Agilent PCR Clean-up Workstation
Application Bulletin

Summary
Agilent PCR Cleanup Workstationconsisting of an Agilent BenchCel
Microplate Handling Workstation (left)
and an Agilent Bravo Automated Liquid
Handling Platform (right).

• A flexible workstation providing
high-throughput PCR clean up• Up to 15 PCR microplates can beprocessed without user intervention• Processing time is approximately 20 min
per microplate (depending on theexact procedure)

System Description

Introduction
The high demand for genomics applications and the considerable improvementin PCR thermocycler speed have createdbottlenecks upstream and downstreamof PCR processes. To address thisdemand, the PCR CleanUp Workstationfrom Agilent Automation Solutions iscustom tailored around the Promega
Wizard SV96 kit, one of the mostsuccessful PCR kits on the market.

The combination of the Agilent Bravo
Automated Liquid Handling Platform and theAgilent BenchCel Microplate HandlingWorkstation provides a flexible, efficient andcompact approach for automated PCR clean
up. The BenchCel robot moves the labware
to and from the Bravo deck. The Bravo gripper assembles and disassembles theVacuum Filtration Station and transports
microplates to and from the station.

Reservoirs and two sets of tipboxes areplaced manually on the Bravo deck at thebeginning of a run. A waste station on theBravo deck can accommodate both tipboxes
and microplates.
The Agilent VWorks Automation Control
software uses a simple drag-and-drop
method to create the event-driven
protocol for the entire process. TheVWorks software includes error checking,error recovery, event reporting, anduser-access management.
This application bulletin outlines a protocol
for the Promega Wizzard SV96 kit using theAgilent PCR Cleanup Workstation. This
workstation setup can process 15 kits in96-well plate format running without manualintervention. The estimated throughput timeis 20 minutes per microplate, depending on
the exact procedures.

Sample and DNA binds tobinding buffer silica membrane
are added to in presence ofbinding plate chaotropic salts

Washing withethanol while
applying vacuum
removes unboundcontaminants

Addition of Nuclease-free water andvacuum releases the bound DNA into thecollection plate

Overview of the PCR cleanup procedure using the Promega Wizzard SV96 kit

MaterialsInstrument Layout

Component List
• Agilent BenchCel Workstation(R-series with 6 stackers)• Agilent Bravo Platform with gripper,
96LT disposable-tip head, 3 x Reservoir, TipWaste, Vacuum Filtration Station• Agilent VWorks Automaton
Control software

The Agilent Bravo deck (top view) withthree reagent reservoirs (locations 1 to3), a waste station (location 6), and a
Vacuum Filtration Station (location 8).
Two tipboxes are manually placed at
locations 4 and 5.

Labware List
• Microplate A: PCR sample plate• Microplate B: Promega Wizard SV
96 binding plates• Microplate C: Promega Wizard SV
96 elution plates• Tipbox A: Agilent Tips 96 LT 200 µL
Reagent List
• Reservoir A: Binding solution• Reservoir B: Ethanol (85%)• Reservoir C: Nuclease-free water

The BenchCel 6 stacker top view with three different microplate types (stackers 1 to 3)
and up to 30 tipboxes (stacker 4).

Conclusions

Protocol Workflow
1. Move tipbox A from BenchCel
stacker 4 to Bravo location 7.

16. Apply vacuum at location 8 for 30 s.

2. Move tipbox A from location 7 to 9.

Loop: Repeat steps 15 and 16 a total of3 times.

3. Move microplate B from BenchCel
stacker 2 to Bravo location 7.

17. Apply vacuum at location 8 for4 min. Wait 1 min.

4. Move microplate B from location 7 to 8.

18. Remove used tips at location 4.

5. Move microplate A from BenchCel
stacker 1 to Bravo location 7.

19. Move microplate B and collar fromlocation 8 to 9.

6. Press on fresh tips at location 9.

20. Move microplate C from BenchCel
stacker 3 to Bravo location 7.

7. Aspirate 100 µL binding solution fromreservoir A and dispense intomicroplate A.
8. Perform mixing with tips.
9. Transfer 200 µL from microplate A tomicroplate B.
10. Remove used tips at location 9.

21. Move microplate C from location 7 to 8.
22. Move microplate B and collar fromlocation 9 to 8.

The Agilent PCR Cleanup Workstation
provides the throughput, flexibility, andwalk-away time necessary to meet thedemands of genomic applications. The
BenchCel Microplate Handling Workstation
handles the wide variety of PCR microplates
on the market and is capable of storing anddelivering a number of different labware types(microplates, tipboxes) simultaneously. The
speed and precision of the BenchCel
Workstation and the Bravo Automated Liquid
Handling Platform can meet the challenge ofa wide range of PCR cleanup demands. TheBravo Platform tip usage is configurable tosupport many reagent layout options.

23. Press on fresh tips at location 5.
24. Aspirate 100 µL water from reservoir Cand dispense into microplate B.

11. Move tipbox A from location 9 towaste at location 6.

25. Wait 1 min. Apply vacuum for 30 s.

12. Move microplate A from location 7 towaste at location 6.

27. Move microplate B from location 8 towaste at location 6.

13. Apply vacuum at location 8 for 30 s.

28. Move collar from location 8 to 9.

14. Press on fresh tips at location 4.

29. Move microplate C from location 8 to 7.

15. Aspirate 200 µL from reservoir B anddispense into microplate B. Wait 1 min.

30. Move collar from location 9 to 8.

26. Remove used tips at location 5.

31. Move microplate C from location 7 to
BenchCel stacker 6.

www.agilent.com/lifesciences/automation
This item is intended for Research Use Only.
Not for use in diagnostic procedures. Information,descriptions, and specifications in this publication
are subject to change without notice.
Agilent Technologies shall not be liable for errors
contained herein or for incidental or consequential
damages in connection with the furnishing,performance, or use of this material.
Promega and Wizard are registered trademarks ofPromega Corporation.
© Agilent Technologies, Inc., 2009
Published in the U.S.A., February 26, 2009
Publication Number 5990-3552EN