Table of Contents
Summary of Contents for OligoMaker X12
- Page 1 Manual January 2nd, 2019 DNA/RNA Synthesizer 2019 OligoMaker X12 220V/60Hz OligoMaker DNA/RNA Synthesizer OligoMaker ApS • Kong Georgs Vej 12 • DK-2000 Frederiksberg • Tel: +45 321 322 00 www.oligomaker.com • email: karl@ross.dk...
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Page 2: Table Of Contents
EAGENTS ............................. 18 RIMING ....................18 EAGENT PRESSURE AND VACUUM TEST ....................... 19 TARTING THE BASIC SYNTHESIS ............................ 19 YNTHESIS ..................19 EMOVING COLUMNS FROM THE EACTION LOCK 10. SYNTHESIS PROTOCOL ........................20 11. MAINTENANCE ..........................25 12. SERVICE ............................26 12.1 ........................26 ERVICE HOLDER POSITION 12.2 ......................... 27 EMOVING THE 12.3 ..........................28 HANGING A VALVE 13. SPARE PARTS ..........................29 14. DECLARATION OF CONFORMITY ....................31 OligoMaker DNA/RNA Synthesizer OligoMaker ApS • Kong Georgs Vej 12 • DK-2000 Frederiksberg • Tel: +45 321 322 00 www.oligomaker.com • email: karl@ross.dk... -
Page 3: Introduction
1. Introduction This manual is a guide in how to operate the OligoMaker X12. OligoMaker is produced by OligoMaker ApS, Kong Georgs Vej 12, DK-2000 Frederiksberg, Denmark - www.oligomaker.com OligoMaker ApS obtained CE marking in May 2009 This manual must be kept in the laboratory next to the OligoMaker. -
Page 4: Touch Screen Manual
Opens for Priming (section 3.3) Manual control Opens for Manual Control (section 3.2) Get data Imports data (section 3.4) Delete Oligo Opens for removing single synthesis Pause Pause in the synthesis Start Synthesis Start the synthesis Center Center the Reaction Block OligoMaker DNA/RNA Synthesizer OligoMaker ApS • Kong Georgs Vej 12 • DK-2000 Frederiksberg • Tel: +45 321 322 00 www.oligomaker.com • email: karl@ross.dk... -
Page 5: Manual Control
Sucktion time can be higher by pushing the button (+50 ms). Time+ Activate the pump. Pump Zero Set Reaction Block in center-position Position Sol Air Switch On and Off the valve from the nitrogen cylinder to acetonitrile (Sol) bottle OligoMaker DNA/RNA Synthesizer OligoMaker ApS • Kong Georgs Vej 12 • DK-2000 Frederiksberg • Tel: +45 321 322 00 www.oligomaker.com • email: karl@ross.dk... - Page 6 For updating the software (instrument) firmware Comments: In order to use the FTP server, the program must introduced to OligoMaker through a USB-stick. OligoMaker will remember the IP address. You can change the log code om12345.log to your own code on both the program on the FTP-server and the USB-stick.
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Page 7: Priming
Release pressure for Acetonitrile DeFlate CpA_Air Release pressure for CapA DeFlate CpB_Air Release pressure for CapB DeFlate Deb_Air Release pressure for Deb DeFlate Ox_Air Release pressure for Ox DeFlate Ox2_Air Release pressure for Ox2 Quit Back to Main (Fig.1) OligoMaker DNA/RNA Synthesizer OligoMaker ApS • Kong Georgs Vej 12 • DK-2000 Frederiksberg • Tel: +45 321 322 00 www.oligomaker.com • email: karl@ross.dk... -
Page 8: Get Data
Opens for Priming (section 3.3) Manual control Opens for Checkpoints (section 3.2) Delete Oligo Opens for removing single syntheses (section 3.6) Pause Pause in the synthesis Start Synthesis Start the synthesis Center Put the Reaction Block into Center-position OligoMaker DNA/RNA Synthesizer OligoMaker ApS • Kong Georgs Vej 12 • DK-2000 Frederiksberg • Tel: +45 321 322 00 www.oligomaker.com • email: karl@ross.dk... -
Page 9: Synthesis
Opens for removing single oligos in the synthesis (section 3.6) Trityl Check The synthesis stops before the Deblock step, insert the holder with tubes, and collect Deblock reagents. Check colour, and press continue in order to proceed the synthesis OligoMaker DNA/RNA Synthesizer OligoMaker ApS • Kong Georgs Vej 12 • DK-2000 Frederiksberg • Tel: +45 321 322 00 www.oligomaker.com • email: karl@ross.dk... -
Page 10: Delete Oligo
3.6 Delete Oligo Delete oligo: Enter the location of the oligo by typing the specific number of the oligo Press Del Press Quit - and the synthesis continue. p.10 OligoMaker DNA/RNA Synthesizer OligoMaker ApS • Kong Georgs Vej 12 • DK-2000 Frederiksberg • Tel: +45 321 322 00 www.oligomaker.com • email: karl@ross.dk... -
Page 11: Terms
The instrument is constructed, so it is possible to add extra valves and bottle holders (upgrade). An engineer from OligoMaker ApS must perform any changes. Operators of the OligoMaker are recommended to attend a workshop on how to use the OligoMaker either at the users location or in the laboratory at OligoMaker ApS in Copenhagen, Denmark. -
Page 12: Safety
OligoMaker cannot start unless the front Lid is in place, and the Reaction Block is filled with 12 columns. When the tubing from the reagents are rinsed (priming), the Valve Manifold has to be placed in the priming position with the waste tub placed below. -
Page 13: Transportation
Service holder position 7. Transportation OligoMaker will be delivered to the customer on a pallet in a wooden box. Unpacking must be done by professionals from OligoMaker ApS. 8. Installation On site requirements: A ventilated hood or similar, connection to power (115 / 220 volts), and connection to Nitrogen (or Argon) bottle (at around 3 bar). -
Page 14: A Quick Guide
8.1 A Quick Guide A Quick Guide to install the OligoMaker X12 DNA synthesizer Provided together with the instrument you will find 5-6 meter of teflon tube (6mm). The 6mm tube should be used for: • Gas inlet (nitrogen or argon) •... - Page 15 From the outlet of the pump you should connect a tubing to the waste container. We recommend that you place the waste container in a ventilated area according to your local safety regulations. p.15 OligoMaker DNA/RNA Synthesizer OligoMaker ApS • Kong Georgs Vej 12 • DK-2000 Frederiksberg • Tel: +45 321 322 00 www.oligomaker.com • email: karl@ross.dk...
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Page 16: Synthesis Start - A Users Guide
OligoMaker X12 has to be operated as intended by a trained operator. The instrument includes an operator’s manual. All valves must be closed, when the OligoMaker is not in use. When the OligoMaker is not in use, keep Reaction Block in Center-position. -
Page 17: Check Reagents
P2 should not fall more than 0,2 during a period of two min. P3 indicates the pressure on the top gas. Manometer Vacuum when pumping Pressure on bottles Wash, Deblock, Cap A, Cap B and Oxidizer Pressure on bottles Activator and Amidites Pressure on Top gas p.17 OligoMaker DNA/RNA Synthesizer OligoMaker ApS • Kong Georgs Vej 12 • DK-2000 Frederiksberg • Tel: +45 321 322 00 www.oligomaker.com • email: karl@ross.dk... -
Page 18: Priming
The tolerated range for the pressure of the vacuum is between -0,2 bar and -0,4 bar. The tolerated range for the pressure for Amidite and special amidite position is between 0,5 bar and 0,6 bar (P1). p.18 OligoMaker DNA/RNA Synthesizer OligoMaker ApS • Kong Georgs Vej 12 • DK-2000 Frederiksberg • Tel: +45 321 322 00 www.oligomaker.com • email: karl@ross.dk... -
Page 19: Starting The Basic Synthesis
When a synthesis is done, the display will show END. 9.7 Removing columns from the Reaction Block The OligoMaker X12 will be delivered with a multi-tool which can be used to remove the columns from the reaction block. Universal tool p.19... -
Page 20: Synthesis Protocol
This short manual will enable you to take advantage of all the flexibility of the synthesis program used by OligoMaker. The standard procedure for loading sequences from your database to the OligoMaker DNA synthesizer is to transfer by using an USB-stick. - Page 21 This is the protocol for setting up communication directly between your database and the OligoMaker Opening time for the valves during the synthesis run. For each reagent you can have individual opening times. All times are calculated in msec. All numbers shown have been used on a demo instrument for 50 nmol DNA synthesis.
- Page 22 All numbers are in msec. When the numbers are adjusted it is important to make sure that all columns are dry before the next reagent is added. The waiting time (3 sec. for DEB) before the vacuum pump will start. p.22 OligoMaker DNA/RNA Synthesizer OligoMaker ApS • Kong Georgs Vej 12 • DK-2000 Frederiksberg • Tel: +45 321 322 00 www.oligomaker.com • email: karl@ross.dk...
- Page 23 Please note: During the synthesis the amidites will be added together with ”TET”. The synthesis protocol for every cycle that contains amidites in position # 1,2,3…0. Some modified reagents require additional coupling time. As above you can add lines or delete lines if required. p.23 OligoMaker DNA/RNA Synthesizer OligoMaker ApS • Kong Georgs Vej 12 • DK-2000 Frederiksberg • Tel: +45 321 322 00 www.oligomaker.com • email: karl@ross.dk...
- Page 24 Copy your sequences from your database and paste them into the “OM data” protocol. Select DMT ”on” or ”off”. ”On” will leave final DMT group on for post synthesis purification. ”Off” will remove the final DMT group according to the DMT protocol. p.24 OligoMaker DNA/RNA Synthesizer OligoMaker ApS • Kong Georgs Vej 12 • DK-2000 Frederiksberg • Tel: +45 321 322 00 www.oligomaker.com • email: karl@ross.dk...
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Page 25: Maintenance
In case of a pump failure, the vacuum pump has to be inspected. The membranes are cleaned with suitable solvent (acetone or ethyl acetate) and the pump is reassembled. If the membranes are damaged, replace the pump. p.25 OligoMaker DNA/RNA Synthesizer OligoMaker ApS • Kong Georgs Vej 12 • DK-2000 Frederiksberg • Tel: +45 321 322 00 www.oligomaker.com • email: karl@ross.dk... -
Page 26: Service
12. Service 12.1 Service holder position Service Holder Position Lift the valve manifold and place it in the service holder position as shown in the picture. p.26 OligoMaker DNA/RNA Synthesizer OligoMaker ApS • Kong Georgs Vej 12 • DK-2000 Frederiksberg • Tel: +45 321 322 00 www.oligomaker.com • email: karl@ross.dk... -
Page 27: Removing The U-Pin
12.2 Removing the U-pin Removing the U-pin When replacing a leaking valve, place the service holder on the OligoMaker. Tighten the two screws which are placed behind the service holder. Place the Valve Manifold on the service holder. To remove the Alu-cover, untie the two screws. Place it behind the row of valves. -
Page 28: Changing A Valve
Ing. Quang Han conducts questions related to the mechanics. The reagent bottles must be opened under a ventilated hood or similar. Power must be switched off, while the instrument is opened during service. p.28 OligoMaker DNA/RNA Synthesizer OligoMaker ApS • Kong Georgs Vej 12 • DK-2000 Frederiksberg • Tel: +45 321 322 00 www.oligomaker.com • email: karl@ross.dk... -
Page 29: Spare Parts
13. Spare parts Spare Parts from OligoMaker ApS will usually be in stock for shipping within 48 hours. OM-1/16-0.5-5 PTFP Tube 1/16” ID 0.5mm 5m OM-1/8-1-5 PTFP Tube 1/8” ID 1mm 5m OM-Va-Bürkert Reagent valve (Bürkert) OM-18-400 Bottle Holder OM-20-400... - Page 30 Peek manifold 1 to 4 OM-Roth-Sieves Molecular Sieves 100g Carl Roth,Germany OM-Display S Display S OM-Display L Display L OM-Manifold Manifold for 96 columns OM-Grease-Tef-70 Teflon Grease 70g OM-KNF-pumpN840 KNF pump N840.1.2FT.18 230V/60Hz OM-KNF-pumpN810USKNF pump N810FT.18 115V/60Hz p.30 OligoMaker DNA/RNA Synthesizer OligoMaker ApS • Kong Georgs Vej 12 • DK-2000 Frederiksberg • Tel: +45 321 322 00 www.oligomaker.com • email: karl@ross.dk...
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Page 31: Declaration Of Conformity
Kong Georgs Vej 12 DK-2000 Frederiksberg Denmark Tel.: +45 321 322 00 VAT no.: DK12783388 www.oligomaker.com Machine: DNA Synthesizer X12 Serial No.: XX-XX-19 2019 Manufacturing Year: 2019 Machinery Directive, ie. Council Directive 2006/42/EC of 17.5.2006 on the approximation of laws relating to macinery.
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