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The ABI 3900 Oligo Synthesizer has become very popular for synthesis of standard and special oligos. ABI has not supported this product for several years even though there are many instruments in service to this day. The ABI 3900 instrument and software have remained fundamentally unchanged since its release. The 3900 continues to maintain great potential to serve our customers' needs.

The Biolytic ABI 3900 Upgrade comes packed with new hardware and software features as well as a new computer and monitor running the latest Windows operating system. Included in the upgrade are state of the art valve and motion control systems. The new software is built for Windows 8 and features flexible protocol construction similar to the world renowned Dr. Oligo Synthesizer. The software supports truly independent protocol operation on each bank of 12 oligos while providing the user with real-time feedback during each synthesis run.

ABI 3900 Upgrade Front Panel
Front Panel

ABI 3900 Upgrade

With over two decades of applied experience in the field of oligonucleotide synthesis automation, Biolytic is able to bring you a 3900 upgrade that dramatically improves its performance, adds hardware features and comes with a completely new software package, written from the ground up.

The patent pending Biolytic ABI 3900 Upgrade – Tier 1, greatly reduces cycle time due to the use of 4 drain stations rather than the original 2. The chamber volume is much lower, requiring less time to pressurize and vent.

The Biolytic ABI 3900 Upgrade is customizable and has multi-tier packages to choose from to fit any of your synthesizing needs.

The ABI 3900 Upgrade adds a mechanism to move reagents slowly through the columns creating maximum reaction site efficiency. This allows the use of less reagent while achieving a high reaction efficiency. Most oligos are synthesized using CPG or polystyrene support columns.

The reaction sites within the solid supports are in tight spaces (such as CPG pores), requiring time for reagent to diffuse to the reaction sites. The ability to precisely control reagent flow through the columns allows more efficient diffusion to reaction sites, resulting in higher reaction efficiency even with the use of smaller volumes of reagents.

ABI 3900 Upgrade Bank Vent & Reagent Spill Trough
Bank Vent & Reagent Spill Trough

ABI 3900 Upgrade

The patent pending Biolytic ABI 3900 Upgrade also allows finely tuned control of reaction chamber pressure above and below synthesis columns, preventing liquid from flowing backwards up through columns and eliminating the risk that back flowing reagents may contaminate adjacent syntheses.

The Chamber Flood Damage Control System redirects chamber flood reagents to waste. In the unlikely event of a reagent overflow, excess liquid in the reaction chamber is directed to a waste trough away from the motion control assembly. This protects the motion control assembly from chemical damage, preventing the need for potentially costly and time-consuming repairs.

Truly independent protocol operation on each bank of 12 oligos. The pressure below each bank of 12 synthesis columns is controlled independently, allowing the simultaneous use of up to 4 different protocols in a single synthesis.

Allows use of up to 10 specials. The amidite delivery is highly customizable, allowing any amidite nozzle to dispense to any column position, permitting the use of up to 10 special amidites in addition to the 4 standard amidites used.

Ability to simultaneously use 2 different Oxidizer reagents.The software package allows the use of more than one oxidizer, and permits the configuration of each amidite to automatically select the correct oxidizer to be used in each step of the synthesis. Among other applications, this allows oxidation and sulfurization to be performed in the same synthesis.

Flexible protocol construction. There is no need to use Excel to edit and create protocols. Biolytic's protocol editor uses familiar Drag-and-Drop to edit and create protocols. Select from a range of standard protocols supplied with the software, or finely tune your protocols to meet you individual synthesis needs.

Don't have an ABI 3900 to upgrade? Biolytic offers a Biolytic 3900 that brings you all the Tier 1 features of the ABI 3900 Upgrade without having to supply a preexisting instrument for an upgrade.

Trade in your ABI 3900 for a Biolytic 3900! Biolytic has a trade in program where you give us your old ABI 3900 or other similar instrument for an assessed value to be placed towards a brand new Biolytic 3900.

Disclaimer - This system is sold as an upgrade to an existing compatible instrument. The upgrade does not include the instrument itself. Biolytic Lab Performance, Inc. does not provide any license for any particular chemistry. If any license is required to perform the chemistry want to perform, it is the end user's responsibility to obtain any license that is required.

Patent Pending - Designed and Manufactured in the United States, Fremont, CA by Biolytic Lab Performance, Inc.

*Windows is a registered trademark of Microsoft Corporation

More Features

  • Increased Performance
  • Increased Efficiency (Reduced Reagent and Gas Consumption)
  • Completely eliminates reverse flow cross contamination
  • Reduces errors rates in oligos used for gene construction
  • Allows use of up to 10 specials
  • Ability to simultaneously use 2 different Oxidizer reagents
  • Fine control of reagent flow rate to minimize reagent consumption
  • Truly independent protocol operation on each bank of 12 oligos
  • Biolytic owned and developed software and hardware
  • Customization of hardware & software available upon request


  • User Control New computer & monitor running latest Windows
  • Valve Control Intelligent valve control boards
  • Motion Control Completely closed loop intelligent motion control
  • Reagent Spill Containment Redirected in chamber bottom away from motor system
  • Pneumatics Requires 60 Psi (0.413 Mpa) to 80 psi (0.551 Mpa)
  • Power 100 to 240 VAC, 50 / 60 Hz, 800 VA
  • Manufactured Made in the U.S.A.