OWL The Otter SGC-1 User manual

The Otter
TM
Sequencing Gel Casters
Model SGC-1 and SGC-2
O
wner’s
Manual
Rev. Date: 3/2003

S
afety Information
i
Important Safety Information!
Please read carefully before operating!
• This manual contains important operating and
safety information. In order to benet from the
use of this apparatus, you must carefully read
and understand the contents of this manual
prior to use of this apparatus.
• 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.

16

Safety Information …………………………………………..…….…. i
Section 1 General Information………………………………………. 2
Introduction ………………………………………….…….……… 2
Unpacking and Checking Your Order …….……….............. 2
Section 2 Using the System …………………………………….… 5
Setting Up …………………….…………………..….......................… 5
Gel Casting ……………………..……...….……..............……............ 6
Operating ....................................................................................... 7
Section 3 Technical Tips …………………………………………..… 9
Section 4 Troubleshooting ……………………..…….…….………… 11
Section 5 Care & Cleaning ……………………..…….…….…………. 13
A Few Tips About Caring for Your System ….…................ 13
Care of Acrylic ……………………..…….…….………….…............... 14
Section 6 Optional Equipment ……………………..…….…….….. 15
1
T
able of Contents

2
UNPACK & CHECK YOUR ORDER
Before starting, unpack the unit and inventory your order. If any parts
are missing, refer to the warranty section on the back cover of this
manual and contact Owl immediately at 800-242-5560.
Reference the order or catalog number on your invoice and check the
corresponding parts list.
INTRODUCTION
The Otter Sequencing Gel Caster provides the user with a simple and
easy-to-use method for casting sequencing gels. Relying on a horizontal
sliding plate procedure, capillary action draws the gel between plates.
Surface tension, not tape, keeps the gel from leaking. No taping or
special assembly is required. The sliding casting method has been
shown to require significantly less time to cast and the clean process
decreases exposure to acrylamide and reduces clean up time. Gels can
be cast in less than one minute. Any standard size sequencing gel can
be cast using either the SGC-1 or SGC-2.
SGC-1
Gel Size: 20-42cmW x 48cmL
Footprint: 21.6cmW x 71cmD (fully closed) x 12.2cmH
SGC-2
Gel Size: 20-42cmW x 65.5cmL
Footprint: 21.2cmW x 102cmD (fully closed) x 12.2cmH
G
eneral Information
SECTION 1

G
eneral Information
SECTION 1
3
Figure 1-1 Parts Diagram
SGC-1, SGC-2
1 Adjustable casting platform
2 knobs for width adjustment (attached)
12 Binder clamps

4

U
sing the System
SECTION 2
5
Setting Up
The following additional equipment may be required for casting.
• One or more pairs of glass plates to fit any standard manual or
automatic sequencing electrophoresis system.
• Matching spacer set and comb for each gel to be cast.
• Binder clamps - 9 per gel cassette. Owl catalog # CL-12.
• Rain-X or Sigmacote (Sigma Chemical, St. Louis, MO)
• Ethanol for washing plates, combs and spacers.

U
sing the System
SECTION 2
6
Gel Casting
Basic laboratory safety procedures should be followed when preparing
sequencing gels. When working with acrylamide solutions always
wear proper protective clothing, gloves and eye protection.
Careful attention must be given during each step of sequencing gel
preparation for consistent results. Begin by cleaning plates thoroughly:
1. To completely clean glass plates of any acrylamide residue, left-
over detergents, and dust, wash plates with warm water and deter-
gent.
2. Rinse plates completely with deionized water then wipe with 95%
ethanol to eliminate any traces of detergent and water marks.
A final wipe should be done using a dust free cloth such as
Kimwipes.

U
sing the System
SECTION 2
7
Operating
1. The caster consists of two
adjustable ends and two side pieces
with a cut out railing. The railing
is open at one end so that long
glass can slide past the length of
the caster. The opposite end has
a stop cut into the sides so that
the bottom plate is held in position.
Loosen knobs on the ends of the
caster and place glass into unit.
Slide the sides of the caster togeth-
er to tightly fit the glass plate.
Tighten knobs.
2. Making sure that the casting area is level, place the blank, longer glass
plate into the caster, pushing it to the end with the stops. The rail it is
sitting on is slightly lower than the rail on the other end of the unit.
3. Moisten spacers with drops of water and place them flush to the edge
of the glass against the side of the rail. Moistening helps to keep the
spacers from moving while sliding the notched plate over them during
casting.
4. Place the notched top plate on top of the blank plate so that the two
overlap by about one inch. The side rail will hold the top plate above
the bottom blank plate. This plate should slide freely up to the top of the
blank plate. Have your gel solution ready at this point.

U
sing the System
SECTION 2
8
5. Slowly pour gel solution onto the
bottom plate at the point where the
two plates overlap. The acrylamide
will flow into the space between
the two plates by capillary action.
Gently slide the top plate across the
bottom plate while pouring gel solu-
tion along the leading edge of the
glass. If a bubble forms, simply
move the top plate backwards until
you have passed the point where the
bubble formed and then proceed for-
ward again until the gel is completly
cast.
6. Clamp along the spacers in the
spaces provided by the caster. Clamp
in the middle of the spacer and not in
the gel area.
7. Insert comb (see page 9 for
Sharktooth and Well Comb instru-
tions) at the top of the gel and clamp
with two or three clamps as space
allows. Clamp in the middle of the
comb and not on the teeth or beyond
the comb into the gel area.
8. After gel has polymerized for
20-30 minutes, the cassette can be
removed from the caster and allowed
to complete polymerization on the
benchtop. Do not move the gel dur-
ing the first minutes of polymeriza-
tion.

echnical Tips
T
SECTION 3
9
The difference between a well comb and a sharktooth
comb:
A well comb has rectangular teeth and is simi-
lar to combs used for protein gels. After
polymerization, these combs must be removed
carefully to avoid destroying the acrylamide
walls that create the wells. A sharktooth comb
has pointed teeth. It is placed with the flat side
down during gel casting to create a flat surface on the top of the gel and
reinserted with the teeth down towards the gel for loading. Samples are
loaded in the space between the teeth.
Sharktooth comb: Carefully insert the flat edge of the sharktooth comb
between the plates to a depth of 2 to 3mm below the shorter plate. If the
flat edge of the comb is inserted too deeply (more than 4 or 5mm) during
gel casting the resulting trough will be too deep to load samples easily
with a pipet. It is wise to make marks on the comb to distinguish the
right/left sides so the comb can be put back in the same orientation for
sample loading later, in the event that the material has any slight variation
in thickness. Place binder clamps over the comb and glass plates along the
upper edge to force the glass plates against the comb. This will ensure a
tight fit of the comb during and after polymerization. If top binder clamps
are not used the comb may not be tight enough to prevent sample leaks
between wells following gel polymerization. Do not clamp the outer edges
over the side spacers. Allow the gel to completely polymerize.
After polymerization, wash out the trough with buffer gently in order to
remove any unpolymerized acrylamide and excess urea. Place the comb
between the glass plates in the correct left to right orientation (the same
orientation the trough was cast in) with the comb teeth pointing down
toward the gel. Slowly and carefully slide the comb until it just makes
contact with the gel surface, without piercing it.
Well comb: Carefully insert the comb. Place binder clamps over the
comb and glass plates along the upper edge to force the glass plates against
the comb. After polymerization, flood the comb with 1X TBE and remove
gently. Rinse the wells out with deionized water or TBE in order to
remove excess urea or unpolymerized acrylamide.

echnical Tips
T
SECTION 3
10
The difference between notched and offset glass:
Notched or eared glass plates face in towards the
upper buffer chamber during a gel run. The “ears”
are glass tabs on each side of the plate, which
prevent buffer from running out of the upper buffer
chamber.
Offset glass plates serve the same purpose as
notched plates. Offset glass is usually about 2 cm
shorter than the front, or blank, glass plate. Instead
of glass ears, pieces of adhesive sponge are adhered
either to the top of the spacers or to the apparatus
itself. These sponge tips wear out and may leak.
Notched glass plates are more fragile and expen-
sive than offset glass and sponge tips, but many
researchers prefer notched glass because it is easier
to use.
The third spacer:
This is a bottom spacer, and can be cut to the
desired length. It is optional. If you use a bottom
spacer when casting, remember to remove it before running the gel.

T
roubleshooting
SECTION 4
5
11
Problem
Bubbles continually form between glass plates while casting.
Solution
Be sure plates are clean of any acrylamide debris and are dust free. If bubbles
do occur even after cleaning plates, simply move the top plate backwards until
the bubble is cleared and then proceed forward. From time to time a more
thorough cleaning of plates is required: 5 minutes in 1N HCl, rinse in hot water,
then rinse in deionized water. Repeat if necessary.
Problem
Gel solution appears to be leaking while pouring.
Solution
Be sure the caster is set up on a level surface. Leveling platforms are available
from Owl, catalog # B-LP.
If gel will not stay between the plates at the bottom of the cassette, this may
be caused by bowed plates. Try another set of glass or flip the top piece
so that the other side is facing the gel solution. Dirty glass can also cause
slight leaking. See cleaning instructions above and in the Gel Casting section
of this manual.
Problem
When loading samples, the samples seem to be running into other well
Solution
This may be due to a slight thickness variation between the comb and the
spacers used to pour the gel. Clamping the plates over the comb as well as
over the spacers will allow the gel to polymerize evenly and should alleviate
this problem. Using glass plates that are not completely flat may also cause
this problem, try flipping the plate over and using the other side for casting or
try a new plate.

12

C
are & Cleaning
SECTION 5
13
A Few Tips About Caring for Your System
WARNING!
Organic solvents cause acrylic to “craze” or crack. Clean all
Owl acrylic systems with warm water and a mild detergent.
Do not use ethanol or other organic solvents to clean Owl
products. Do not autoclave, bake, or microwave your unit.
Temperatures over 50°C can do damage to the acrylic.
NOTE:
If an RNase free electrophoresis system is desired, there are various methods to
rid the system of RNA contamination. For fast and easy decontamination, use
RNase Away®*. Spray, wipe or soak labware with RNase Away® then wipe or
rinse the surface clean; it instantly eliminates RNase. RNase Away® eliminates
the old methods that include treatment with 0.1% Diethyl Pyrocarbonate (DEPC)
treated water and soaking in dilute bleach. DEPC is suspected to be a carcinogen
and should be handled with care. This electrophoresis system should never be
autoclaved, baked, or placed in a microwave.
To order RNase Away® (not available through Owl), contact Molecular BioProd-
ucts 800-995-2787 (U.S. and Canada) or 858-453-7551:
Part Number
7000 250ml bottle
7002 475ml spray bottle
7003 1 liter bottle
7005 4 liter bottle
*Rnase AWAY® is a registered trademark of Molecular BioProducts

C
are & Cleaning
SECTION 5
14
Care of Acrylic
This list does not include all possible chemical incompatibilities and safe compounds.
Owl’s acrylic products should be cleaned with warm water, a mild detergent such as
Alconox™, and can also be exposed to a mild bleach solution (10:1). In addition, RNAse
removal products are also safe for acrylic. Please contact Owl’s Technical Service at
1-800-242-5560 with any questions.
The following chemical compatibility chart is supplied for the convenience of our custom-
ers. Although acrylic is compatible with most solvents and solutions found in the biochemi-
cal laboratory, some solvents can cause substantial damage. Keep this chart handy to avoid
harm to your apparatus by the use of an inappropriate solvent.
Codes:
S–Safe (No effect, except possibly some staining)
A–Attacked (Slight attack by, or absorption of, the liquid)
(Slight crazing or swelling, but acrylic has retained most of its strength)
U–Unsatisfactory (Softened, swollen, slowly dissolved)
D–Dissolved (In seven days, or less)
Table 7-1 Chemical Compatibility for Acrylic-Based Products
Chemical Code Chemical Code Chemical Code
Acetic acid (5%) S Ethyl alcohol (50%) A Naptha S
Acetic acid (Glacial) D Ethyl alcohol (95%) U Nitric acid (10%) S
Acetic Anhydride A Ethylene dichloride D Nitric acid (40%) A
Acetone D Ethylene glycol S Nitric acid concentrate U
Ammonia S 2-Ethylhexyl Sebacate S Oleic acid S
Ammonium Chloride (saturated) S Formaldehyde (40%) S Olive oil S
Ammonium Hydroxide (10%) S Gasoline, regular, leaded S Phenol 5% solution U
Hydroxide (10%) S Glycerine Heptane (commercial grade) S Soap solution (Ivory) S
Ammonium Hydroxide concentrate S Hexane S Sodium carbonate (2%) S
Aniline D Hydrochloric acid (10%) S Sodium carbonate (20%) S
Benzene D Hydrochloric acid concentrate S Sodium chloride (10%) S
Butyl Acetate D Hydrouoric acid (40%) U Sodium hydroxide (1%) S
Calcium chloride (saturated) S Hydrogen peroxide (3% solution) S Sodium hydroxide (10%) S
Carbon tetrachloride U Hydrogen peroxide (28% solution) U Sodium hydroxide (60%) S
Chloroform D Isooctane S Sodium hydrochlorite (5%) S
Chromic acid (40%) U Isopropyl alcohol (100%) A Sulfuric acid (3%) S
Citric acid (10%) S Kerosene (no. 2 fuel oil) S Sulfuric acid (30%) S
Cottonseed oil (edible) S Lacquer thinner D Sulfuric acid concentrate U
Detergent Solution (Heavy Duty) S Methyl alcohol (50%) A Toluene D
Diesel oil S Methyl alcohol (100%) U Trichloroethylene D
Diethyl ether U Methyl Ethyl Ketone U Turpentine S
Dimethyl formamide U Methylene chloride D Water (distilled) S
Dioctyl phthalate A Mineral oil (white) S Xylene D
Ethyl acetate D

O
ptional Equipment
SECTION 6
Contact the customer service department at Owl to order replacement
parts 800-242-5560.
15
Optional Accessories Catalog No.
Binder Clamps (pkg of 12) CL-12
Stainless Steel Clamps (pkg of 12) CL-12S
Glass Plate Dimensions Type Catalog No.
20cmW x 45cmL x 3/16"T Notched Glass S1S-45R
Blank Glass S1S-45G
20cmW x 43cmL x 3/16"T Offset Glass S1S-43G
35cmW x 45cmL x 3/16"T Notched Glass S2S-45R
Blank Glass S2S-45G
35cmW x 43cmL x 3/16"T Offset Glass S2S-43G
35cmW x 65cmL x 3/16"T Notched Glass S2SL-65R
Blank Glass S2SL-65G
35cmW x 63cmL x 3/16"T Offset Glass S2SL-63G
Spacers (set includes 2 side and 1 bottom) Catalog No.
45cmL 1.0cmW x 0.4mm thick S2S-SA4
1.0cmW x 0.2mm thick S2S-SA2
65cmL 1.0cmW x 0.4mm thick S2SL-SA4
1.0cmW x 0.2mm thick S2SL-SA2

W
arranty Information
THE OWL SEPARATION SYSTEMS WARRANTY
A three-year quality and material warranty covers all products manu-
factured by Owl Separation Systems. Owl will repair or replace any
equipment found to be defective at no cost. This warranty does not
cover equipment damage due to misuse or abuse. After the warranty
expires, Owl will repair products at a reasonable cost. All shipping
claims must be made within 48 hours from date received.
To activate your warranty, complete and return the enclosed postage
paid warranty card. Please note that the card must be completely filled
out in order to process your warranty.
RETURNING EQUIPMENT
Be environmentally friendly – and speed up your return – by saving
all packing materials cartons and documents until you have thoroughly
inspected your shipment. Should you find that your order is incorrect or
damaged, verify the problem with the shipper, save all packing mate-
rial, and call Owl for return instructions within 48 hours. All returns,
exchanges, and credits must be pre-approved by Owl.
55 Heritage Avenue
Portsmouth, NH 03801
T. [phone]
[phone]
F. [phone]
Website: www.owlsci.com
E-mail: [email protected]
Thank You!
We at Owl Separation Systems
thank you for your order and
appreciate your business.
Please contact us regarding our
complete line of electrophoresis
equipment and reagents
for DNA, RNA and protein
separations. While innovation
and quality are our foremost
objectives, we pride ourselves
on exceptional customer
response and service.
IMPORTANT DOCUMENTS ENCLOSED
Model #:
Serial #:
C.T.: