Multiple Oligo Synthesis System (MOSS) - Thermo … · Multiple Oligo Synthesis System (MOSS) for the Expedite 8900 Nucleic Acid Synthesis System User’s Guide

Multiple Oligo Synthesis System (MOSS)for the Expedite 8900 Nucleic Acid Synthesis System

User’s Guide

© Copyright 2001, Applied Biosystems. All rights reserved.

Printed in the United States of America. This book or parts thereof may not be reproduced in any form without the written permission of the publishers.

For Research Use Only. Not for use in diagnostic procedures.

NOTICE

Information in this document is subject to change without notice and does not represent a commitment by Applied Biosystems. Applied Biosystems assumes no responsibility for any errors that may appear in this document. This manual is believed to be complete and accurate at the time of publication. In no event shall Applied Biosystems be liable for incidental or consequential damages in connection with or arising from the use of this manual.

U.S and foreign patents pending.

Applied Biosystems grants the customer of synthons in the accompanying package a license to manufacture PNA oligomers for internal use only. Sale of PNA oligomers manufactured with the synthons, or resale of the synthons, is prohibited and may constitute patent infringement.

Applied Biosystems is a registered trademark, and Expedite is a trademark, of Applera Corporation or its subsidiaries in the U.S. and certain other countries.

Waters and Delta-Pak are trademarks of Waters Corporation. Millipore is a trademark of Millipore Corporation.

WARNING

Most of the reagents and solvents used in nucleic acid synthesis are hazardous. Wear a lab coat, gloves, and eye protection when handling reagents. Adequate ventilation is essential and working under a fume hood is recommended. Consult Appendix B, Reagent Safety in the Expedite 8900 Nucleic Acid Synthesis System User’s Guide.

AVERTISSEMENT

La plupart des réactifs et solvants employés en synthèse PNA sont dangereux. Portez une blouse, des gants et des lunettes de protection lorsque vous manipulez des réactifs. Une ventilation adéquate est nécessaire et il est recommandé de travailler sous une hotte. Consultez la partie Appendix B, "Reagent Safety," du manuel Expedite 8900 Nucleic Acid Synthesis System User’s Guide.

US Safety and EMC (Electromagnetic Compliance) Standards

SafetyThis instrument has been tested to and complies with standard ANSI/UL 1262, “Electrical Equipment for Laboratory Use; Part 1: General Requirements”, 1st Edition. It is an ETL Testing Laboratories listed product.

EMCThis device complies with Part 15 of the FCC Rules. Operation is subject to the following two conditions: (1) This device may not cause harmful interference, and (2) this device must accept any interference received, including interference that may cause undesired operation.

Warning: Changes or modifications to this unit not expressly approved by the party responsible for compliance could void the user’s authority to operate the equipment.

Note: This equipment has been tested and found to comply with the limits for a Class A digital device, pursuant to Part 15 of the FCC Rules. These limits are designed to provide reasonable protection against harmful interference when the equipment is operated in a commercial environment. This equipment generates, uses, and can radiate radio frequency energy and, if not installed and used in accordance with the instruction manual, may cause harmful interference to radio communications. Operation of this equipment in a residential area is likely to cause harmful interference in which case the user will be required to correct the interference at his own expense.

Note: Shielded cables must be used with this unit to ensure compliance with the Class A FCC limits.

Canadian Safety and EMC (Electromagnetic Compliance) Standards

SafetyThis instrument has been tested to and complies with standard C22.2 No. 151, “Safety Requirements for Electrical Equipment for Measurement, Control, and Laboratory Use; Part 1: General Requirements”. It is an ETL Testing Laboratories listed product.

SécuritéCet instrument a été vérifié avec la norme C22.2 No. 151, «Spécifications de sécurité du matériel électrique utilisé pour les mesures, les contrôles et dans les laboratoires ; Partie 1 : Spécifications générales», et il est conforme à cette norme. C’est un produit homologué par les ETL Testing Laboratories.

EMCThis Class A digital apparatus meets all requirements of the Canadian Interference-Causing Equipment Regulations.

Cet appareil numérique de la classe A respecte toutes les exigences du Règlement sur le materiel brouilleur du Canada.

European Safety and EMC (Electromagnetic Compliance) Standards

Declaration of Conformity

Application of Council Directive(s): 73/23/EEC “Low Voltage”

89/336/EEC “Electromagnetic Compatibility”

Standard(s) to which conformity is declared:

IEC 1010-1 “Safety Requirements for Electrical Equipment for Measurement, Control and Laboratory Use”

EN55011:1991, Group 1, Class B “Radiated Emissions”

EN50082-1:1992 “Generic Immunity”

Manufacturer’s Name: Applied Biosystems

Manufacturer’s Address: 500 Old Connecticut Path

Framingham, Massachusetts 01701 USA

Type of Equipment: Laboratory Instrumentation

Model Name & Number: Expedite Nucleic Acid Synthesis System, Models 8905 and 8909

Part Number: GEN600041 or GEN600042

Serial Number: FX???8200? and laterQuestion marks represent date and manufacturing codes that are part of the serial number.

Year of Manufacture: 1995 and later

Table of Contents

Table of Contents

How to Use This Guide .............................................................................. ix

Chapter 1 Overview of the MOSS Option ..................................1-1

Chapter 2 Performing a Synthesis2.1 Overview .............................................................................. 2-2

2.2 Creating the Sequences ........................................................... 2-3

2.3 Defining the Synthesis Set ........................................................ 2-3

2.4 Checking Reagent Resources .................................................... 2-9

2.5 Priming the System ................................................................ 2-11

2.6 Installing the Reaction Columns ................................................ 2-17

2.7 Emptying the Waste ............................................................... 2-19

2.8 Starting the Synthesis Set ........................................................ 2-20

2.9 Monitoring the Syntheses......................................................... 2-22

Chapter 3 Maintenance Procedures3.1 Replacing Inline Filters ............................................................. 3-2

3.2 Replacing Post-Column Filters ................................................... 3-4

3.3 Replacing the Gas Cylinder ....................................................... 3-7

Appendix A Performance Specifications .................................. A-1

Appendix B Technical Support and Training.......................... B-1

Index

Expedite 8900 MOSS User’s Guide vii

How to Use This Guide

How to Use This GuidePurpose of this

guideThe Applied Biosystems Multiple Oligo Synthesis System (MOSS) for the Expedite 8900 Nucleic Acid Synthesis System User’s Guide describes the features and use of the Multiple Oligo Synthesis System (MOSS) for the Expedite Nucleic Acid Synthesis System.

Structure of thisguide

Applied Biosystems Multiple Oligo Synthesis System (MOSS) for the Expedite 8900 Nucleic Acid Synthesis System User’s Guide is divided into chapters. The table below describes the material covered in each chapter.

Chapter 1, Overview ofthe MOSS Option

Describes the Multiple Oligo Synthesis System (MOSS) for the Expedite Nucleic Acid Synthesis System.

Chapter 2, Performing a Synthesis

Provides the procedure for synthesizing a set of sequences on the Expedite system with the MOSS option.

Chapter 3, Maintenance Procedures

Explains how to replace inline filters, post-column filters, and the gas cylinder.

Chapter 4, Installing the Software

Describes how to install the Expedite Macintosh Interface software.

Appendix A, Performance Specifications

Provides specifications for the performance of the MOSS system, and miscellaneous specifications.

Appendix B, Technical Support and Training

Describes how to contact Technical Support, obtain technical documents, and obtain customer training information.

Expedite 8900 MOSS User’s Guide ix

How to Use This Guide

Conventions This guide uses the following conventions to make text easier to understand.

Generalconventions

• Bold indicates user action:

“Type 0 and press Enter for the remaining fields.”

• Italic text denotes new or important words, and is also used for emphasis:

“Before analyzing, always prepare fresh matrix.”

Notes, Cautions,and Warnings

A note calling out important information to the operator appears as:

NOTE: Record your result before proceeding with the next step.

A caution calling out information to avoid damage to the system or equipment appears as:

CAUTION

Changing reagent bottles during a synthesis is not recommended. Check the reagent resources prior to initiating a synthesis to make sure that there is a sufficient supply.

A warning calling out information essential to the safety of the operator appears as:

WARNING

The Expedite Cabinet weighs 102 pounds (46 kg). Two people are required to safely lift the instrument cabinet.

x Applied Biosystems

1Overview of the MOSSOption 1

Features The Multiple Oligo Synthesis System (MOSS) Option is a column expansion module for the Expedite 8909 Nucleic Acid Synthesis System.

The MOSS Option provides:

• Sixteen column positions (expanded from 2 column positions)

• Unattended synthesis of up to 16 sequences

• Low reagent consumption

• A full range of synthesis protocols

• Ability to monitor all syntheses

The MOSS column expansion module sits on top of the Expedite instrument (Figure 1-1). No additional bench space is required.

Expedite 8900 MOSS User’s Guide 1-1

Chapter 1 Overview of the MOSS Option

1

Figure 1-1 Expedite Instrument with MOSS Option

Parts of the MOSSoption

The MOSS Option includes:

• MOSS column expansion module• Expedite instrument software version 2.1 or later • Expedite Workstation software version 2.1 or later• A 2-liter halogenated waste bottle

Workstationcontrol

You control the MOSS option with the Expedite 8900 Workstation Software, version 2.1 or later. Refer to the Expedite 8900 Workstation Software User’s Guide for more information on the Workstation software.

A single Expedite Workstation can control up to:

• Six instruments with no MOSS option attached

• Four instruments if one or more MOSS options are attached

The same workstation can control standard Expedite instruments, Expedite instruments with MOSS option, and instruments with different chemistries specified.

PB100394

Moss moduleon top ofExpedite Instrument

1-2 Applied Biosystems

1
Initial installation The MOSS Option must be installed on the Expedite Model 8909 system by an Applied Biosystems Service Representative.
Your Applied Biosystems Service Representative installs appropriate fluidic, electronic, power, and communications (RS-422/485) connections between the MOSS option and the Expedite instrument.

Supportedprotocols

You must run supported MOSS protocols with the MOSS unit installed. The fluidics system is modified with the MOSS option and does not support protocols designed for Expedite instruments without MOSS options.

NOTE: The 15 µmole scale DNA protocol is not currently supported on Expedite instruments with the MOSS option.

UPS The Expedite instrument with the MOSS option can synthesize up to sixteen unattended sequences. The Expedite instrument contains sensors that detect a failure in the gas system. We recommend an Uninterruptable Power Source (UPS) that protects the instrument and computer from utility line failures that could result in loss of synthesis.

In the event of a blackout, brownout, or sag, the UPS rapidly transfers the instrument to an alternative power source. The alternative power source is derived from a rechargeable battery within the UPS and provides you with ample time (up to 30 minutes) to continue the synthesis to a chemically safe stopping point.

You can configure the stopping point in the user profile. You can also specify in the user profile whether you want the synthesis to resume after the power is restored and a UPS is installed.


Chapter 1 Overview of the MOSS Option

1
Waste disposalprecautions
The MOSS option can produce more than 4 liters of waste when using an 800-cycle reagent kit. Keep the waste bottles in a spill tray and empty all waste before starting a synthesis run.

WARNING

Make sure that you use a 2 L halogenated waste bottle provided with the MOSS instead of the standard 1 L halogenated waste bottle.

AVERTISSEMENT

Faites toujours en sorte d’utiliser un flacon d’écoulement << halogéné >> de 2 litres, fourni avec le système MOSS, au lieu du flacon << halogéné >> d’un litre, fourni avec le moniteur de trityle.


2
2Performing a Synthesis
This chapter contains the following sections:

2.1 Overview ................................................... 2-2

2.2 Creating the Sequences ............................ 2-3

2.3 Defining the Synthesis Set ......................... 2-3

2.4 Checking Reagent Resources.................... 2-9

2.5 Priming the System................................... 2-11

2.6 Installing the Reaction Columns............... 2-17

2.7 Emptying the Waste................................. 2-19

2.8 Starting the Synthesis Set ....................... 2-20

2.9 Monitoring the Syntheses ........................ 2-22


Chapter 2 Performing a Synthesis

2

2.1 Overview

This chapter describes the step-by-step procedure for synthesizing a set of sequences on the Expedite system with the MOSS option.

Synthesis sets The MOSS option allows you to run syntheses on up to sixteen columns. You specify the synthesis parameters for columns in a synthesis set.

Overview Operation is very similar to standard Expedite operation, with the differences noted below.

The key steps to running a synthesis set are:

1. Create or edit sequences.

2. Define the synthesis set (new with MOSS option).

3. Print the synthesis set list (new with MOSS option).

4. Check the reagent resources and install the necessary reagents.

5. Prime the system (different with MOSS option).

6. Install the reaction columns.

7. Empty the waste.

8. Start the synthesis.

9. Monitor the syntheses.


Creating the Sequences

2

2.2 Creating the Sequences

Create or edit sequences as described in Section 3.2, Creating or Editing the Sequence, in the Expedite 8900 Workstation Software User’s Guide.

2.3 Defining the Synthesis Set

A synthesis set defines the synthesis to run on each column.

NOTE: If you are running an Expedite instrument with the MOSS option, this section replaces Section 3.4.1, Specifying the Synthesis Parameters, in the Expedite 8900 Workstation Software User’s Guide.

Specifying thechemistry

Before defining the synthesis set, define the chemistry to use in the user profile.

To change chemistry type, see Section 3.6.7, Changing the Chemistry, in the Expedite 8900 Nucleic Acid Synthesis System User’s Guide.

Defining thesynthesis set

To select the sequences and specify the synthesis parameters:

1. Select Synthesis from the Run menu in the Workstation Main Window.

The Run Synthesis dialog box (Figure 2-1) is displayed.



2

Figure 2-1 Run Synthesis Dialog Box

1. Click on a column position. The bottom portion of the screen displays the parameters for the selected column.

2. Click the arrow next to the Sequence field and do one of the following:

• Select a sequence name

• Select database to retrieve a sequence from the Expedite database

• Select foreign to open a foreign sequence

You can also enter a new sequence by clicking on the Edit sequence button.


Defining the Synthesis Set

2

The 3' base connected to the solid support is displayed in the Column field (specified in the selected sequence).

3. In the Protocol field, select a protocol name from the drop-down list. You can use different protocols (scales) for each column.

NOTE: The 15 µmole scale DNA protocol is not currently supported on Expedite instruments with the MOSS option.

4. Click the Final DMT On or Off button to specify whether you want the final 5' DMT group on or off.

If you choose to keep the final DMT on, it can be removed by performing the final deblock routine from the Prime menu on the instrument after the synthesis has been completed (see Section 3.5.5, Final Deblock, in the Expedite 8900 Nucleic Acid Synthesis System User’s Guide).

NOTE: The observed intensity of the orange-colored solution released by the final deprotection is a qualitative indication of the success of a synthesis.

NOTE: The Universal Support option is not currently available for use with the MOSS option.

5. Repeat step 1 through step 4 for each column.

NOTE: For efficient operation, set up syntheses on both column 1 and column 2 positions, instead of setting up all syntheses on column 1 or column 2. The instrument runs syntheses on column 1 and 2 positions simultaneously using alternating phase delivery of reagents.



2

Editing thesynthesis set

You can display the Run Synthesis dialog box at any time to:

• View the status of the column positions

• Edit syntheses that have not yet run (Ready status)

• Add new syntheses to positions that are finished (Done status) or empty (Idle status).

To edit the synthesis set:

1. Select a column position that is not currently running on the instrument (Ready or Done status).

2. Edit settings as needed, or click Clear Item to remove the selected synthesis from the set. Click Clear All to remove all syntheses from the list.

Printing thesynthesis set

After defining the synthesis set, click the Print List button to print a listing of the each syntheses with synthesis parameters (Figure 2-2).

Use the printout to determine the correct column to install in each column position in the MOSS unit, described in Section 2.6, Installing the Reaction Columns.


Defining the Synthesis Set

2

Figure 2-2 Print Listing

Transferring theprotocol

Click OK to accept all the changes and transfer the first protocol from each column to the instrument. Click Close to close the Run Synthesis dialog box without transferring.

During the transfer, the dialog box shown in Figure 2-3 is displayed.

Figure 2-3 Transferring the Protocols

Run DNA-Chemistry Synthesis on MOSS12 (12) Page 1 *Expedite(TM) Nucleic Acid Synthesis System (Workstation) ** Wed Oct 25 17:38:34 1995 ***************************************************************************Position Column Sequence Protocol DMT Status 1a 50 nmol G sequence1 *MOSS .05 umole On Ready 1b 1 umol T new sequence *MOSS 1 umole On Ready 1c 1 umol A sbd8 *MOSS 1 umole Off Ready 1d On 1e 200 nmol A aa *MOSS 0.2 umole On Ready 1f On 1g On 1h On 2a 1 umol A sbd8 *MOSS 1 umole Off Ready 2b 200 nmol T new sequence *MOSS 0.2 umole Off Ready 2c 50 nmol G sequence1 *MOSS .05 umole On Ready 2d On 2e On 2f On 2g On 2h On



2

Reminder dialogbox

When the transfer of the first syntheses to the instrument is complete (or any time after the synthesis set is run to completion and a new synthesis set is started), the Reminder dialog box shown in Figure 2-4 is displayed.

Figure 2-4 Reminder Dialog Box

The dialog box reminds you to:

• Check the reagent resources and waste containers.• Prime the system.• Prime the column positions.• Load the columns on the instrument.• Start the synthesis.

Click OK to continue.

The Workstation Main Window is displayed and the system is ready to begin the synthesis.


Checking Reagent Resources

2

2.4 Checking Reagent Resources

To check the reagent resources, do one of the following:

• Click the Rsrc button at the bottom of the Workstation instrument window.

• In the Run menu, select Resources.

The Resources dialog box (Figure 2-5) is displayed.

Figure 2-5 Resources Dialog Box

The Resources dialog box lists the following volumes:

• Req—Volume needed for current synthesis

• Current—Volume in reagent bottle

• Total Reqd.—Volume needed to complete the entire synthesis set (all syntheses with Ready or Running status), including the current synthesis



2

If the required volume of any reagent is less than or equal to its current volume, that reagent is flagged with an exclamation point (!) (see Figure 2-5). The total count of the reagents with insufficient volumes is displayed below the list.

In this dialog box, you can click:·

• Print—To print current resource requirements• Close—To close the dialog box• Help—For related information

If additional reagents are required to complete the synthesis run, install them on the instrument (see Section 2.4, Preparing and Loading the Reagents, of the Expedite 8900 Nucleic Acid Synthesis System User’s Guide).


Priming the System

2

2.5 Priming the System

CAUTION

Run the priming routines before you install columns. The priming procedures deliver the reagents through the column positions and could damage the column.

RecommendedPriming Routine

Priming is critical to the success of your synthesis. Insufficient priming can cause your synthesis to fail. To ensure that your system is primed sufficiently, always:

• Use the Prime All option to prime column 1 two times.

• Use the Prime All option to prime column 2 one time.

NOTE: If all reagents have been changed, or if water has been introduced into the system, use Prime All three times on each column.

• Use the Prime Individual option to prime all other column positions the synthesis uses. Prime each of these column positions two times with wash (internal).

When to prime thereagents

Prime the reagents using the options on the MOSS Prime menu if:

• The instrument has been idle for more than 12 hours• This synthesis is the first since instrument power-up• The reagents have been changed or replenished



2

Priming Options Use Table 2-1 to choose a MOSS priming option.

NOTE: Each priming pulse moves 16 ml of fluid.

Table 2-1 MOSS Priming Options

If you select . . . This happens . . .

Prime Individual • You can choose individual reagents

• The system delivers 20 pulses of selected reagent

Prime All • The system primes all reagents

• The system delivers:

• 10 pulses from monomers• 20 pulses from activator, caps, and

auxiliary• 30 pulses from Wash (internal)• 120 pulses from Wash A (external)• 120 pulses of deblock• A gas flush to dry the lines

Prime Reagents • The system primes ancillary reagents including activator and wash


• 20 pulses from activator, caps, and auxiliary

• 30 pulses from Wash (internal)• 120 pulses from Wash A (external)• 120 pulses of deblock• A gas flush to dry the lines

Prime Monomers • The system primes monomers only


• 10 pulses from monomers• 20 pulses from activator• 30 pulses from Wash (internal)• A gas flush to dry the lines


Priming the System

2

Fluid PathVolumes

Use Table 2-2 to calculate fluid path volumes.

Table 2-2 Fluid Path Volumes (ml)

Position FritTube to

PlatePlate

VolumePlate to Column

Total to Column

A 250 70 7 320 647

C 250 70 11 320 651

G 250 70 16 320 656

T 250 70 20 320 660

5 250 70 24 320 664

6 250 70 27 320 667

7 250 70 30 320 670

8 250 70 34 320 674

9 250 70 37 320 677

Act 250 120 43 320 733

Wash 250 120 46 320 736

Dblk 250 1200 6 320 1776

Aux 250 120 9 320 699

Ox 250 120 14 320 704

Cap B 250 120 18 320 708

Cap A 250 120 22 320 712

Wsh A 250 1200 26 320 1796



2

PrimingProcedure

NOTE: Watch the waste lines during the first full prime to make sure all valves are functioning.

The procedure for using Prime Individual is different from the procedure for using Prime All, Prime Reagents, and Prime Monomers. Therefore, this section provides two priming procedures:

• Prime Individual• Prime All, Prime Reagents, and Prime Monomers

Prime Individual To use the Prime Individual option:

1. Install a union in the column positions to be primed.

2. Choose Prime from the Main menu on the instrument.

The Prime menu is displayed.

3. Select Prime Individual.

4. Choose either Individual Positions or All Positions and the appropriate column (Figure 2-6).

Figure 2-6 Individual or All Positions Prompt

If you choose:

• Individual Positions, go to step 5.• All Positions, go to step 6.


Priming the System

2

5. Choose the MOSS position if needed (Figure 2-7).

Figure 2-7 MOSS Position Prompt

The Prime Individual window appears. It prompts you to put unions on all positions.

6. Choose the reagent to prime from the Reagent menu. You may need to select the option MORE to find the reagent you need.

Priming starts. During the prime, the current action is displayed on the screen. Press the Stop key to abort the priming procedure.

7. When priming for that reagent stops, choose Pulse, Cycle, Next, or Cancel:

• Pulse delivers a single pulse• Cycle repeats the routine• Next primes the next position with the reagent• Cancel returns you to the Reagent menu

8. Repeat step 6 to step 7 for each additional reagent you need to prime.

9. When priming is completed, choose Exit to return to the Prime menu.

10. Choose Exit to return to the Main menu.



2

Prime All, PrimeReagents, or Prime

Monomers

Follow this procedure to use the Prime All, Prime Reagents, or Prime Monomers option on the Prime menu.

1. Install a union in the column positions to be primed.

2. Choose Prime from the Main menu on the instrument.

The Prime menu appears.

3. Select Prime All, Prime Reagents, or Prime Monomers.

4. Under Individual Positions, choose the appropriate column (Figure 2-8).

Figure 2-8 Individual Positions Prompt

5. Choose the MOSS position (Figure 2-9).

Figure 2-9 MOSS Position Prompt

6. Select OK to confirm that a union is in place.

Priming starts. During the prime, the current action is displayed on the screen. Press the Stop key to abort the priming procedure.


Installing the Reaction Columns

2

7. When priming for that reagent stops, choose Cycle, Next, or Cancel:

• Cycle repeats the routine• Next primes the next position with the reagent• Cancel returns you to the Reagent menu

8. Choose Exit to return to the Main menu.

2.6 Installing the Reaction Columns

CAUTION

Run priming routines before you install the columns. The priming procedures deliver the reagents through the column positions and could damage the column.

Use the printout from the synthesis list (see Figure 2-2) as a guide to place each column type (3' base and scale) in the appropriate position.

Column locations Figure 2-10 shows the column locations in the MOSS unit.

Figure 2-10 Column Positions

This figure is also printed on the inside of the door of the MOSS column expansion module.

1a 1b 1c 1d

1e 1f 1g 1h

2a 2b 2c 2d

2e 2f 2g 2h



2

Installing To install the columns:

1. Remove the union from the column position. Place the union on the pins located in front of each column.

NOTE: CPG columns are bidirectional and can be attached in either orientation.

2. Firmly insert the columns onto the Luer fittings on the base of the column expansion module. Use a slight twisting motion—about one quarter turn.

3. Insert a post-column filter into the column outlets. Use a slight twisting motion—about one quarter turn.

NOTE: Replace post-column filters at the intervals specified in Section 3.2, Replacing Post-Column Filters.

4. Insert the upper column fittings into the top of the post-column filter. Use a slight twisting motion—about one quarter turn. Make sure that the label on the upper column fitting matches the position label below the lower column fitting.


Emptying the Waste

2

2.7 Emptying the Waste

Keep all waste containers in a spill tray.

Before starting the synthesis, empty each waste reservoir. This is particularly important when using the MOSS option for the Expedite instrument because the increased synthesis capability leads to a greater volume of chemical waste. The 4-liter waste bottle can contain all the waste from an 800-cycle reagent kit.

WARNING

Make sure that you use a 2 L halogenated waste bottle provided with the MOSS instead of the 1 L halogenated waste bottle provided with the trityl monitor.

AVERTISSEMENT

Faites toujours en sorte d’utiliser un flacon d’écoulement << halogéné >> de 2 litres, fourni avec le système MOSS, au lieu du flacon << halogéné >> d’un litre, fourni avec le moniteur de trityle.



2

2.8 Starting the Synthesis Set

To start the synthesis set when the workstation is in Local mode, do one of the following:

• Click the Start button at the bottom of the instrument window.

• In the Run menu, select Start.

• Press the Start button in the Main menu on the instrument keypad.

NOTE: In Remote mode, you must use the Expedite instrument keypad to start the synthesis set.

During thesynthesis

The synthesis on the first positions of each column begins. When a synthesis is completed on a column, the synthesis information from the next position is downloaded to the instrument and automatically started.

Keeping theExpedite

workstationsoftware running

You must keep the Expedite workstation software running during a synthesis.

NOTE: Do not exit the Expedite software when a sequence is running on the MOSS unit. If you exit the software, the currently running syntheses on the instrument run to completion, but the next sequences cannot be sent to the instrument. The Expedite software can be running in the background while you are running another Windows application in the foreground.


Starting the Synthesis Set

2

If you exit theExpedite software

If you exit the Expedite software during a synthesis, do the following to initiate remaining syntheses in the set:

1. Open the Expedite workstation software.

2. Display the Run Synthesis dialog box and re-enter the synthesis information for the columns that have not been run.

Refer to the Instrument Status screen to determine the last columns completed. Refer to the print listing for the information on remaining columns that you need to re-enter. See Section 2.3, Defining the Synthesis Set.

3. Click OK.

4. Start the synthesis again.



2

2.9 Monitoring the Syntheses

After the synthesis set is started, all the operations of the instrument and Workstation are the same as for a standard Expedite instrument (except new sequences are automatically downloaded and started on the instrument).

Monitoring the currently running syntheses is the same as on the standard Expedite (see Section 3.5, Monitoring the Synthesis, of the Expedite 8900 Workstation Software User’s Guide).

Holding,stopping, or

aborting

The procedures for stopping, holding, and aborting currently running syntheses are also the same. See the following sections in the Expedite 8900 Workstation Software User’s Guide for more information:

• Section 3.7.1, Holding a Synthesis• Section 3.7.2, Stopping a Synthesis• Section 3.7.3, Aborting a Synthesis

If a synthesis is aborted, the Workstation automatically downloads the next synthesis to the instrument.

Data storage When a sequence is completed, the synthesis information is stored in the Expedite database. Reports include all standard Expedite report information and the MOSS column position.

Trityl data Trityl data can be displayed with the report. You may notice some difference in the magnitude of the trityl data from the first column position (a) to the last (h). This does not reflect a problem in the synthesis of the sequences on the later column positions but a difference in the length of the lines through which the trityl fraction travels. This variability in line lengths may result in different positioning of the DMT color in the trityl monitor which can affect the calculation of the trityl number, and therefore the trityl histogram.


3
3Maintenance Procedures
This chapter contains the following sections:

3.1 Replacing Inline Filters ........................... 3-2

3.2 Replacing Post-Column Filters................ 3-4

3.3 Replacing the Gas Cylinder .................... 3-7


Chapter 3 Maintenance Procedures

3

3.1 Replacing Inline Filters

Inline filters Inline filters in the column compartment of the Expedite instrument prevent particulate matter from entering the MOSS unit and blocking fluid pathways. Figure 3-1 shows the location of the inline filters.

Figure 3-1 Location of Inline Filters

When to replace Replace inline filters every 3 to 4 months.

PB100398

C1

C1

C2

C

2

Inlinefilterslocated incouplings


Replacing Inline Filters

3

Replacing 1. Carefully slide the MOSS unit 1 to 1.5 inches to the back of the Expedite instrument to allow access to the column door of the instrument.

CAUTION

Do not stress the tubing connection between the MOSS and the instrument.

2. Open the column door and locate the fluid lines labeled C1 and C2 in the compartment. These are the column inlet lines from the fluidic delivery system to the MOSS unit.

3. Unscrew the top PEEK fitting on line C1 from the knurled coupling that holds the filter (Figure 3-2).

Figure 3-2 Replacing Inline Filters

4. Remove the old filter from the knurled coupling.

PB100395

C1

C1

Recess infilterfacing upFilter

Knurledcoupling

PEEKfitting

To MOSSunit



3

5. Hold a new filter with the recess pointing up. Drop the filter into the knurled coupling.

6. Screw in the top PEEK fitting.

7. Repeat step 3 through step 6 for line C2.

3.2 Replacing Post-Column Filters

Post columnfilters

Post-column filters prevent particulate matter from leaving the column and blocking fluid pathways in the MOSS unit.Figure 3-3 shows the location of the inline filters.

Figure 3-3 Location of Post-Column Filters

PB100397

Post-columnfilter


Replacing Post-Column Filters

3

When to replace Replace post-column filters:

• After 5600 couplings (or seven 800-cycle reagent kits)

• If the volume of WashA delivered during the fluidic diagnostic test is less than 1.6 mL

After 5,600couplings

Replace post-column filters after 5,600 couplings (or seven 800-cycle reagent kits). Table 3-1 lists the recommended schedule for changing post-column filters.

If WASHA volumeis less than 1.6 mL

Replace post-column filters if the volume of WashA delivered during the fluidic diagnostic test is less than 1.6 mL from any MOSS column position.

To check WASHA volume, run a Fluid diagnostic test and measure the volume dispensed from the waste tube with a graduated cylinder. See the Expedite 8900 Nucleic Acid Synthesis System User’s Guide, “Fluid Test” on page 3-74.

Table 3-1 Replacing Post-Column Filters

Usage When to replace

Continuous daily use Every 14 days

Moderate use Every month

Occasional use Every 2 months



3

Replacing 1. Remove the column outlet line from the old filter (Figure 3-4).

Figure 3-4 Replacing Post-Column Filters

2. Remove the old filter from the column outlet and discard the filter.

3. Place a new filter on the column and press down to secure.

4. Insert the column outlet line into the filter and press down to secure.

5. Repeat step 2 through step 4 for each column position on the MOSS unit.

Priming afterreplacing filters

Prime after replacing filters to check for leaks. See “Prime Individual” on page 2-14.

PB100396

Column outlet

Filter

line


Replacing the Gas Cylinder

3

3.3 Replacing the Gas Cylinder

The recommended system pressurization gases are helium, argon, or nitrogen (high purity, 99.995%). It will be necessary to replace the gas cylinders at regular intervals.

To replace the cylinder:

1. Decrease the gas pressure on the cylinder regulator to zero (0).

2. Turn the gas off at the cylinder.

3. Disconnect the gas supply line from the rear of the instrument cabinet by pressing the quick release tab (Figure 3-5).

Figure 3-5 Rear of Instrument Cabinet

INLET PRESSURE

25 PSI MAX

(1.7 kg/cm2)

ACINLET

90-260 VAG 47-63Hz

FUSE 3 AG 250V 1A SLOW

100VA MAX

FOR CONTINUED PROTECTION

AGAINST RISK OF FIRE, REPLACE

ONLY WITH FUSE OF SPECIFIED

TYPE AND CURRENT RATING.

WARNING

Gas Hookup



3

4. Remove the regulator from the cylinder.

5. Install the regulator on the new cylinder.

6. Reconnect the gas line to the reagent instrument cabinet.

CAUTION

Increasing the pressure too quickly may damage the internal gas pressure system.

7. Increase the gas pressure slowly to 25 psi for optimum operation with the MOSS option.


A PerformanceSpecifications A

Table A-1 Performance Specifications

Condition Specification

Column Positions Up to 16, unattended

Synthesis Strategy Alternating phase (2 independent columns)

Synthesis cycle time <4 minutes per base addition (0.05 and 0.2 µmole scales)

Synthesis Scale/Protocol 0.05 µmole DNA, 0.20 µmole DNA, 1.0 µmole DNA

(Thioated and RNA protocols will be available in the future)

Oligonucleotide Quality >98% Average Stepwise Coupling Efficiency (measured by Ion Exchange HPLC on a Random 31 mer standard test sequence)

Monomer Consumption < 5 mg at 0.20 µmole scale

Reagent Consumption <5.5 mL per cycle

Expedite 8900 MOSS User’s Guide A-1

Appendix A Performance Specifications

A
Monitoring Expedite Trityl Monitor
Reagent Capacity ~800 cycles with 0.2 µmole protocol (requires Model 8909 Nucleic Acid Synthesis System)

Table A-1 Performance Specifications (Continued)


Table A-2 Miscellaneous Specifications


Dimensions 39 cm W x 33 cm D x 13 cm H (module placed on top of Expedite System)

External Computer Requires Expedite PC Workstation Configuration (with RS422 Communications Port)

A-2 Applied Biosystems

B Technical Supportand Training B

This appendix contains the following sections:B.1 Contacting Technical Support .......................... B-2

B.2 Obtaining Technical Documents ...................... B-9

B.3 Obtaining Customer Training Information........ B-11

Expedite 8900 MOSS User’s Guide B-1

Appendix B Technical Support and Training

B

B.1 Contacting Technical Support

Overview You can contact Applied Biosystems for technical support:

• By e-mail• By telephone or fax• Through the Applied Biosystems Technical Support

web site

NOTE: For information on obtaining technical documents such as Applied Biosystems user documents, MSDSs, and certificates of analysis, see “Obtaining Technical Documents” on page -9.

By E-mail You can contact technical support by e-mail for help in the product areas listed below.

Product/Product Area E-Mail Address

Genetic Analysis (DNA Sequencing) [email protected]

Sequence Detection Systems and PCR [email protected]

Protein Sequencing, Peptide, and DNA Synthesis [email protected]

BiochromatographyPerSeptive DNA, PNA and Peptide Synthesis systemsFMAT 8100 HTS SystemCytoFluor® 4000 Fluorescence Plate ReaderMariner Mass SpectrometersVoyager Mass SpectrometersMass Genotyping Solution 1™ (MGS1) System

[email protected]

LC/MS (Applied Biosystems/MDS Sciex)

[email protected]

Chemiluminescence (Tropix) [email protected]

B-2 Applied Biosystems

Contacting Technical Support

B

By telephone orfax (NorthAmerica)

To contact Applied Biosystems Technical Support in North America, use the telephone or fax numbers in the table below.

NOTE: To schedule a service call for other support needs, or in case of an emergency, dial 1.800.831.6844, then press 1.

Product/Product Area Telephone Fax

ABI PRISM ® 3700 DNA Analyzer 1.800.831.6844, then press 8a

1.650.638.5981

DNA Synthesis 1.800.831.6844, press 2, then press 1a

1.650.638.5981

Fluorescent DNA Sequencing 1.800.831.6844, press 2, then press 2a

1.650.638.5981

Fluorescent Fragment Analysis (including GeneScan® applications)

1.800.831.6844, press 2, then press 3a

1.650.638.5981

Integrated Thermal Cyclers (ABI PRISM® 877 and Catalyst 800 instruments)


1.650.638.5981

ABI PRISM® 3100 Genetic Analyzer 1.800.831.6844, press 2, then press 6a

1.650.638.5981

Peptide Synthesis (433 and 43x Systems)


1.650.638.5981

Protein Sequencing (Procise® Protein Sequencing Systems)


1.650.638.5981



B

PCR and Sequence Detection 1.800.762.4001, then press:

1 for PCRa

2 for TaqMan® applications and Sequence Detection Systems including ABI Prism‚ 7700, 7900, and 5700a

6 for the 6700 Automated Sample Prep Systema

or

1.800.831.6844, then press 5a

1.240.453.4613

Voyager MALDI-TOF Biospectrometry Workstations

Mariner ESI-TOF Mass Spectrometry Workstations

Mass Genotyping Solution 1™ (MGS1) System

1.800.899.5858, press 1, then press 3b

1.508.383.7855

Biochromatography (BioCAD®, SPRINT, VISION, and INTEGRAL® Workstations and POROS® Perfusion Chromatography Products)


1.508.383.7855

Expedite Nucleic Acid Synthesis Systems


1.508.383.7855

Peptide Synthesis (Pioneer and 9050 Plus Peptide Synthesizers)


1.508.383.7855




B

By telephone orfax (outside North

America)

To contact Applied Biosystems Technical Support or Field Service outside North America, use the telephone or fax numbers below.

PNA Custom and Synthesis 1.800.899.5858, press 1, then press 5b

1.508.383.7855

FMAT 8100 HTS System

CytoFluor® 4000 Fluorescence Plate Reader


1.508.383.7855

Chemiluminescence (Tropix) 1.800.542.2369 (U.S. only),or 1.781.271.0045c

1.781.275.8581

LC/MS (Applied Biosystems/MDS Sciex)

1.800.952.4716 1.508.383.7899

a. 5:30 A.M. to 5:00 P.M. Pacific time.

b. 8:00 A.M. to 6:00 P.M. Eastern time.

c. 9:00 A.M. to 5:00 P.M. Eastern time.


Region Telephone Fax

Africa and the Middle East

Africa (English Speaking; Fairlands, South Africa)

27 11 478 0411 27 11 478 0349

Africa (French Speaking; Courtaboeuf Cedex, France)

33 1 69 59 85 11 33 1 69 59 85 00

South Africa (Johannesburg) 27 11 478 0411 27 11 478 0349



B

Middle Eastern Countries and North Africa (Monza, Italia)

39 (0)39 8389 481 39 (0)39 8389 493

Eastern Asia, China, Oceania

Australia (Scoresby, Victoria) 61 3 9730 8600 61 3 9730 8799

China (Beijing) 86 10 64106608 or86 800 8100497

86 10 64106617

Hong Kong 852 2756 6928 852 2756 6968

India (New Delhi) 91 11 653 3743/3744 91 11 653 3138

Korea (Seoul) 82 2 5936470/6471 82 2 5936472

Malaysia (Petaling Jaya) 60 3 79588268 603 79549043

Singapore 65 896 2168 65 896 2147

Taiwan (Taipei Hsien) 886 2 2358 2838 886 2 2358 2839

Thailand (Bangkok) 66 2 719 6405 662 319 9788

Europe

Austria (Wien) 43 (0)1 867 35 75 00 43 (0)1 867 35 75 11

Belgium 32 (0)2 532 4484 32 (0)2 582 1886

Czech Republic and Slovakia (Praha) 420 2 35365189 420 2 35364314

Denmark (Naerum) 45 45 58 60 00 45 45 58 60 01

Finland (Espoo) 358 (0)9 251 24 250 358 (0)9 251 24 243

France (Paris) 33 (0)1 69 59 85 85 33 (0)1 69 59 85 00

Germany (Weiterstadt) 49 (0) 6150 101 0 49 (0) 6150 101 101

Hungary (Budapest) 36 (0)1 270 8398 36 (0)1 270 8288

Italy (Milano) 39 (0)39 83891 39 (0)39 838 9492

Norway (Oslo) 47 23 12 06 05 47 23 12 05 75




B

Poland, Lithuania, Latvia, and Estonia (Warszawa)

48 22 866 4010 48 22 866 4020

Portugal (Lisboa) 351.(0)22.605.33.14 351.(0)22.605.33.15

Russia (Moskva) 7 502 935 8888 7 502 564 8787

South East Europe (Zagreb, Croatia) 385 1 34 91 927/838 385 1 34 91 840

Spain (Tres Cantos) 34.(0)91.806.1210 34.(0)91.806.12.06

Sweden (Stockholm) 46 (0)8 619 4400 46 (0)8 619 4401

Switzerland (Rotkreuz) 41 (0)41 799 7777 41 (0)41 790 0676

The Netherlands (Nieuwerkerk a/d IJssel)

31 (0)180 392400 31 (0)180 392409 or31 (0)180 392499

United Kingdom (Warrington, Cheshire)

44 (0)1925 825650 44 (0)1925 282502

All other countries not listed (Warrington, UK)

44 (0)1925 282481 44 (0)1925 282509

Japan

Japan (Hacchobori, ChuoKu, Tokyo) 81 3 5566 6230 81 3 5566 6507

Latin America

Caribbean countries, Mexico, and Central America

52 55 35 3610 52 55 66 2308

Brazil 0 800 704 9004 or 55 11 5070 9654

55 11 5070 9694/95

Argentina 800 666 0096 55 11 5070 9694/95

Chile 1230 020 9102 55 11 5070 9694/95

Uruguay 0004 055 654 55 11 5070 9694/95




B

Through theTechnical Support

web site

To contact Technical Support through the Applied Biosystems web site:

T

1. Access the Applied Biosystems Technical Support web site at www.appliedbiosystems.com/techsupp.

2. Under the Troubleshooting heading, click Support Request Forms, then select the support region for the product area of interest.

3. In the Personal Assistance form, enter the requested information and your question, then click Ask Us RIGHT NOW.

4. In the Customer Information form, enter the requested information, then click Ask Us RIGHT NOW.

Within 24 to 48 hours, you will receive an e-mail reply to your question from an Applied Biosystems technical expert.


Obtaining Technical Documents

B

B.2 Obtaining Technical Documents

Overview You can obtain technical documents, such as Applied Biosystems user documents, MSDSs, certificates of analysis, and other related documents for free, 24 hours a day. You can obtain documents:

• By telephone• Through the Applied Biosystems Technical Support web

siteOrdering

documents bytelephone

To order documents by telephone:

1. From the U.S. or Canada, dial 1.800.487.6809, or from outside the U.S. and Canada, dial 1.858.712.0317.

2. Follow the voice instructions to order documents (for delivery by fax).

NOTE: There is a limit of five documents per fax request.

Obtainingdocumentsthrough the

web site

To view, download, or order documents through the Applied Biosystems Technical Support web site:

1. Access the Applied Biosystems Technical Support web site at www.appliedbiosystems.com/techsupp.

2. Under the Resource Libraries heading, select the type of technical document you want.

3. In the search form, enter or select search criteria, then click Search.



B

4. In the results screen, do any of the following:

• Click to view a PDF version of the document.

• Right-click , then select Save Target As to download a copy of the PDF file.

• Select the Fax check box, then click Deliver Selected Documents Now to have the document faxed to you.

• Select the Email check box, then click Deliver Selected Documents Now to have the document (PDF format) e-mailed to you.

NOTE: There is a limit of five documents per fax request, but no limit on the number of documents per e-mail request.


Obtaining Customer Training Information

B

B.3 Obtaining Customer Training Information

The Applied Biosystems Training web site at www.appliedbiosystems.com/techsupp/training.html provides course descriptions, schedules, and other training-related information.


I

DEX

N

Index

AAborting a synthesis 2-22

BBench space required 1-1

CCertificates of analysis

obtaining B-9Chemistry, setting 2-3Columns

installing 2-17location 2-17

Customer training, information B-11

EE-mail

contacting technical support B-2

FFeatures 1-1Field Service in North America,

contacting B-3Filters

inline, replacing 3-2post-column, replacing 3-4

GGas cylinder, replacing 3-7

HHolding a synthesis 2-22

IInstallation 1-3

MMaintenance

filters, inline 3-2filters, post-column 3-4gas cylinder 3-7

Monitoring the synthesis 2-22MSDSs, obtaining B-9

OOverview 1-1

PPriming the system 2-11Printing synthesis set 2-6Protocol

supported 1-3transferring to instrument 2-7

RReagents, checking 2-9

Expedite 8900 MOSS User’s Guide Index-1

I

DEX

N
SSequence, creating 2-3Stopping a synthesis 2-22Synthesis
chemistry 2-3monitoring 2-22overview 2-2priming 2-11reagents, checking 2-9starting 2-20stopping 2-22

Synthesis setdefining 2-3definition of 2-2editing 2-6printing 2-6starting 2-20transferring to instrument 2-7

TTechnical documents, obtaining B-9Technical support, contacting

Africa and the Middle East B-5Eastern Asia, China, Oceania B-6e-mail B-2Europe B-6Japan B-7Latin America B-7telephone or fax in North

America B-3Trityl data, difference in

magnitude 2-22

UUPS 1-3User‘s guide structure ix

WWaste

container requirement 1-4disposal 1-4emptying 2-19

Workstation control 1-2

Index-2 Applied Biosystems

Headquarters850 Lincoln Centre DriveFoster City, CA 94404 USAPhone: +1 650.638.5800Toll Free: +1 800.345.5224Fax: +1 650.638.5884

Worldwide Sales OfficesApplied Biosystems vast distribution and

service network, composed of highly trained support and applications personnel, reaches into 150 countries on six continents. For international office locations, please call our local office or refer to our web site at www.appliedbiosystems.com.

www.appliedbiosystems.com

Applera Corporation is committed to providing the world’s leading technology and information for life scientists. Applera Corporation consists of the Applied Biosystems and Celera Genomics businesses.

Printed in the USA, 06/2001Part Number PB601307 Rev. 2

an Applera business