Agarose: Gel Volumes And Percentage; Ethidium Bromide - VWR Peqlab PerfectBlue Mini S Instruction Manual

Instruction Manual PerfectBlue

Agarose: Gel volumes and percentage

VWR offers an extensive range of high quality agaroses, for many specific applications (see
'TECHNICAL SUPPORT AND ORDERING INFORMATION').
The required volume of the gel is calculated using the following formula.
gel width (cm) x gel length (cm) x gel thickness (cm) = required volume agarose solution (ml)
The following volumes will result:
Model
PerfectBlue Mini S
PerfectBlue Mini M
PerfectBlue Mini L ('Revolution')
The optimal range of DNA fragment sizes separated by any electrophoresis experiment is dependent on
the agarose concentration of the gel. The higher the agarose concentration, the better small fragments
are separated from each other and vice versa. However, for the smallest or largest fragment lengths, the
usage of specialized agaroses or polyacrylamide gels should be considered (see table below) since a
3 % agarose solution solidifies rapidly and a 0.3 % agarose gel is very soft and difficult to handle.
Agarose content (w/v)
0.3 %
0.5 %
0.7 %
1.0 %
1.2 %
1.5 %
2.0 %
3.0 %

Ethidium bromide

The gel may be stained during or following the run with a variety of stains for photo documentation. The
most common stain for DNA is ethidium bromide. Because of its capacity to intercalate into double
stranded nucleic acids and alter the conformation of DNA, ethidium bromide is judged to be highly
mutagenic. Therefore appropriate safety measures must be applied.
Ethidium bromide may be added directly to the gel before pouring it at a concentration of 0.1 to
0.5 µg/ml. However, being positively charged, ethidium bromide will migrate to the cathode during the
electrophoresis leading to uneven staining. Improved results can be obtained by incubating the gel after
the electrophoresis is finished in electrophoresis buffer containing 0.5 µg/ml ethidium bromide for 5 to
20 min. Subsequently the gel should get rinsed in electrophoresis buffer without ethidium bromide for up
to 20 min in order to reduce background signal.
VWR_v0617_E
Horizontal Mini Gel Systems
TM
Gel size (cm)
7 x 8 (W x L)
9 x 11 (W x L)
12 x 14 (W x L)
Agarose (g)
0.3
0.5
0.7
1.0
1.2
1.5
2.0
3.0
Gel thickness (cm)
0.25 0.5
14 ml 28 ml
25 ml 50 ml
42 ml 84 ml
Buffer (ml)
100
100
100
100
100
100
100
100
8
0.75 1.0
42 ml 56 ml
75 ml 100 ml
126 ml 168 ml
optimal separation range (kb)
5 - 30
1 - 15
0.8 - 10
0.5 - 7
0.3 - 6
0.2 - 4
0.1 - 3
< 0.1