Long Ranger® 50% Gel Solutions ® Accugene TBE Buffers
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Lonza Rockland, Inc. www.lonza.com [email protected] Tech Service: 800-521-0390 Customer Service: 800-638-8174 Document # 18693-1007-05 Rockland, ME 04841 USA Long Ranger® 50% Gel Solutions ® AccuGENE TBE Buffers Complete Solutions for DNA Sequencing and Genotyping Specifications Let Lonza partner with you to meet your sequencing Components: 5X 10X and STR analysis research goals. We are committed 0.445 M Tris Base 0.89 M Tris Base to offering you a family of products and services 0.445 M Boric Acid 0.89 M Boric Acid designed to increase your throughput, efficiency and 0.01 M 0.02 M 2 2 2 2 quality. We continue to work with many world class Na EDTA• H2O Na EDTA• H2O genome facilities and core laboratories offering them 18 MΩ water 18 MΩ water the best products for their specific research needs Filtered: 2 µm 2 µm through our varied product line, technical support and Conductivity: 3.14-3.50 mS/cm 3.8-5.06 mS/cm application development. Allow us to contribute to your pH: 8.25-8.38 8.0-8.5 research success. Storage: 18°C-24°C 18°C-24°C Long Ranger® Gel Solution - Long Ranger® Gel Storage Conditions Solution is the core of our sequencing and genotyping TBE buffers should be stored at room temperature and product line. Due to its patented gel formulation, Long out of direct sunlight. TBE buffers are stable for up to 3 Ranger® gels produce longer, accurate reads. months from date of manufacture. AccuGENE TBE Buffer - Our buffer is prepared from the same qualified reagents used to produce our gel Preparing Diluted Solutions solutions. Liquid concentrates are quality tested to Dilute the liquid concentrates with deionized water. Do ensure lot-to-lot consistency. not store diluted solutions for longer than 24 hours. Precautions Buffer Preparation Handling and use of Long Ranger® Gel Solution are 10X TBE identical to handling conventional acrylamide solutions. Concentration grams/L Wear gloves and use all safety precautions required for 0.89 M Tris Base 108.0 g 0.89 M Boric Acid 55.0 g handling acrylamide solutions. Please read the material 2 safety data sheets (MSDS) prior to use. 0.02 M Na EDTA•2H20 7.44 g Storage Conditions Add deionized water to a final volume of 1L, mix Avoid storing solutions in direct sunlight. thoroughly and filter through ≤0.45 µm membrane. Storage Shelf Life NOTE: To obtain optimal results and prevent Temperature precipitation of TBE stock solution, do not allow any dust ® Long Ranger 50% Gel Solution Room 24 months particles to enter the container and pour from the bottle temperature ® rather than inserting a pipette. Make in ≤1 L amounts. AccuGENE 5X and 10X TBE Room 3 months Buffers temperature Do not store in carboy. Store at room temperature. Do not use if precipitate forms. ® AccuGENE 5X and 10X TBE Buffers ® Long Ranger 50% Gel Solution for Automated DNA Liquid Concentrate for Automated DNA Sequencing Sequencing Prepared from qualified reagents, which are used in ® Long Ranger 50% Gel Solution works with all Long Ranger®,AccuGENE® 5X and 10X TBE liquid automated sequencers and is compatible with both dye concentrates, are quality tested to ensure lot-to-lot ® terminator and dye primer chemistry. Long Ranger consistency. Supplied in a convenient container with a Gels offer uniform spacing and sharp peaks, resulting spigot. in long, high-accuracy read lengths. We typically 1 observe a 25% to 30% increase in read length and an increase in base calling accuracy on automated 6. Filter the solution through Whatman® #1 filter paper sequencers when comparing the Long Ranger® matrix (11mM) or a Nalgene® cellulose acetate filter (≤0.45 with standard polyacrylamide gels. µm). 7. If desired, degas the solution for 5 minutes. Storage Conditions 8. Add the appropriate amount of TEMED and APS. Mix Long Ranger® 50% Gel Solution is stable for 24 months gently. from the date of manufacture when stored at room temperature. Store solutions away from direct sunlight. Gel Casting The following steps must be completed without For Best Results delay. • Do not prepare and store premix solutions made from 1. Cast gel and insert comb according to your standard ® Long Ranger 50% Gel Solution. procedure. • Ensure the glass plates are thoroughly clean and 2. Once the gel is polymerized (approximately 30 dust free. Glass plates can accumulate fluorescent minutes), place paper towels soaked in contaminants from many sources including electrophoresis buffer over the ends of the plates and detergents, marker pens, ethanol and other solvents, then cover with plastic wrap. This will prevent poor quality water, and hands or gloves. These moisture loss as the polymerization process invisible contaminants can seriously affect data continues. collection. 3. Allow 2 hours for complete gel polymerization. • Once the gel is polymerized (approximately 30 minutes), place paper towels soaked in Preparing for Electrophoresis electrophoresis buffer over the ends of the plates and 1. Remove the comb and wash the plates as described then cover with plastic wrap. This will prevent in the ABI Automated Sequencer Manual. moisture loss as the polymerization process 2. Prepare a sufficient quantity of electrophoresis buffer continues. Wrapped gels may be stored at 4°C to fill both anodal and cathodal chambers by diluting overnight. 10X TBE stock with deionized water to 1X. • New instrument (matrix) files may need to be 3. Mount the gel cassette onto the sequencing prepared for ABI machines when changing reagents apparatus according to the manufacturer’s or dye sets. instructions. 4. To assure plates and gel are clean, perform the Plate Electrophoresis with the ABI Automated Check module specific to the dye set you are using. DNA Sequencers Gel Preparation 1. Assemble glass plates and spacers in the cassette following the method described in your automated sequencer instructions, or use the Owl Otter™ Sequencing Gel Caster (Model #SGC-1). 2. Mix the gel solution appropriate for your sequencer according to the formulations in the table below. 377-36 cm plates 377-48 cm plates 373-48 cm plates 373-34 cm plates 5% LR/6 M Urea 4.75% LR/6 M Urea 5% LR/8.3 M Urea 5.75% LR/7 M Urea Components 1X TBE 1X TBE 1X TBE 1X TBE Total Volume 50 ml 50 ml 100 ml 100 ml Urea 18.0 g 18.0 g 50.0 g 42.0 g dd Water 26 ml 26.25 ml 42 ml 46.5 ml Long Ranger® 5 ml 4.75 ml 10 ml 11.5 ml 50% 10X TBE 5 ml 5 ml 10 ml 10 ml Fresh 10% 250 µl 250 µl 500 µl 500 µl APS TEMED 35 µl 35 µl 70 µl 70 µl 3. Place the specified quantity of the first four components into a clean beaker and mix gently. 4. To facilitate dissolving the urea, the solution may be warmed, but cool the solution to room temperature prior to the addition of TEMED and APS. 5. If necessary, after the urea has dissolved, bring up to volume with deionized water. 2 ABI Prism® 377 with 36 and 48 cm Plates Electrophoresis with the LI-COR® Sequencing NOTE: Prepare an analysis matrix standard file for Long Ranger® Gel Solution as described in the ABI Systems Prism 377 Automated Sequencer Manual. Gel Preparation 1. Assemble glass plates and spacers in the cassette ® 1. Prepare sample sheet as normal using an following the method described in the Li-COR appropriate setting. Automated Sequencer Manual. 2. Pre-run the gel using the desired module until a 2. Mix the gel solution appropriate for your gel temperature of 51°C is achieved,about 10-20 concentration according to the formulation in the minutes. Do not pre-run longer than necessary to table below. reach 51°C. Gel Length 33 or 41 cm plates 3. Prepare DNA samples as you would for standard automated sequencing gels. Spacer Thickness 0.25 mm 0.2 mm 4. After pre-run is complete, pause the instrument ® 5.5% Long Gel Composition 6% Long Ranger ® and rinse the wells thoroughly with electrophoresis Ranger buffer. 7 M Urea/1.2X TBE 7 M Urea/1X TBE 5. Load samples as described in the ABI Automated Urea 25.2 g 25.2 g Sequencer Manual. ® 6. Run the gel using the desired module. Long Ranger 7. Analyze data as usual. 50% Gel Solution 7.2 ml 6.6 ml 10X TBE 7.2 ml 6.0 ml ABI 373A with 48 cm Plates dd Water (fill to) 60.0 ml 60.0 ml NOTE: Prepare an analysis matrix standard file for ® Long Ranger Gel Solution as described in the ABI 3. Place a 100 ml beaker with a stir bar on a balance 373A Automated Sequencer Manual. and tare the balance. 1. Set the run parameters to 48-cm run length, full scan 4. Measure 25.2 g of urea into the beaker. mode, 4.0% gel type, 31W power and 16-18h 5. Add the recommended amounts of acrylamide and collection time. Set the parameters for the data 10X TBE to the beaker. collection software as usual. 6. Add distilled-deionized water to a target weight of 2. Pre-run the gel for 10-20 minutes, then press “abort 67.5 grams (= 60 ml of gel solution). run” to stop the pre-run. Rinse the wells thoroughly 7. To facilitate the dissolving of urea, the solution may with electrophoresis buffer. be warmed. Prior to the addition of APS and TEMED, 3. Load samples as described in the ABI Automated cool to room temperature.