Enzymatic DNA Synthesis Technology
- What is Enzymatic DNA Synthesis (EDS)?
Enzymatic DNA synthesis (EDS) is a new type of technology for DNA production. It employs three core components: (i) highly engineered terminal deoxynucleotidyl transferase (TdT) enzyme, (ii) reversibly terminated nucleotides, and (iii) solid supports that are preloaded with a short, predefined initiator DNA (iDNA). EDS is performed in an open-air, aqueous medium and without the use of harsh organic solvents. Synthesis occurs, as it would in nature, in the 5′-to-3′ direction in a template-independent manner. Final oligos include a native phosphate group at the 5′ end.
- What role does terminal deoxynucleotidyl transferase (TdT) play in EDS?
TdT is one of the three core components that makes EDS possible. Specialized TdT enzymes, chosen for their unique ability to add diversity during gene recombination, are used to add reversibly-terminated nucleotides to the 3’-end of any single DNA strand with high dependability and coupling efficiency.
- What are some of the benefits of enzymatic vs. chemical synthesis?
Chemically synthesized DNA may use harsh chemicals and may require a third-party to manufacture and ship your oligos, which may cause a delay in your research. Enzymatic synthesis is water-based, accessible to any laboratory, and can produce custom oligos in your laboratory within a day. Enzymatic synthesis also offers the unique capability to add any desired sequence to the 3’-end of an existing, native, single-stranded DNA.
- Can DNA Script assist with long oligo synthesis?
The SYNTAX System synthesizes oligos of up to 80 nt in length. We have used our EDS technology to produce oligos of over 200 nt in length and are developing products to make this capability commercially available .
Synthesizing Oligos with the SYNTAX Instrument
- How many DNA oligos can I synthesize using the SYNTAX System?
The SYNTAX System can synthesize 1-96 different oligos in parallel in a 96-well plate.
- How long does it take to synthesize a 96-well plate of DNA oligos using the SYNTAX System?
- Approximately 6 hours for ninety-six, 20 nt oligos
- Approximately 23 hours for ninety-six, 120 nt oligos
- What is the length of the DNA oligos that can be synthesized on the SYNTAX System?
The SYNTAX System, Model STX-200 can synthesize oligos from 15-80 nt in length using the SYNTAX DNA Synthesis Kit and the SYNTAX 96 Standard Kit. The SYNTAX System, Model STX-200 can synthesize oligos from 15-120 nt in length using the SYNTAX DNA Synthesis Kit and the SYNTAX 96 Hi-Fidelity Kit.
- How much does enzymatic DNA synthesis cost?
The SYNTAX System enables custom DNA oligo printing on a benchtop instrument, giving you full control over oligo production and freeing you from delays and backorders due to third-party manufacturing and logistics challenges. To discuss instrument costs and individual pricing terms, contact us.
SYNTAX System Hardware and Installation
- What are the dimensions of the SYNTAX System?
The SYNTAX System fits on most laboratory benchtops.
- Instrument (benchtop):
Weight: 159 kg | 350 lb
Dimensions (W x H x D): 122 x 66 x 74 cm | 48 x 26 x 29 in
- Vacuum cabinet (freestanding):
Weight: 59 kg | 130 lb
Dimensions (W x H x D): 84 x 66 x 65 cm | 33 x 26 x 26 in
- Instrument (benchtop):
- What electrical or other requirements do I need to consider for installation?
The SYNTAX System requires one 100-240 VAC, ≥15 A, 50/60 Hz single-phase power outlet. Typical power draw is less than 1000 W . For more information regarding bench and laboratory requirements, please contact our Customer Support team at support@DNAScript.com.
- What type of water do I need to provide for post-run and maintenance washes?
The SYNTAX System requires ASTM Type II water or better for these washes. Most water filtration systems in laboratories produce ASTM Type I or II water, which are both acceptable for use with the SYNTAX System. Do not use deionized water supplied by laboratory plumbing because it may contain particulates that can clog the SYNTAX System. For more information regarding bench and laboratory requirements, please contact our Customer Support team at support@DNAScript.com.
- What is involved in installation of a SYNTAX System?
Delivery and installation of a SYNTAX System is coordinated with a DNA Script representative. A site preparation guide is provided to ensure that your laboratory meets installation requirements. After delivery, the instrument will be set up, qualification runs will be performed to ensure proper function, and training will be provided.
- Should I power off the SYNTAX System after each run?
The SYNTAX System is designed to be left running. Shutting down the system between synthesis runs is not necessary. However, if the system will be idle for more than a week, a maintenance wash should be performed immediately following reagent disposal. Afterward, the maintenance wash should be repeated every two weeks if the system sits idle.
- What kind of warranty and support is available for the SYNTAX System?
12 or 24 months of warranty service is included with the purchase of a SYNTAX System and is performed by a trained engineer from DNA Script. Service agreements for additional service coverage for the SYNTAX System can be purchased directly from DNA Script.
- What are the synthesized DNA oligos eluted into?
All synthesized DNA oligos are eluted into biology-grade water.
- What oligo modifications are supported on the SYNTAX System? Probes containing up to two labels per probe can be synthesized using the SYNTAX System. Currently supported labels include five fluorophores (Green 488, Yellow 532, Orange 550, Red 565, and Deep Red 647), three quenchers, and biotin.
- What is the maximum length of a biotin-labeled probe that can be synthesized? Biotin-labeled probes of up to 80 nt in length can be synthesized using a SYNTAX system.
- What are the correct storage conditions for the components of the SYNTAX kits?
- Nucleotides and enzyme reagents: -20°C
- Synthesis reagents: 4°C
- Consumables: 4°C
- Post-processing reagents: RT
- Can SYNTAX reagents be used on other instruments? No, SYNTAX reagents can only be used with the SYNTAX System.
- What preparation is needed for SYNTAX reagents before use? Enzymes are added to the S1 Solution, P1 Solution, and P2 Solution bottles during run setup. The user must also supply ethanol, isopropanol, and ASTM Type II water or better for each run. Please see the SYNTAX System User Guide for detailed instructions.
- I have SYNTAX reagents remaining at the end of the run. Can I use them in a subsequent run? SYNTAX reagents are stable on-board the instrument for 7 days. User-supplied reagents and the consumables need to be fresh/new for each run.
- Can a synthesis plate and other SYNTAX consumables be used more than once? No, plates and other consumables are single-use items. New consumables should be used for each run.
- How much waste is generated per run using the SYNTAX System? The final fluid volume from a full 60-mer and 80-mer run is approximately 2 L and 2.7 L, respectively, with a pH value ranging from 5-7. Please see the SYNTAX System User Guide for more details on the typical waste composition.
- How do I dispose of the waste from a SYNTAX run? Treat used consumables and reagents in accordance with good laboratory practice guidelines. Inquire about appropriate collecting points and approved methods of disposal in accordance with all national, regional, and local regulations..
SYNTAX System and Console Software
- What software do I need to use the SYNTAX System?
The browser-based Console Software enables you to centrally create, manage, and share synthesis design runs and results. The Console Software automatically transfers the print job specifying the oligo sequences to be synthesized to the instrument.
The SYNTAX System Software is accessed using the instrument’s touchscreen, providing run setup guidance, run progress, and results reporting.
- Where is the Console Software hosted? The Console Software has both cloud (online) and on-premises (offline) options. We can work with you to determine the solution that best fits your need and network policies.
- What kind of file format can I use to specify my oligos? The sequences of the oligos to be synthesized can be uploaded using .csv or .xls/.xlsx file formats to the Console Software. Downloadable file templates including a sample sequence are available within the Console Software. In addition, sequences may also be entered directly by typing the text in the sequence editor or using a FASTA file.
- What type of validation of input sequences is performed by the Console Software? Sequences entered will be verified based on length, acceptable bases, valid modifications, and whether the target concentration is supported whether the SYNTAX 60-Cycle Kit or SYNTAX 80-Cycle Kits is being used for the run. In addition, the user is alerted to any oligos that contain regions that are predicted to be challenging to synthesize.
- What concentration can I request for my oligos? The SYNTAX System can produce oligos with concentrations ranging from 4-7 µM for the SYNTAX 60-Cycle Kit and 4-10 µM for the SYNTAX 80-Cycle Kits.
- How do I access the SYNTAX System Software? You access the SYNTAX System Software using the instrument touchscreen. The software automatically starts when the SYNTAX System is powered on.
- Where can I find my list of print jobs in the SYNTAX System Software? Press Start a Run on the SYNTAX instrument’s Home screen to display a list of print jobs.
- Where can I find the run reports for my print jobs in the SYNTAX System Software? Press View Run Results on the SYNTAX instrument’s Home screen and select the appropriate run report.
- Can I view the run reports for my print jobs in the Console Software? Yes, you can view run reports by selecting Synthesis Data > Runs from the Console Software menu.