|Types of controls
||EMSA Positive controls
||EMSA Negative controls
EMSA is a well-established technique for
detecting the activity of DNA/RNA-binding
proteins. As other gel electrophoresis, a
reference standard is important to locate the
target molecule. However, common standards used
in Western blots or molecular size markers for
DNA/RNA electrophoresis can not be used for EMSA
because the location of DNA/RNA-binding proteins
is based to the combination of shape, size,
charge and interaction of the native proteins.
The use of EMSA controls in EMSA can save time
and precise location of target proteins.
Some EMSA kits contain controls. For example, Light Shift
kit includes EBNF controls. However, EBNF control is
not a good one for
1. EBNF band locates at the
position just above free probes, much
smaller that that of most nucleic acid-protein
complexes. It is too
small to locate most of target proteins.
2. Probes & samples of
EBNF control are completely
different from that customer want to use,
therefore, the control cannot provide information for
the real reaction of target probes & samples. If
specific shifted bands cannot be observed, the problems could be 1) low level of
nuclear extracts, 2) proteins degradation, 3)
inactivated protein factors or 4) non-working probes
etc, no of which has
relationship with EBNF controls.
control was considered to be an indicator for working EMSA as EBNF
band cannot be seen if electrophoresis,
trans-blotting, UV crosslinking, biotin/avidin
reaction, reagents or non-working ECL substrates etc. do/does not
work. However, if problems mentioned above happen, free probe
bands could not be seen either. Since
free probes can be used
as indicators, why needs EBNF
4. EMSA pictures with free
probe lane(s) can be used for publication directly,
however, it would be strange if EMSA pictures include EBNF band(s).
Viagene Biotech Biotech
provides largest number of EMSA
negative/positive controls than other companies;
such as NFkB/NK-kB, AP1, SP1, OCT1, OCT2, NRF2,
GATA, STATs, WT-1, E2F, P53...