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User Bulletin
Applied Biosystems 3900 DNA Synthesizer
September 22, 2006
SUBJECT: 3900 Software v2.0 Issue Notification
In This User
Bulletin
This user bulletin covers:
•“Overview” on page 1
•“No Cap A Solution Delivered” on page 1
•“Excess Volume Delivery” on page 2
•“Degenerate Base Usage” on page 3
•“FW Values Empty” on page 3
•“Post Process Trityl Off ” on page 3
Overview This User Bulletin describes the currently known issues in the 3900 v2.0 software
and provides workarounds. While the No Cap A Solution Delivered and Excess
Volume Delivery issues are also known to occur in earlier versions of the software,
the remaining issues are limited to the v2.0 software. The No Cap A Solution
Delivered issue and the Post Process Trityl Off issue can affect the chemistry.
No Cap A
Solution
Delivered
When column position 24 has the Disable option button selected in bank 2, no
CAP A solution is delivered to any bank 1 column positions. Similarly, when column
position 48 has the Disable option button selected in bank 4, no CAP A solution is
delivered to any bank 3 column positions. Verify this delivery pattern by watching
the Cap A solution delivery during the synthesis or by viewing the log file.
Use Table 1, “No Cap A Solution Delivered issue workarounds,” to avoid losing runs
in banks 1 or 3.
Table 1 No Cap A Solution Delivered issue workarounds
Bank If ... Then ...
1 Column location 24 contains a
sequence that is not to be used
Delete the sequence and do not
use the Disable option button for
column position 24.
3 Column location 48 contains a
sequence that is not to be used
Delete the sequence and do not
use the Disable option button for
column position 48.
Applied Biosystems 3900 DNA Synthesizer
User Bulletin
2Applied Biosystems 3900 DNA Synthesizer User Bulletin
DRAFT
October 11, 2006 1:29 pm, 3900 UB.fm
3900 Software v2.0 Issue Notification
Excess Volume
Delivery
A software issue has been identified that causes Valve Array 1and 2 to deliver excess
amidite re-prime volume. The software contains default settings in the Service
window on the Dispense tab under Priming Defaults as shown in Figure 1.
Figure 1 Dispense tab in the Service window
The default setting for the Prime Volume is 400µL. This is the volume used when the
valves are primed before a synthesis is begun if you decide to prime at the start of the
synthesis. The default setting for Amidite Re-Prime Every is 30 minutes. This option
specifies the time that amidites will be re-primed if they are about to be used and
have not been used for at least the specified time. The default volume for this Re-
Prime is 30 µL.
If the table value in Figure 1 is not modified by the user, the software will re-prime
the amidites more frequently than every 30 minutes and cause the prime volume to be
greater than 30 µL.
To minimze the occurance of Excess Volume Delivery:
1. Open the 3900 Software.
2. Select Instrument Service.
3. Enter the password 94404.
4. Select the Dispense tab and change the Amidite Re-Prime Every to 120 min.
3Applied Biosystems 3900 DNA Synthesizer User Bulletin
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October 11, 2006 1:29 pm, 3900 UB.fm
Degenerate Base
Usage
Degenerate bases can only be used in banks 1 and 3. If you are using all four banks
(banks 1, 2, 3, and 4) and attempt a synthesis with a degenerate base in bank 2 or 4,
the error messages shown in Figure 2 are generated and the synthesis does not
proceed.
Figure 2 Error messages
To resolve the problem, perform one of the following:
• Group sequences containing degenerate bases together on banks 1 and 3 (a
maximum of 24 degeneracies per run). Non-degeneracies can occupy any
remaining vacant positions, including banks 2 and 4.
or
• When synthesizing 24 or fewer oligonucleotides, degeneracies may be used in
banks 2 and 4 provided banks 1 and 3 do not contain sequences.
FW Values Empty The FW Values Empty issue occurs during software installation and the message
“FW Values Empty” is generated.
If you see this message, close the software and then reopen it. The values should
appear as zeros. If they still do not show as zero, then manually enter 0 into the FW
fields.
Post Process
Trityl Off
If a specialty base (from bottle positions 5, 6, 7, 8, 9, 0) is added to the 5’ position of
the oligonucleotide, all other non 5’-modified oligonucleotides will not execute the
post-process portion of the cycle file method. The post-process method includes the
final detritylation step (if a trityl off synthesis is chosen) and the final wash steps.
The result is that what you expect to be a Trityl Off synthesis is really a Trityl On
synthesis for the unmodified oligonucleotides. (However, the 5’-modified
oligonucleotides will be detritylated if that was specified.)
When synthesizing 5’-modified oligonucleotides, ensure that they are run separately
from the unlabeled oligonucleotides.
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10/2006
Part Number 4379043 Rev. A
Stock Number 108UB18-01
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