Thermo Scientific A2-OK Operating instructions

Horizontal System
Model A2-OK
Operating and Maintenance Manual 7219011 Rev. 0
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Thermo Scientific
MANUAL NUMBER 7219011
0 -- 4/13/12 Transfer to Marietta (was 11/2002) ccs
REV ECR/ECN DATE DESCRIPTION By
Preface
Horizontal System i

Thermo Scientificii Horizontal System
Preface
Important Read this instruction manual. Failure to read, understand and follow the instructions in this manual
may result in damage to the unit, injury to operating personnel, and poor equipment performance. s
Caution All internal adjustments and maintenance must be performed by qualified service personnel. s
Warning To avoid the risk of personal shock, always disconnect the gel box from the power supply. Further, the
power supply must be equipped with a shut-down-on-disconnect circuit. Do not move the unit unless the power
source to the unit has been disconnected. s
Statement of Proper Use: Use this product only for its intended purpose as described in this manual. Do not use
this product if the power leads are damaged or if any of its surfaces are cracked.
Warning Running conditions for this unit should not exceed the name plate readings found on the lower buffer
chamber. s
This Owl System is designed to meet IEC 1010-1 safety standards (IEC 1010-1 is an internationally accepted
electrical safety standard for laboratory instruments).
Material in this manual is for information purposes only. The contents and the product it describes are subject to
change without notice. Thermo Fisher Scientific makes no representations or warranties with respect to this
manual. In no event shall Thermo be held liable for any damages, direct or incidental, arising out of or related to
the use of this manual.
©2012 Thermo Fisher Scientific. All rights reserved.

Thermo Scientific Horizontal System iii
Preface
Important operating and/or maintenance instructions. Read the accompanying text carefully.
Potential electrical hazards. Only qualified persons should perform procedures associated with this
symbol.
Equipment being maintained or serviced must be turned off and locked off to prevent possible injury.
Hot surface(s) present which may cause burns to unprotected skin, or to materials which may be
damaged by elevated temperatures.
Marking of electrical and electronic equipment, which applies to electrical and electronic equipment
falling under the Directive 2002/96/EC (WEEE) and the equipment that has been put on the market
after 13 August 2005.
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Equipment (WEEE) Directive 2002/96/EC. It is marked with the WEEE symbol. Thermo Fisher
Scientific has contracted with one or more recycling/disposal companies in each EU Member State
European Country, and this product should be disposed of or recycled through them. Further
information on Thermo’s compliance with this directive, the recyclers in your country and
information on Thermo products will be available at www.thermofisher.com.
4Always use the proper protective equipment (clothing, gloves, goggles, etc.)
4Always dissipate extreme cold or heat and wear protective clothing.
4Always follow good hygiene practices.
4Each individual is responsible for his or her own safety.

Thermo Scientificiv Horizontal System
Preface
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Horizontal System vThermo Scientific
Table of Contents
General Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1-1
Setting Up . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2-1
Preparing the Gel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .2-2
Using the System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .3-1
Finishing Up . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .4-1
Specifications and Recommended Running Conditions . . . . . . . . . . .4-1
Technical Tips . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-1
Combs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-1
Reagent Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .5-2
Troubleshooting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .6-1
Care and Cleaning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .7-1
Optional Equipment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .8-1
Replacement Parts . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .8-1
Section 1
Section 2
Section 3
Section 4
Section 5
Section 6
Section 8
Section 7

Horizontal System 1-1Thermo Scientific
Section 1 General Information
The Opossum Multiple Gel system is ideal for teaching labs or labs that
need to run multiple gels simultaneously. Up to six minigels (7cmW x
8cmL) can be run on this versatile system. Along with optional combs the
Opossum can screen up to 144 samples at once (120 with supplied
combs). EasyCast casting design allows the casting of gels without tape or
plugs. UV transmissible gel trays may be placed directly on the
transilluminator for photodocumentation.
Before starting, unpack the unit and inventory your order. If any parts are
missing, contact Technical Services immediately.
Reference the order or catalog number on your invoice and check the
corresponding parts list.
Table 1-1. Parts List
Buffer Chamber
Combs 10 well comb, Double Sided, 1.0/1.5mm Thick (12)
Super Safe Lid with attached power supply leads
Multiple Gel Caster (2)
Gel Tray Holder
UV Transmissible gel trays (6)

1-2 Horizontal System Thermo Scientific
Section 1
General Information
Figure 1-1. Exploded Parts Diagram
Table 1-1. Specifications
Gel size . . . . . . . . . . . . . . . . . . . . . . .7cmW x 8cmL
Running Buffer . . . . . . . . . . . . . . . . . .Volume 2.3L
Footprint . . . . . . . . .28cm W x 37.5cm L x 10cm H
Power Supply
Leads Super Safe Lid
UVT Gel
Tray (6)
Gel Tray
Holder
Buffer
Chamber
Bubble Level
Double Sided
Comb (12)
Multiple Gel
Caster (2)
Gasket (12)
1.5 Thick
1.0 Thick

Horizontal System 2-1Thermo Scientific
Section 2 Setting Up
1. For shipping and convenient storage, the gel tray is packaged inside the
unit with the gasketed end gates in
position upon arrival. Lift the casting
tray out of the buffer chamber.
2. To cast gels, place the gel tray(s) into
the external multiple gel caster. The
gasketed sides of the UVT gel tray
form a leak proof seal along the side
of the gel caster.
3. Prepare and pour warm (>60) agarose solution onto UVT gel tray.
Place comb(s) into slots provided on walls of UVT gel tray.
4. One the gel has solidified, place the UVT gel tray (s) into the gel tray
holder.
5. Level the casting chamber using the thumbscrews on each side of the
unit by slowly turning one thumbscrew at a time and lining up the
bubble in the level with the center circle. Place the gel tray holder in
the buffer chamber, add buffer, remove combs, load samples and run
the gel.
Figure 2-1. Casting Tray
Figure 2-2. Pour Agarose Figure 2-3. Place Combs

2-2 Horizontal System Thermo Scientific
Section 2
Setting Up
Preparing the gel - Using electrophoresis-grade agarose and compatible
electrophoresis buffer the gel may be prepared in various ways. The
percentage of agarose and the electrophoretic buffer used is determined by
the size of the samples to be separated and further recovery of the samples.
The agarose and buffer are mixed and heated over a heat source, in a
microwave oven, or in an autoclave until the agarose is completely
dissolved. The prepared gel then must be cooled to below 60° before
casting to avoid warping the UVT gel tray due to excessive heat. If
numerous gels are to be run in one day, a large volume of gel may be
prepared and placed in a covered bottle stored between 40°-60° in a water
bath. This provides a ready gel supply in a warm liquid form that will
solidify quickly when gels are cast.
Pour or pipet warm agarose (<60°). Immediately after pouring, insert the
desired comb or combs into the comb slots to form the sample wells. If
only a small portion of gel is required for proper sample separation,
multiple combs may be used to run 1 or 2 sets of equal distance samples
simultaneously expanding the number of samples per gel that may be run.
Repeat for up to 6 gels (3 per external multiple gel caster).

Horizontal System 3-1Thermo Scientific
Section 3 Using the System
1. Once the gel (s) is completely
solidified, lift the gel tray (s) out of
the external gel caster. Place the gel
tray (s) onto the gel tray holder.
Place the gel tray holder in the
buffer chamber in the running
position. The running position
exposes the open ends of the agarose
to the buffer. Standard agarose
should solidify completely in about
30 minutes.
2. Pour enough compatible running
buffer into the unit to fill the
chamber and completely cover and
submerge the gel. Correct buffer
level is clearly marked on the units
side wall as “FILL LINE”. See
Recommended Running Conditions
for approximate buffer volumes
needed for your unit. Too little
buffer may cause the gel(s) to dry
out during the run, while excess
buffer may decrease DNA mobility
and cause band distortion.
3. Carefully remove the comb (or combs) by tapping lightly to loosen,
and slowly lifting straight up out of the gel tray to avoid damage to the
wells.
Figure 3-1. Place Gel Tray
Figure 3-2. Place Gel Tray Holder

3-2 Horizontal System Thermo Scientific
Section 3
Using the System
4. Load prepared samples into the wells. Samples should be mixed with a
sample loading buffer; giving weight to the samples so that they drop
evenly into the wells and containing tracking dyes to monitor the gel
run. After the gel solidifies, remove the gel tray from the external
casting tray and place the tray on the lab bench. Carefully remove the
sample combs by tapping and lifting straight up. Samples mixed with
loading buffer that does not contain dye may be easier to load dry,
especially in larger gel units to avoid cross contamination. After
loading all sample lanes, place the gel tray into the gel tray holder in
the running position with the gel edges facing out toward the buffer
chambers and slowly fill as described in Step #2. It is wise to always
run a sample lane of a known “standard ladder” to determine
concentration and size of separated fragments after the gel run, and to
aid in photo documentation and analysis.
Note It is sometimes easier to load the sample wells dry before placing the
gel tray into the running position.
5. Carefully slide the Supersafe lid with attached power supply leads onto
the unit. This will connect the power cords to the banana plug
electrodes and complete the circuit. Plug other end of the power cords
into appropriate power supply.
6. Turn on power supply (see Recommended Running Conditions).
Carefully monitor the gel run to avoid samples running into the path
of another set of samples.

Horizontal System 4-1Thermo Scientific
Section 4 Finishing Up
1. When the gel run is complete and tracking dye has migrated as far
through the gel as desired, or to the end of the gel, turn off the power
supply and slide off the lid to disconnect from the power source.
Carefully remove the tray (s) containing the gel (wear gloves if
ethidium bromide is present). The UV Transmissible (UVT) gel tray
makes visualization and photography with a UV light source easy
without the need to remove the gel from the tray.
2. The gel box should be rinsed under warm running water after each
use, including the UVT gel tray (s). Rinsing the UVT gel tray (s) will
avoid salt build up in the gasket material from the electrophoretic
running buffer, extending the gasket life and ensuring leak-free gel
casting. An RNase/DNase decontaminate may be used. This
electrophoresis system must never be autoclaved, baked, or
microwaved!
Specifications and Recommended Running Conditions
Gel Size: . . . . . . . . . . . . . . . . . . . . . .7cmW x 8cmL
Buffer Capacity: . . . . . . . . . . . . . . . . . . . . . . . . .2.3L
There are various types of agarose commerically available that may be used.
Besides standard ultra pure electrophoresis grade agarose, there are also
numerous low melting point products for easy sample recovery, as well as
speciality products formulated for specific uses to separate/recover very
small or very large fragments etc. To visualize and photograph the samples
after the gel run for a permanent record, the gel may be stained during or
following the run with a variety of stains. The most common stain for
DNA is ethidium bromide. Ethidium bromide may be added directly to
the gel and running buffer to quickly and easily visualize and photograph
the separated fragments following the gel run without the need for
additonal staining. If this is not added, then following the gel run the gel
may also be soaked in a concentrated ethidium bromide solution and
rinsed for the same visualization. The ethidium bromide is added to the gel
(after heating) and the electrophoresis buffer at a concentration of
0.5ug/ml.
Warning Ethidium bromide is a potential carcinogen. Care in handling
the powder and stock solution must be taken. Always wear gloves when
handling the powder, solutions and all gels that contain any amount of
ethidium bromide. s

Horizontal System 5-1Thermo Scientific
Section 5 Technical Tips
Combs
Standard
• 1.0mm (C) and 1.5mm (D)
thickness for all models.
Double Sided
• Double Sided Molded Combs
combine 1.0mm and 1.5mm tooth
thickness on one comb.
Preparative
• One long well and one marker
lane.
Wall Comb
• See page 33 for details.
Multi-Load Comb
• F or use with 8 channel pipet.
Custom Combs
Call Technical Services for more information.
Standard
Double Sided
Preparative
Wall Comb
Multi Load Comb

5-2 Horizontal System Thermo Scientific
Section 5
Technical Tips
Chart A
Mobility range of DNA in different percentage agarose gels
Agarose % (w/v) . . . .Approximate range of separated DNA fragments (kb)
0.3 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .60 to 5
0.5 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .30 to 1
0.7 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .12 to 0.8
1.0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .10 to 0.5
1.2 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .7 to 0.3
1.5 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .4 to 0.2
2.0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .3 to 0.1
3.0 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .<0.1
It should be noted, an increased agarose % gives better separation of small
fragments and also bands very close together that tend to be more difficult
to separate, visualize and photograph. A specialty agarose product
formulated to increase resolution of low molecular mass samples may also
be used.
Example: A good mid-range gel percentage would be 0.7%, or 0.7g.
agarose in 100mls. electrophoresis buffer (TBE or TAE), following heating
and dissolving the agarose, 10ul of ethidium bromide stock solution
(5mg/ml) is added. The gel would be run with compatible electrophoretic
running buffer (1X TBE or 1X TAE) that also contained ethidium
bromide. 1 liter of the running buffer would contain 100ul of this 5mg/ml
ethidium bromide stock solution.
Reagent Information

Chart B
Preparation & Properties of TAE and TBE Electrophoresis Buffer
Systems:
These buffers are used because they both have a basic pH which gives the
phosphate group of the DNA a net negative charge allowing migration of
the DNA toward the positive anode in the electrophoresis chamber.
TAE - Tris acetate with EDTA (40mM Tris base 40mM acetic acid,1mM EDTA)
50X stock solution, pH 8.5: 1X working solution:
242 g. Tris base 40 mM Tris acetate
57.1 ml. glacial acetic acid 1 mM EDTA
18.61 g. Na EDTA “ 2H2O (MW 372.24)
Distilled H2O to 1 liter final volume
TBE - Tris borate with EDTA (89mM Tris base, 89mM boric acid, 2mM EDTA)
10X stock solution: 1X working solution:
108 g Tris base 89 mM Tris base
55 g boric acid 89 mM boric acid
7.44g Na2EDTA “ 2H2O (MW 372.24) 2 mM EDTA
(or 40 ml 0.5 M EDTA, pH 8.0)
Distilled H2O to 1 liter final volume
Do not adjust pH
Buffer: Suggested Uses and Comments:
TAE Buffer Use when DNA is to be recovered. For electrophoresis of
large (>20kb) DNA Applications requiring high resolution.
Has low ionic strength and low buffering capacity -
recirculation may be necessary for long runs (> 4hrs).
TBE Buffer For electrophoresis of small (<1kb) DNA. Better resolution
of small (<1kb) DNA. Decreased DNA mobility. High
ionic strength and high buffering capacity - no
recirculation needed for extended run times.
TBE buffer reacts with the agarose making smaller pores and a tighter
matrix. This reduces broadening of the DNA bands for sharper resolution.
Horizontal System 5-3Thermo Scientific
Section 5
Technical Tips

Ethidium Bromide -
Ethidium bromide is ideal for the flurometric detection of nucleic acids in
gel electrophoresis. The addition of ethidium bromide to both the prepared
gel and running buffer is a convenient way to monitor separation and keep
a photographic log of gel runs. Ethidium Bromide is prepared as 10mg/ml
in distilled water and used as a stock working solution of 5.0ug/ml in the
electrophoresis buffer and gel. Mix ethidium bromide powder or tablet
thoroughly into solution checking for any precipitate and store at room
temperature protected from light.
Chart C
Amount of Agarose to prepare:
All approximate well volumes given in the chart below are based on a gel of
0.5cm thickness. Gel volume is determined by the following formula and
may be adjusted according to need or preference:
gel width(cm) x gel length (cm) x gel thickness (cm) = ml of agarose
Agarose Gel Loading Buffer
Samples are prepared and combine with gel loading buffer before applying
to the prepared gel. Sample buffer usually contains similar components to
the running buffer, dyes for visibility, and glycerol to provide some weight
to the samples. This increased sample density and color allows easy
visualization of the samples and ensures samples load evenly into the wells
and do not float out during loading. Dyes also migrate toward the anode
end of the electrophoresis chamber at predictable rates allowing the gel run
to be monitored.
The most commonly used loading buffer is glycerol, bromophenol blue,
and xylene cyanol.
5-4 Horizontal System Thermo Scientific
Section 5
Technical Tips
Unit Agarose Volume in ml per gel thickness in cm.
Model # Gel size(cm) 0.25cm 0.5cm 0.75cm 1.0cm
A2-OK

Section 6 Troubleshooting
Horizontal System 6-1Thermo Scientific
Problem Solution
Agarose leaks into chamber
when casting the gel
Check to see if the gasket is correctly seated in groove and
even all the way around. Remove gasket and reseat by smooth-
ing out gently with your thumb from one end to the other.
Gasket material may have a tendency to absorb salts from the
running buffer. After each use, rinse the end gates under warm
running water to bring back spongelike consistence of the gas-
ket material. Gaskets may eventually become brittle with fre-
quent use. Contact Technical Services to purchase replacement
gaskets.
Bands seem to be running at
an angle.
Check to be sure that the unit is properly leveled for casting
and running the gel by using the thumbscrews on the base.
Thumbscrews should be adjusted until the bubble in the level
lines up with the levels center circle. Always center the gel
tray holder on the platform and cool the agarose to below 60°
before pouring to avoid warping the UVT gel tray (s).
Samples seem to be running
unevenly in certain areas.
Check that the platinum electrode wire is intact running flat
and evenly across the outer corners and up the side to the
junction of the banana plug area. This problem could also be
caused by regular casting with very hot agarose gel (>60° )
which may damage the gel tray over time. Always cool the
melted agarose to below 60o before casting to avoid warping
the UVT gel tray (s). Warping the UVT gel tray will cause all
subsequent gels to be cast unevenly.
Samples do not band sharply
and appear diffuse in the gel.
Gels should be no more than 5mm thick and allowed to
solidify completely before running. For standard agarose, this
would be about 30 minutes, if low melting point agarose is
used, it may be necessary to completely solidify gels at a
cooler temperature in the refrigerator or cold room. Gels
should be submerged in 3-5mm of buffer to avoid gel dry out,
but excess buffer >5mm can cause decreased DNA mobility
and band distortion.