, the protocol described in this contribution offers the possibility of exploring the use of nuclease activity as a biomarker.
Figure 1: Bacteria cultures and workflow of the screening process. Preparation of bacteria cultures and supernatants (left). Description of the workflow for the two screening rounds. First screening: The preference for DNA or RNA is evaluated using 10 probes. Second screening: Based on nucleic acid preference, additional probes containing chemically modified nucleotides are evaluated to identify the best performing substrates for a given nuclease activity. Please click here to view a larger version of this figure.
Figure 2: First kinetic screening round. Kinetic profiles of Salmonella, E. coli and culture media (TSB) using DNA and RNA probes. Nuclease activity is represented by relative fluorescence units (RFU). The graphs are representative for at least 3 individually performed experiments. The different samples are labeled as indicated in the graph's legend. Fold difference (FD) values were calculated using the rate coefficients of Salmonella and E. coli for each probe. Please click here to view a larger version of this figure.
Figure 3: Second kinetic screening round. Kinetic profiles of Salmonella, E. coli and culture media (TSB) using chemically modified probes. Nuclease activity is represented by relative fluorescence units (RFU). The graphs are representative for at least 3 individually performed experiments. The different samples are labeled as indicated in the graph's legend. Fold difference (FD) values were calculated using the rate coefficients of Salmonella and E.coli for each probe. Please click here to view a larger version of this figure.
Table 1: Nucleic acid probe sequences. List of all the nucleic acid probes used in this study. Please click here to view a larger version of this figure.
Supplementary Figure 1: Measurement set up. Button clicks and dialog windows describing the stepwise process performed in the acquisition software to set up the different measurement parameters. (A) Desktop icon. (B) Task manager dialog window. (C) Procedure and Temperature Set up dialog windows. (D) Procedure and Kinetic Step dialog windows. (E) Procedure and Read Method dialog windows. Please click here to view a larger version of this figure.
Supplementary Figure 2: Measurement set up. Button clicks and dialog windows describing the stepwise process performed in the acquisition software to set up the different measurement parameters. (A) Procedure and Read Step (Kinetic) Dialog windows. (B) Procedure dialog window (C) "Protocol" menu bar. (D) Well selection dialog window. (E) File name input box. (F) Run New icon used to start the acquisition within the software. Please click here to view a larger version of this figure.
Supplementary Figure 3: Data analysis. Button clicks and dialog windows describing the stepwise process performed in the acquisition software to export acquired data into a spread sheet for further analysis. (A) Plate Matrix dialog window. (B) Plate and Well Selection dialog windows. (C) Plate dialog window and Quick Export context menu. Please click here to view a larger version of this figure.
Supplementary Figure 4: Third screening round (Sequence preference optimization). Description of the different steps involved in an additional screening round aimed at assessing sequence variations. Please click here to view a larger version of this figure.
Supplementary Figure 5: Fourth screening round (Specificity evaluation round). Description of the different steps involved in an additional screening round aimed at increasing specificity. Please click here to view a larger version of this figure.
Supplementary Figure 6: Fifth screening round (Reaction parameter optimization). Description of the different steps involved in an additional screening round aimed at reducing non-target cross reactivity by modulating nuclease activity. Please click here to view a larger version of this figure.
Supplementary Table 1: Raw data from the first screening round. For each probe (labeled in red, on top), the acquisition time and the raw fluorescence values were reported for TSB, E. coli and Salmonella, along with the calculated rate value for each interval. The calculations were carried out as described in the methods section. Please click here to download this file.
Supplementary Table 2: Raw data from the second screening round. For each probe (labeled in red, on top), the acquisition time and the raw fluorescence values were reported for TSB, E. coli and Salmonella, along with the calculated rate value for each interval. The calculations were carried out as described in the methods section. Please click here to download this file.
Supplementary Table 3: Data analysis for the first screening round. For each probe (labeled in red, on top), the following values were obtained for TSB, E. coli and Salmonella: maximum rate values, minimal and maximal interval time points, rate coefficient, fold difference values between Salmonella and E. coli over TSB and fold difference values between Salmonella and E. coli (highlighted in yellow). The calculations were carried out as described in the methods section and the calculation formulas and the step by step calculations are shown in the spreadsheet. Please click here to download this file.
Supplementary Table 4: Data analysis for the second screening round. For each probe (labeled in red, on top), the following values were obtained for TSB, E. coli and Salmonella: maximum rate values, minimal and maximal interval time points, rate coefficient, fold difference values between Salmonella and E. coli over TSB and fold difference values between Salmonella and E. coli (highlighted in yellow). The calculations were carried out as described in the methods section and the calculation formulas and the step by step calculations are shown in the spreadsheet. Please click here to download this file.
Black bottom, non-treated 96 well plate | Fisher Scientific | 10000631 | |
Cytation1 | BioTek | CYT1FAV | |
Eppendorf tubes | Thermofisher | 11926955 | |
Escherichia coli | ATCC | 25922 | |
Microbank cryogenic storage vial containing beads | Pro-Lab Diagnostics | 22-286-155 | |
Nucleic acid probes | Biomers.net | # | |
Phosphate Buffer Saline containing MgCl2 and CaCl2 | Gibco™ | 14040117 | |
Salmonella enterica subs. Enterica | ATCC | 14028 | |
Tris-EDTA | Fisher Scientific | 10647633 | |
Tryptone Soya Agar with defibrinated sheep blood | Thermo Fisher Scientific | 10362223 | |
Tryptic Soy Broth | Sigma Aldrich | 22092 |
Nucleases are a class of enzymes that break down nucleic acids by catalyzing the hydrolysis of the phosphodiester bonds that link the ribose sugars. Nucleases display a variety of vital physiological roles in prokaryotic and eukaryotic organisms, ranging from maintaining genome stability to providing protection against pathogens. Altered nuclease activity has been associated with several pathological conditions including bacterial infections and cancer. To this end, nuclease activity has shown great potential to be exploited as a specific biomarker. However, a robust and reproducible screening method based on this activity remains highly desirable.
Herein, we introduce a method that enables screening for nuclease activity using nucleic acid probes as substrates, with the scope of differentiating between pathological and healthy conditions. This method offers the possibility of designing new probe libraries, with increasing specificity, in an iterative manner. Thus, multiple rounds of screening are necessary to refine the probes' design with enhanced features, taking advantage of the availability of chemically modified nucleic acids. The considerable potential of the proposed technology lies in its flexibility, high reproducibility, and versatility for the screening of nuclease activity associated with disease conditions. It is expected that this technology will allow the development of promising diagnostic tools with a great potential in the clinic.
Nucleases are a class of enzymes that break down nucleic acids by catalyzing the hydrolysis of the phosphodiester bonds that link the ribose sugars. Nucleases display a variety of vital physiological roles in prokaryotic and eukaryotic organisms, ranging from maintaining genome stability to providing protection against pathogens. Altered nuclease activity has been associated with several pathological conditions including bacterial infections and cancer. To this end, nuclease activity has shown great potential to be exploited as a specific biomarker. However, a robust and reproducible screening method based on this activity remains highly desirable.
Herein, we introduce a method that enables screening for nuclease activity using nucleic acid probes as substrates, with the scope of differentiating between pathological and healthy conditions. This method offers the possibility of designing new probe libraries, with increasing specificity, in an iterative manner. Thus, multiple rounds of screening are necessary to refine the probes' design with enhanced features, taking advantage of the availability of chemically modified nucleic acids. The considerable potential of the proposed technology lies in its flexibility, high reproducibility, and versatility for the screening of nuclease activity associated with disease conditions. It is expected that this technology will allow the development of promising diagnostic tools with a great potential in the clinic.
Nucleases are a class of enzymes that break down nucleic acids by catalyzing the hydrolysis of the phosphodiester bonds that link the ribose sugars. Nucleases display a variety of vital physiological roles in prokaryotic and eukaryotic organisms, ranging from maintaining genome stability to providing protection against pathogens. Altered nuclease activity has been associated with several pathological conditions including bacterial infections and cancer. To this end, nuclease activity has shown great potential to be exploited as a specific biomarker. However, a robust and reproducible screening method based on this activity remains highly desirable.
Herein, we introduce a method that enables screening for nuclease activity using nucleic acid probes as substrates, with the scope of differentiating between pathological and healthy conditions. This method offers the possibility of designing new probe libraries, with increasing specificity, in an iterative manner. Thus, multiple rounds of screening are necessary to refine the probes' design with enhanced features, taking advantage of the availability of chemically modified nucleic acids. The considerable potential of the proposed technology lies in its flexibility, high reproducibility, and versatility for the screening of nuclease activity associated with disease conditions. It is expected that this technology will allow the development of promising diagnostic tools with a great potential in the clinic.