Preparation of
Agarose Gels

Section II: Preparation of Agarose Gels

In This Section
Agarose Selection Guide
Agarose and Compatible Techniques
Agarose Types
Agarose Analytical Specifications
Suggested Agarose Concentrations& Dye Migration Information
Buffers for Electrophoresis
Dissolving Agarose
Casting Agarose Gels

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80
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Section II: Preparation of Agarose Gels
Agarose Selection Guide

fragment size, sample type and application. The selection
tools below will get you started. The following pages will
guide you to the right concentration, buffer and marker
to use for best performance in your experiment.

Selecting the best agarose for your application canminimize opportunity for error, optimize results, and evenreduce cost. Lonza offers a wide range of agarose types
that are specifically engineered to optimize results by
Choose the Agarose that is Right for You

Agarose and Applications

SeaKem® Gold Agarose
SeaPlaque® GTG® Agarose

200 bp - 25 kb

SeaPlaque® Agarose

200 bp - 25 kb

SeaKem® GTG® Agarose

100 bp - 23 kb

SeaKem® LE Agarose

100 bp - 23 kb

NuSieve® GTG® Agarose

50 bp - 1 kb

NuSieve® 3:1 Agarose

50 bp - 1 kb

Preparation of
Agarose Gels

MetaPhor® Agarose
0

1 kb - 10 Mb

200 bp400 bp

GTG

GTG

GTG

GTG

20 bp - 800 bp
600 bp800 bp1,000 bp

10,000,000 bp

25,000 bp
GTG

Fragment Size Range

Performance Certified
Genetic Technology Grade™

High Gel Strength

Low Melting
Temperature

Agarose and Compatible Techniques
Recovery Method
In-Gel Reactions
ß-Agarase
Phenol/Chloroform
Recovery Columns
Electroelution
Freeze/Squeeze
Blotting
Southern <1 kbSouthern >1 kb
Northern <1 kb
Northern >1 kb
Specialty Applications
Viral Plaque Assays
Preparation of
Megabase Samples
PFGE
Cell Culture
Encapsulation &Embedding of Cells
DNA Identity Testing
Comet Assays

SeaKem®
LE■■■

SeaKem®
GTG®

■
■
■

SeaPlaque®

■
■
■
■
■

SeaPlaque®
GTG®
■
■
■
■
■
■

NuSieve®
3:1

■
■
■

NuSieve®
GTG®
■
■
■
■
■
■

MetaPhor®

SeaKem®
Gold

■
■
■

■
■
■

SeaPrep®

InCert®

I.D. NA®

■
■
■

■
■
■
■
■

■
■
■

■

■

■

■
■
■

■

■
Low Melting
Temperature

Low Melting
Temperature

Low Melting
Temperature

Low Melting
Temperature

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Section II: Preparation of Agarose Gels
Agarose Types

Introduction

Molecular Biology Grade Agaroses

Nucleic acid applications take advantage of the specificproperties of different agaroses and derivatizedagaroses. The appropriate choice of agarose
depends on the size of the DNA to be analyzed andany subsequent manipulations required. Gelling/melting temperatures, electroendosmosis and gel
strength are all important factors in choosing theright agarose for your application. Refer to page 79 foranalytical specifications of Lonza agarose.

Molecular biology grade agaroses are suitable for general
analytical separation of DNA.

Genetic Technology Grade™ (GTG®) Agaroses
Our Genetic Technology Grade™ (GTG®) Agarose
Products are specially prepared and certified for
demanding molecular biology applications for nucleic
acids, including PCR amplified products. Lonza's GTG®
Agarose quality tests go beyond standard assays suchas, DNase and RNase testing, to include enzymatic
performance measurements. Our additional testing
provides a more realistic index of overall product quality
and reliability. You no longer need to screen agarose lots
to find those that yield biologically active DNA.

■ The following agaroses are considered molecularbiology grade agaroses:–– MetaPhor® Agarose–– SeaKem® LE Agarose–– NuSieve® 3:1 Agarose–– SeaPlaque® Agarose (low melting temperature
agarose)■ Lonza screens our molecular biology grade agaroses

for the following parameters:–– DNA binding–– DNase and RNase activity–– Gel background staining

Preparation of
Agarose Gels

Returnto Main■ The following agaroses are GTG® Certified:–– SeaKem® GTG® Agarose–– SeaPlaque® GTG® Agarose (low melting temperature
agarose)–– NuSieve® GTG® Agarose (low melting temperature
agarose)–– SeaKem® Gold Agarose■ Lonza performs the following tests on GTG® Certified

Agaroses:–– DNA binding–– DNase and RNase activity–– DNA resolution–– Gel background-gel exhibits low background
fluorescence after ethidium bromide staining–– In-gel cloning (low melt agarose)–– In-gel restriction digestion (low melt agarose)–– Restriction-ligation assay (SeaKem® GTG®)

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Section II: Preparation of Agarose Gels
Agarose Types — continued

DNA resolution examples
The photographs below show the different resolution
properties of Lonza agaroses.
SeaKem® GTG®
A

B

NuSieve® 3:1
A B

NuSieve® GTG®
A

B

MetaPhor®
A

B

SeaPlaque® GTG®
A

B

1,000 bp –– 622 bp
– 23,130 bp– 4,361 bp

2,500 bp –– 238 bp
– 242 bp

400 bp –Preparation of
Agarose Gels

Separation of DNA markers in 1% SeaKem® GTG® and SeaPlaque® GTG®
Agarose gels in 1X TBE Buffer (Prepared from AccuGENE® 10X TBE
Buffer).
Lane A: Lonza's 50 - 2,500 bp DNA Marker (~0.25 ng/band)
Lane B: New England BioLabs Hind III digest of lambda DNA (0.125
mg/lane) 20 cm long gels were run at 6 V/cm for ~ 2.5 hrs. Gels werepost stained using Lonza’s 1X GelStar® Nucleic Acid Gel Stain for 30
minutes. No destain.

Resolution Performance of Lonza agaroses for DNA <1 kb
Separation of DNA markers in 3% NuSieve® 3:1, NuSieve® GTG® and
MetaPhor® Agarose gels in 1X TBE (Prepared from AccuGENE® 10X TBE
Buffer).
Lane A: Lonza’s 50 - 1,000 bp DNA Marker (~25 ng/band)
Lane B: New England BioLabs Msp I digest of pBR322 (0.125 mg/lane)
20 cm long gels were run at 6 V/cm for 2 hrs. & 20 mins. Gels were post
stained using Lonza’s 1X GelStar® Nucleic Acid Gel Stain for 30 minutes.
No destain.

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Section II: Preparation of Agarose Gels
Agarose Analytical Specifictions

Introduction
Lonza performs routine analytical testing on every
lot of agarose to ensure lot-to-lot consistency for thecritical characteristics that can impact functional
performance. Specifications for properties such as gel
strength, gelling temperature, electroendosmosis, andothers are established at the optimal level for the target
applications of the various agarose types. However,analytical specifications alone may not be sufficient for

judging the best agarose for a specific application, nor are
they the best means to compare agaroses from different
vendors. The best way to find out if an agarose is rightfor your application, is to speak to our Scientific Support
representatives, and test a sample of the recommended
agarose type(s) based on your application. Lonza
has extensive capabilities for modification of agarose
properties to fit unique applications and requirements.
Ask about our custom capabilities if one our standard
products does not meet your needs.

Agarose Analytical Specifications
AgaroseMelting
Temperature

Gel Strength
g/cm2

Gelling Temperature

EEO (-mr)MoistureSulfateDNA <1 kb

NuSieve® 3:1
MetaPhor®
NuSieve® GTG®

≤90ºC at 4%≤75ºC at 3%≤65ºC at 4%≥1,400 at 4%≥300 at 3%≥500 at 4%32.5ºC – 38ºC at 4%≤35ºC at 3%≤35ºC at 4%

≤0.13
≤0.05
≤0.15

≤10%
≤10%
≤10%

≤0.15%
NA≤0.15%

DNA >1 kb

SeaKem® LE
SeaKem® GTG®
SeaPlaque®
SeaPlaque® GTG®

NA
NA
≤65ºC at 1.5%
≤65ºC at 1.5%

≥1,200 at 1%≥1,200 at 1%≥200 at 1%≥200 at 1%

36ºC ± 1.5ºC at 1.5%
36ºC ± 1.5ºC at 1.5%
26ºC – 30ºC at 1.5%
26ºC – 30ºC at 1.5%

0.09 – 0.13
0.09 – 0.13
≤0.10
≤0.10

≤10%
≤10%
≤10%
≤10%

≤0.15%≤0.15%≤0.10%≤0.10%PFGE

SeaKem® GoldNA

34.5ºC –37.5ºC at 1.5%

≤0.05

≤10%

≤0.10%

26ºC – 30ºC at 1.5%

≤0.10

≤10%

≤0.15%

InCert®

≤70ºC at 1.5%

≥1,800 at 1%≥3,500 at 1.5%≥350 at 1%

Identity Testing

I.D.na®

NA≥1,300 at 1%

36ºC ± 1.5ºC at 1.5%

≤0.10

≤10%

≤0.15%

Protein Electrophoresis

SeaKem® ME
SeaKem® HE
SeaKem® HEEO
SeaKem® HGT

NA
NA
NA
NA

≥1,000 at 1%≥650 at 1%≥650 at 1%≥800 at 1%

36ºC ± 1.5ºC at 1.5%
36ºC ± 1.5ºC at 1.5%
36ºC ± 1.5ºC at 1.5%
42ºC ± 1.5ºC at 1.5%

0.16 – 0.19
0.23 – 0.26
≥0.30
≤0.10

≤10%
≤10%
≤10%
≤10%

≤0.20%≤0.20%≤0.25%≤0.30%

von Willenbrand’s Factor
Separation

SeaKem® HGT(P)NA≥1,000 at 1%

42ºC ± 1.5ºC at 1.5%

≤0.10

≤10%

≤0.20%

Isoelectric Focusing

IsoGel®

NA≥500 at 1.5%

35ºC – 45ºC

Not
Detectable≤10%≤0.20%

Cell Culture

SeaPrep®

≤50ºC at 1%≥75 at 2%

8ºC – 17ºC at 0.8%

≤0.05

≤10%

≤0.10%

Preparation of
Agarose Gels

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Section II: Preparation of Agarose Gels
Suggested Agarose Concentrations and Dye Migration Infomation

Table 1: Suggested agaroses for particular applications

Table 2: Properties of TAE and TBE Buffer Systems

Size Range(Base Pairs)

Agarose Type

BufferSuggested Uses and Comments

20 – 800

MetaPhor®
AgaroseHigh resolution analysis;
2% size differences

TAE Buffer

50 – 1,000

NuSieve® 3:1
AgaroseAnalysis and blotting;
4% – 6% size differences resolved

Use when DNA is to be recovered
Use for electrophoresis of large (>12 kb) DNA
Low ionic strength
Low buffering capacity – recirculation may be necessaryfor extended electrophoretic times

NuSieve® GTG®
AgaroseAnalysis and blotting; In-gel;
6% size differences resolved

TBE Buffer

SeaKem® GTG®
AgaroseAnalysis and blotting;recovery required

Use for electrophoresis of small (<1 kb) DNA
Decreased DNA mobility
High ionic strength
High buffering capacity – no recirculation required for extended
run times

SeaPlaque®
GTG® Agarose

In-gelSeaKem® Gold
AgaroseAnalysis

10,000

Table 4: Migration of double-stranded DNA in relation to
Bromophenol Blue (BPB) and Xylene Cyanol (XC) inagarose gels

Table 3: Suggested agarose concentrations for DNA sizes
Final Agarose Concentration % (w/v)

Preparation of
Agarose Gels

Size Range (Base Pairs)
1X TAE Buffer
SeaKem® LE and SeaKem® GTG® Agarose
1,000 – 23,000
0.60
800 – 10,000
0.80
400 – 8,000
1.00
300 – 7,000
1.20
200 – 4,000
1.50
100 – 3,000
2.00
NuSieve® 3:1 Agarose
500 – 1,000
3.0
100 – 500
4.0
10 – 100
6.0
MetaPhor® Agarose
150 – 800
2.0
100 – 600
3.0
50 – 250
4.0
20 – 130
5.0<80—
SeaPlaque® and SeaPlaque® GTG® Agarose
500 – 25,000
0.75
300 – 20,000
1.00
200 – 12,000
1.25
150 – 6,000
1.50
100 – 3,000
1.75
50 – 2,000
2.00
NuSieve® GTG® Agarose
500 – 1,000
2.5
150 – 700
3.0
100 – 450
3.5
70 – 300
4.0
10 – 100
4.5
8 – 50
5.0
SeaKem® Gold Agarose†
5,000 – 50,000
0.3
1,000 – 20,000
0.5
800 – 10,000
0.8
400 – 8,000
1.0

1X TBE Buffer
0.50
0.70
0.85
1.00
1.25
1.75
2.0
3.0
5.0
1.8
2.0
3.0
4.0
5.0
0.70
0.85
1.00
1.25
1.50
1.75
2.0
2.5
3.0
3.5
4.0
4.5
—
—
—
—

† TBE Buffer is not recommended for separation of DNA >12,000 bp.

1X TAE Buffer
XC
BPB% Agarose
SeaKem® LE and SeaKem® GTG® Agarose
24,8002,900
0.30
11,0001,650
0.50
10,200
1,000
0.75
6,100
500
1.00
3,560
370
1.25
2,800
300
1.50
1,800
200
1.75
1,300
150
2.00
NuSieve® 3:1 Agarose
950
130
2.50
650
80
3.00
350
40
4.00
200
30
5.00
120
20
6.00
MetaPhor® Agarose
480
70
2.00
200
40
3.00
120
35
4.00
85
30
5.00
SeaPlaque® and SeaPlaque® GTG® Agarose
11,700
1,020
0.50
4,000
500
0.75
2,300
350
1.00
1,500
200
1.25
1,000
150
1.50
700
100
1.75
550
60
2.00
320
30
2.50
NuSieve® GTG® Agarose
750
175
2.50
400
120
3.00
115
<20
4.00
100
<20
5.00
85
<20
6.00
SeaKem® Gold Agarose
24,8003,550
0.30
12,200
2,050
0.50
9,200
1,050
0.75
6,100
760
1.00
4,100
600
1.25
2,600
400
1.50
2,000
330
1.75
1,500
250
2.00

1X TBE Buffer
XC
BPB
19,40012,000
9,200
4,100
2,500
1,800
1,100
850

2,850
1,350
720
400
260
200
110
70

700
500
250
140
90

70
40
20
8
4

310
140
85
60

40
35
30
15

6,100
2,850
1,700
1,000
700
500
400
250

400
280
180
100
70
50
30
10

460
210
150
80
50

75
35
<20
<20
<20

19,000
9,200
7,100
4,000
2,550
1,900
1,400
1,000

2,550
1,500
800
500
350
250
180
100

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Agarose Gels

1,000 – 10,000

Application

Section II: Preparation of Agarose Gels
Buffers for Electrophoresis

Introduction

DNA Electrophoresis in TAE or TBE Buffer

During electrophoresis, water is electrolyzed, which
generates protons at the anode, and hydroxyl ions at thecathode. The cathodal end of the electrophoresis chamberthen becomes basic and the anodal end acidic. The use ofa buffering system is therefore required when charged
molecules are electrophoresed through a separation
medium. The two buffers commonly used for DNA
electrophoresis are Tris-acetate with EDTA (TAE; 40 mM
Tris-acetate, 1 mM EDTA) and Tris-borate with EDTA (TBE;
89 mM Tris-borate, 2 mM EDTA). Because the pH of thesebuffers is neutral, the phosphate backbone of DNA has a
net negative charge and migrates towards the anode.

When DNA will not be recovered, either 1X TAE or TBE (1X or
0.5X) Buffer is suitable for use when the DNA is less than
12 kb to 15 kb. For larger DNA, the best buffer to use forelectrophoresis is TAE in combination with a low field strength(1-2 V/cm). During these extended electrophoretic runs,
larger apparent gel porosity, lower EEO and low field strength
decrease the tendency of large DNA to smear.
TBE Buffer is preferred for separation of small DNA(<1 kb) when DNA recovery is not required. TBE Buffer’s
interaction with agarose results in a smaller apparent
pore size. The tighter gel reduces the broadening of DNA
bands due to dispersion and diffusion.

Properties of TAE and TBE Buffer Systems
Despite the apparent similarity of TAE and TBE Buffers,
each has different properties which make it best suitedfor different applications (see table below).
BufferSuggested Uses and Properties

TAE

Use when DNA is to be recovered
Use for electrophoresis of large (>12 kb) DNA

	Low buffering capacity – recirculation may benecessary for extended electrophoretic times(>6 hours)
TBE%

1X TAE Buffer

1X TBE Buffer

0.75 1.00 1.25 0.75 1.00 1.25

12 kb –

3 kb –

1 kb –
0.5 kb –Separation of DNA
markers in 0.75% to1.25% SeaKem® GTG®
– 12 kb Agarose gels in 1X TAE
and TBE Buffers. 1 kb
DNA ladder (Invitrogen,– 2 kb Inc.); 1 µg/lane. The gelswere cast in a 25.5
cm framing gel of 1%– 1 kb
SeaKem® GTG® Agarose
in a submarine chamber– 0.5 kb and run under 5 mmof buffer overlay at 5
V/cm for 3 hours, 30
minutes (TBE Buffer),
3 hours (TAE Buffer).

Preparation of
Agarose Gels

Returnto Main

Use for electrophoresis of small (<1 kb) DNA
Increased resolution of small (<1 kb) DNA
Decreased DNA mobility
High buffering capacity – no recirculation
required for extended run times

1X TBE Buffer

1X TAE Buffer

2%

3%

A B

A

4%

B

A

B

2%

3%

A B

A

4%

B

A

B

– 1,353 bp

Lonza offers ready-to-go buffers for electrophoresis.
Refer to AccuGENE® Buffer products on page 41.

1,000 bp –– 603 bp

100 bp –Separation of DNA fragments in 2% to 4% NuSieve® 3:1 Agarose gel in
1X TAE and TBE Buffers.
Lane A: Lonza’s 100 bp Extended Range DNA Ladder (4 - 7.5 ng/band)
Lane B: Invitrogen, Inc.'s Hae III digest of φX174 (0.25 ng/band)
20 cm long gels were run at 6 V/cm for 2.5 hrs. in 1X TBE (Preparedfrom AccuGENE® 10X TBE Buffer). Gels were post stained using Lonza’s
1X GelStar® Nucleic Acid Gel Stain for 30 minutes. No destain.

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Section II: Preparation of Agarose Gels
Buffers for Electrophoresis — continued

Buffer Depth
Whichever buffer is used, the depth over the gel in ahorizontal electrophoretic system should be 3 mm - 5
mm. Excessive buffer depth will decrease DNA mobility,
promote band distortion and can cause excessive heating
within the system. Less buffer and the gel may dry out
during electrophoresis.
The photograph below depicts the effect of buffer depth
on DNA electrophoresis. The DNA mobility in the gel with a
10 mm buffer overlay is slower than the gel with a 3 mm
buffer overlay. In the Hae III digested φX174 marker, the281/271 bands are starting to resolve in the gel with the
3 mm buffer overlay whereas in the gel with the 10 mm
buffer overlay they are not.
10 mm Buffer
OverlayA

Preparation of
Agarose Gels

1,353 bp –B

3 mm Buffer
OverlayA

271 bp –100 bp –50 bp –

Effects of buffer depletion and development of a pH
gradient can be reduced by recirculating the buffer. Thisis usually necessary only when electrophoresis is donefor extended times or the electrophoresis buffer has a low
buffering capacity.
Buffer Preparation
Alternatively, Lonza offers AccuGENE® TBE Buffer in 5X
and 10X stock solutions and AccuGENE® TAE Buffer in 10X
and 50X stock solutions.
50X TAE(Tris-acetate) stockB– 1,353 bp

700 bp –400 bp –281 bp –1.5 L to 2 L capacity will tolerate 40 to 50 Watt hours
before buffer depletion, and buffer depletion will not occur
in mini-electrophoresis chambers for 10 to 13 Watt hours.
Consult the electrophoresis chamber manufacturer for
specific values.

– 700 bp		– 400 bp		– 281 bp		
– 271 bp
– 234 bp		– 100 bp		– 50 bp

Separation of DNA markers in a 3% NuSieve® 3:1 Agarose gel preparedand run in 1X TBE Buffer.
Lane A: DNA marker 50 bp - 1,000 bp DNA Marker (Lonza); 0.4 µg/lane.
Lane B: Hae III digested φX174 DNA (New England Biolabs); 0.5 µg/lane.
The gels were run at 5 V/cm until the bromophenol blue tracking dye
was 1 cm from the bottom of each gel.

(1X=40 mM Tris base,
40 mM acetic acid, 1 mM
EDTA)
242.0 g Tris base

5X TBE (Tris-borate) stock(1X=89 mM Tris base,89 mM boric acid, 2 mM
EDTA)
(0.5X=45 mM Tris-borate,
1 mM EDTA)

57.1 ml Glacial acetic acid18.61 g Na2EDTA • 2H2O

54.0 g Tris baseTo 1 liter with distilledwater

3.72 g Na2EDTA • 2H2O

27.5 g Boric acidTo 1 liter with distilled
water

Other Buffering Systems
Tris-phosphate Buffer (TPE) may also be used for DNA
electrophoresis. Like TBE Buffer, TPE has a high buffering
capacity, and will not interfere with DNA recovery
procedures. However, TPE can not be used when recovered
DNA will be used in a phosphate-sensitive reaction.
10X Tris-phosphate Stock (TPE)(1X=90 mM Tris base, 90 mM phosphoric acid, 2 mM
EDTA)

Buffer Depletion

108.0 g Tris base

The rate of buffer depletion is influenced by the buffer used
and its buffering capacity. Evidence of buffer depletionis gel melting, smearing of DNA and/or overheating. A
0.5X TBE Buffer has greater buffering capacity thana 1X TAE Buffer at the pH used because the pKa of borate iscloser to the initial Buffer pH than that of acetate. Standardsized electrophoresis chambers (15 cm x 30 cm) with a

15.5 ml 85% Phosphoric acid
7.44 g Na2EDTA • 2H2O
To 1 liter with distilled water
Alkaline electrophoresis buffer is used for the analysis ofsingle-stranded DNA.

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Section II: Preparation of Agarose Gels
Dissolving Agarose

Introduction

5.

Weigh the beaker and solution before heating.

Agarose undergoes a series of steps when it is dissolved;
dispersion, hydration and melting/dissolution.

6.

Cover the beaker with plastic wrap.

7.

Pierce a small hole in the plastic wrap for ventilation.

8.

Heat the beaker in the microwave oven on HIGH
power until bubbles appear.

Dispersion simply refers to the separation of the particles
by the buffer without clumping. Clumping occurs when
the agarose starts to dissolve before it is completely
dispersed, coating itself with a gelatinous layer which
inhibits the penetration of water and keeps the powder
inside from dispersing. Dissolution then becomes a longprocess.

Hydration

Preparation of
Agarose Gels

Hydration is the surrounding of agarose particles by asolution (e.g., water or running buffer). Problems are
sometimes encountered with hydration when using a
microwave oven to dissolve agarose. In part, this occurs
because hydration is time dependent and microwave
ovens bring the temperature up rapidly. The problem
is exacerbated by the fact that the agarose is not being
agitated to help dilute the highly concentrated solution
around each particle and dissolution is slowed.
Melting and Dissolution
The final stage in dissolving the agarose is the melting anddissolution. Melting can be done in either a microwave
oven or on a hot plate. As the particles hydrate, they
become small, highly concentrated gels. Since themelting temperature of a standard agarose gel is about
93°C, merely heating a mixture to 90°C will not completely
dissolve agarose. Even low melting temperature
agaroses should be boiled to ensure that all the agarose
is fully dissolved. Microwave instructions for agarose
preparation for gel concentrations of ≤2% w/v
Microwave Instructions for Gel Concentrations <2%w/v
1.

Choose a beaker that is 2 - 4 times the volume ofthe solution.

Caution: Any Microwave solution may becomesuperheated and foam over when agitated.
9.

Remove the beaker from the microwave oven.

10.

GENTLY swirl the beaker to resuspend any settled 		
powder and gel pieces.

11.

Reheat the beaker on HIGH power until the solution 		comes to a boil.

12.

Hold at boiling point for 1 minute or until all of the 		particles are dissolved.

13.

Remove the beaker from the microwave oven.

Caution: Use oven mits when removing beaker frommicrowave, as container will be hot and may causeburns.
14.

GENTLY swirl the beaker to mix the agarose solution 		
thoroughly.

15.

After dissolution, add sufficient hot distilled water to 		obtain the initial weight.

16.

Mix thoroughly.

17.

Cool the solution to 60°C prior to casting.

Preparation of
Agarose Gels

Dispersion■■ Materials–– Microwave oven or hot plate–– Beaker that is 2 - 4 times the volume of the solution–– Teflon®-coated magnetic stir bar–– Magnetic stir plate–– Plastic wrap–– Oven mitts or other heat protection for hands■■ Reagents2.

Add room temperature 1X or 0.5X buffer and a stir
bar to the beaker.

–– Distilled water3.

Sprinkle in the premeasured agarose powder while 		the solution is rapidly stirred.

–– Agarose powder

4.

Remove the stir bar if not Teflon® coated.

–– 1X TAE, 1X TBE or 0.5X TBE Electrophoresis Buffer
Caution: Always wear eye protection, and guard
yourself and others against scalding solutions.

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Section II: Preparation of Agarose Gels
Dissolving Agarose — continued

Microwave instructions
For agarose preparation for gel concentrations ≥2% w/v
1.

Choose a beaker that is 2 - 4 times the volume of thesolution.

2.

Add room temperature or chilled buffer (for MetaPhor®
and NuSieve® GTG® Agarose) and a stir bar 		to the beaker.
Sprinkle in the premeasured agarose powder while thesolution is rapidly stirred to prevent the formation ofclumps.

3.

4.

Remove the stir bar if not Teflon® coated.

5.

Soak the agarose in the buffer for 15 minutes before
heating. This reduces the tendency of the agarose
solution to foam during heating.

6.

Weigh the beaker and solution before heating.

7.

Cover the beaker with plastic wrap.

8.

Pierce a small hole in the plastic wrap for ventilation.

Preparation of
Agarose Gels

For agarose concentrations >4%, the following
additional steps will further help prevent the agarose
solution from foaming during melting/dissolution:

16.

After dissolution, add sufficient hot distilled water toobtain the initial weight.

17.

Mix thoroughly.

18.

Cool the solution to 60°C prior to gel casting.

Hot plate instructions for preparing agarose
1.

Choose a beaker that is 2 - 4 times the volume of thesolution.

2.

Add room temperature or chilled buffer (for MetaPhor®
or NuSieve® GTG® Agarose) and a stir bar to the beaker.

3.

Sprinkle in the premeasured agarose powder while thesolution is rapidly stirred to prevent the formation ofclumps.

4.

Weigh the beaker and solution before heating.

5.

Cover the beaker with plastic wrap.

6.

Pierce a small hole in the plastic wrap for ventilation.

7.

Bring the solution to a boil while stirring.

8.

Maintain gentle boiling until the agarose is dissolved(approximately 5 -10 minutes).

9.

Add sufficient hot distilled water to obtain the initial
weight.

8a.

Heat the beaker in the microwave oven on
MEDIUM power for 1 minute.

10.

Mix thoroughly.

8b.

Remove the solution from the microwave.

11.

Cool the solution to 60°C prior to casting.

8c.

Allow the solution to sit on the bench for 15
minutes.

Heat the beaker in the microwave oven on MEDIUM
power for 2 minutes.

9.

Caution: Any microwaved solution may becomesuperheated and foam over when agitated.
10.

Remove the beaker from the microwave oven.

Caution: Use oven mits when removing beaker frommicrowave, as container will be hot and may causeburns.
11.

GENTLY swirl to resuspend any settled powder andgel pieces.

12.

Reheat the beaker on HIGH power for 1 - 2 minutes oruntil the solution comes to a boil.

13.

Hold at the boiling point for 1 minute or until all of
the particles are dissolved.

14.

Remove the beaker from the microwave oven.

15.

GENTLY swirl to mix the agarose solution thoroughly.

■■ Materials–– Microwave oven or hot plate–– Beaker that is 2 - 4 times the volume of the solution–– Teflon®-coated Magnetic Stir Bar–– Magnetic stir plate–– Plastic wrap■■ Reagents–– Distilled water–– 1X TAE, 1X TBE or 0.5X TBE Electrophoresis Buffer–– Agarose powder
Caution: Always wear eye protection, and guard
yourself and others against scalding solutions.

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Section II: Preparation of Agarose Gels
Casting Agarose Gels

Introduction

Horizontal gel casting instructions

For optimal resolution, cast horizontal gels 3 mm - 4
mm thick (see figure below). The volume of gel solution
needed can be estimated by measuring the surface
area of the casting chamber, then multiplying by the gel
thickness. Thinner gels can be cast on GelBond® Film and/or in a vertical electrophoresis apparatus.

1.

Allow the agarose solution to cool to 60°C.

1.

While the agarose solution is cooling:

The photographs below depict the effect of gel depth on
DNA electrophoresis. Gel thickness has a profound effecton the resolution of smaller fragments. The smaller DNA
fragments in the 10 mm thick gel are fuzzy, whereas in
the 3 mm thick gel the resolution is sharp throughout
the gel. There is also a higher background staining in gelsthicker than 5 mm.

10 mm Thick Gel
A

B

A

B

A

23,130 bp –			– 23,130 bp

4,361 bp –			– 4,361 bp

			– 2,027 bp

			– 1,078 bp

2,027 bp –1,078 bp –			Separation of DNA markers in 1% SeaKem® GTG® Agarose gels preparedand run in 1X TBE Buffer.
Lane A: Hind III digest of lambda DNA (Boehringer Mannheim);
0.1 µg/lane.
Lane B: Hae III digested φX174 DNA (New England Biolabs); 0.5 µg/lane. 20 cm long gels were run at 6 V/cm for 2 hours 15 minutes(10 mm thick gel) and 2 hours 10 minutes (3 mm thick gel).

Lonza offers a wide range of precast gels.
Refer to page 17 for information.

2b.

Level the casting tray prior to pouring the agarose
solution.

2c.

Check the comb(s)* teeth for residual dried
agarose. Dried agarose can be removed byscrubbing the comb teeth with a lint-free tissue
soaked in hot distilled water.

2d.

Allow a small space (approximately 0.5 mm 1 mm) between the bottom of the comb teeth
and the casting tray.

Pour the agarose solution into the gel tray.

4.

Replace the comb(s).

5.

Allow the agarose to gel at room temperature for 30
minutes.

6.

Low melting temperature agaroses and MetaPhor®
Agarose require an additional 30 minutes of gellingat 4°C to obtain the best gel handling. The additionalcooling step is essential for obtaining fine resolution in
MetaPhor® Agarose.

7.

Once the gel is set, flood with running buffer.

8.

Slowly remove the comb.

9.

Place the gel casting tray into the electrophoresis
chamber.

10.

Fill the chamber with running buffer until the buffer 		reaches 3 mm - 5 mm over the surface of the gel.

11.

Gently flush the wells out with electrophoresis bufferusing a Pasteur pipette to remove loose gel fragments
prior to loading the samples.

12.

Load DNA and electrophorese.

– 310 bp

310 bp –Assemble the gel casting tray.

3.

3 mm Thick Gel
A

2a.

Preparation of
Agarose Gels

Returnto Main*The thickness of the comb in the direction of the electric field can affectthe resolution. A thin comb ( 1 mm) will result in sharper DNA bands. Witha thicker comb, more volume can be added to the well but the separated
DNA bands may be broader.

■■ Materials–– Horizontal electrophoresis apparatus–– Combs–– Pasteur pipette■■ Reagents–– Agarose solution–– Electrophoresis buffer
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Section II: Preparation of Agarose Gels
Casting Agarose Gels — continued

Vertical Gel Casting Instructions
Follow the steps below to cast a vertical agarose gel. This
protocol is divided into the following segments:—— Cassette assembly—— Cassette sealing—— Casting the gel—— Preparing for electrophoresis
Cassette assembly
Unlike polyacrylamide gels, agarose gels do not adhere
to glass plates and may slide out during electrophoresis.
To prevent this from happening, frosted glass plates orplastic plates can be used.

■■ Materials–– Vertical electrophoresis apparatus–– Combs and side spacers–– Whatman® 3MM Chromatography Paper–– Clamps–– Silicone tubing or electrical tape–– Two 60 ml syringes with16-gauge needles–– Heat gun or 55°C oven–– Scalpel or razor blade■■ Reagents–– Agarose solution–– Electrophoresis buffer

Follow the steps below to assemble the glass plates.

Preparation of
Agarose Gels

1.

Use clean glass plates. Clean with soap and water, rinse
with distilled water and dry.

2.

Wipe the plates with ethanol and a lint-free tissue.

3.

Place two side spacers on the back plate. Follow thesteps below if using glass plates.
3a.

For 1 mm thick standard size gels, cut a strip ofWhatman® 3MM Chromatography paper (1 mmthick and 5 - 10 mm wide) long enough to fit
between the two spacers.*

3b.

Wet with running buffer.

3c.

Place at the bottom of the back plate in contact
with the spacers on each side (see Figure 1, page
87).

4.

Put on the front plate.

5.

Clamp the glass plates together.

6.

Use the manufacturer’s casting apparatus or seal thecassette against leaks with silicone tubing or tape.

*Alternatively, use GelBond® Film as a support for the gel, which obviates theneed for the use of Whatman® 3MM Chromatography paper to hold the gel inthe cassette during electrophoresis (see Chapter IX). GelBond® Film is put into
the casting cassette and the gel attaches to the film during the gelling process.
After electrophoresis, the gel may be dried down on the GelBond® Film andkept as a permanent record. However, GelBond® Film blocks UV light below
300 nm and exhibits background fluorescence. To overcome these problems,gels cast on GelBond® Film may be photographed inverted (gel side down)on the UV light box. Background fluorescence can be screened out by using
red, orange (Wratten® #22 or #25 gelatin filter) and UV filters (Wratten® #2B
gelatin filter).

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Section II: Preparation of Agarose Gels
Casting Agarose Gels — continued

Cassette Sealing

Figure 1.

Follow one of the methods below to seal the cassette prior to casting the gel.
Silicone tubing method1.

Use silicone tubing which is the same diameter as the spacer thickness.

2.

Cut a piece long enough to extend along the bottom and up both sides of thecassette.

3.

Place the tubing across the bottom of the back plate below the blotting paper
strip (see Figure 2).

4.

Place the top plate over the bottom plate.

5.

Clamp the glass plates together at the bottom.

6.

Run the tubing up either side of the plates and finish clamping the plates together(see Figure 3).

Tape method
1.

Place the top plate over the bottom plate.

2.

Tape the sides of the cassette with separate pieces of tape.

3.

T ape the bottom of the cassette with a separate piece of tape. This way the tapeon the bottom can be removed for electrophoresis without disturbing the tape atthe sides of the gel (see Figure 4).

4.

Clamp the plates together.

Whatman® 3MM
Chromatography Paper
Figure 2.

Figure 3.

Preparation of
Agarose Gels

Returnto MainFigure 4.

Casting a Vertical Agarose Gel
1.

Prepare agarose solution as described previously.

2.

Pre-warm the assembled cassette and a 60 ml syringe for 15 minutes by placing
in a 55°C oven or by using a heat gun.

3.

Cool the dissolved agarose to 60°C.

4.

Pour into a pre-warmed 60 ml syringe fitted with a 16-gauge needle.

5.

Wedge the needle tip between the plates in the upper corner of the cassette with
the needle opening directed toward the back plate (see Figure 5).

6.

Inject the agarose solution at a moderate, steady rate. Keep a constant flow toprevent air bubble formation (see Figure 5).

7.

A ngle the cassette while pouring so the agarose solution flows down one side
spacer, across the bottom and up the other side.

8.

Fill until the agarose solution goes just above the glass plates.

9.

Insert one end of the comb, then slowly insert the rest of the comb until theteeth are at an even depth. Insert the comb into the agarose to the minimal
depth necessary to accommodate your samples (see Figure 6, page 88).

Figure 5.

Continued on next page.

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Section II: Preparation of Agarose Gels
Casting Agarose Gels — continued

10.

Place extra clamps on the side of the glass plates to hold the comb in place.

11.

Cool the gel at room temperature for 15 minutes.

12.

Place the gel at 4°C for 20 minutes.

13.

Remove the clamps at the top of the gel.

14.

Remove any excess agarose with a scalpel or razor blade.

15.

Squirt running buffer in the spaces between the comb and the gel.

16.

Slowly and gently lift the comb straight up. Allow air or buffer to enter the wellarea to release the vacuum which forms between the agarose and the comb.

17.

The wells can be further cleaned by flushing with running buffer.

18.

The gel can be stored overnight in a humidity chamber or in a sealed bag with abuffer-dampened paper towel.

Figure 6.

Preparing for electrophoresis
1.

Remove the silicone tubing or tape at the bottom of the cassette

Preparation of
Agarose Gels

note: If you have placed Whatman® 3MM Chromatography Paper between the plates atthe bottom, it is not necessary to remove it as it will not interfere with electrophoresis.
2.

Place the cassette into the chamber at an angle to minimize the number of
bubbles which can collect in the well area.

3.

Rinse out well area with a syringe.

note: Since agarose does not adhere well to glass, leave as many clips in place aspossible. For some electrophoresis chambers, it is helpful to seal the spacers at the topof the gel with molten agarose.

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