Thermo Fisher Scientific 3900 Software Owner's manual

Brand: Thermo Fisher Scientific

Model: 3900 Software

Type: Owner's manual

DRAFT

October 11, 2006 1:29 pm, 3900 UB.fm

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

DRAFT

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.

• 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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Fax: +1 650.638.5884

10/2006

Part Number 4379043 Rev. A

Stock Number 108UB18-01

Information in this document is subject to change without notice. Applied Biosystems assumes no

responsibility for any errors that may appear in this document.

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Thermo Fisher Scientific 3900 Software Owner's manual

Brand: Thermo Fisher Scientific

Model: 3900 Software

Type: Owner's manual

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Thermo Fisher Scientific 3900 Software Owner's manual

Thermo Fisher Scientific 3900 Software Owner's manual

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