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Problems | Possible reasons | Solutions |
---|---|---|
No shifted bands & no free
probes |
Poor labeling of nucleic acid. | Check IR dye labeling efficiency. |
No enough amount of IR probes used. | Increase amounts of IR dye probes. | |
Degrated DNA/RNA probes | The solutions should be DNase free or RNase free. | |
Incorrect operation of imager or scanner | Read and follow operation manuals | |
Probes unable to bind to target proteins | Label DNA/RNA with large molecules may prevent probes from binding to target proteins. | |
All bands are smeared or
streaked |
Uneven gel polymerization |
Use fresh gel components. Degas thoroughly
before polymerization. If polymerization
interfered with casting gel, reduce TEMED
concentration. If gel requires greater than 1 h
to polymerize, increase ammonium persulfate
concentration |
Excessive gel heating | Check concentrations of gel and running buffer. If they are correct, reduce voltage during electrophoresis | |
Sample conductivity too high | Reduce salt concentration in nucleic acid or sample buffer | |
Only free probe bands can be observed | Proteins degrated | Use high quality extraction kits with
proteinase inhibitor. Nuclear extration at low temperature. Store extracts at -80 or liquid nitrogen Include RNase inhibitor with reaction if probe is RNA Perform Western bot to check target protein. |
Not enough Proteins | Protein concentration should be 1-3 ug/ul. Total protein 2-3ug is used for EMSA. | |
Used Too much poly[dI:dC] | Poly[dI:dC] non-specifically bind proteins. Too much Poly[dI:dC] would reduced specific complexes. | |
High volum of samples are used. | Nuclear proteins is extracted by buffer with high salts. High volum of samples with increase salt concentration and reduce or prevent formation of DNA/RNA-protein complexes. | |
Only free probe bands and non-specific bands can be observed | Sample without target proteins | Express target protein by an extral gene or change a cell line with target protein |
Target proteins are inactivated | Treat cells with proper cell factors or other stimulating factors | |
Target proteins are degradated | Treat cells with proper cell factors or other stimulating factors | |
Free nucleic acid migrates normally. Nucleic acid mobility unchanged in presence of protein | No target protein or low expression of target protein. | Perform Western bot to check target protein. |
Total protein concentration is low. | Not enough cells/tissues are used or nuc. proteins are lost during extraction. Nuc. proteins should be >1ug/ul. Verify protein concentration. Use larger volumes of protein stock or more concentrated stock in preparing sample | |
Protein is inactive | Run Western blot to check level of total and
nuc. proteins. Activated TF would migrates into
nucleus. If the binding protein is an enzyme, test for activity. Test higher concentrations of protein to detect residual binding activity. A new, more active preparation of protein may be necessary |
|
Target proteins are decayed. | Run Western blot with fresh extracts and extracts in storage. | |
Protein is negatively charged and comigrates with nucleic acid | Check migration of protein alone under EMSA
conditions. If protein comigrates with nuclei
acid, reduce pH of binding and electrophoresis buffers. |
|
Free nucleic acid migrates normally. No nucleic acid detectable in samples containing protein | Nucleic acid degradation | Verify that nucleic acid is intact. If nuclease activity is suspected, treat glassware and buffers with diethyl pyrocarbonate. Exclude divalent cations wherever possible. Use commercial RNase and phosphatase inhibitors |
Binding occurred but complexes dissociated
during electrophoresis. Liberated nucleic acid is too diffuse to detect |
Minimize gel running times; use more
concentrated gel; include stabilizing solutes in
gel buffer; reduce salt concentration in binding and electrophoresis buffers to increase electrostatic stabilization; lower electrophoresis temperature (run gel in cold room); reduce or eliminate competing nucleic acid (this can be added back with care once a useful binding signal is obtained) |
|
Free nucleic acid migrates normally. Complex bands smeared or streaky | Binding occurred but complexes dissociated in gel during electrophoresis | Minimize gel running times; use more
concentrated gel; include stabilizing solutes in
gel buffer; reduce salt concentration in binding and electrophoresis buffers to increase electrostatic stabilization; lower electrophoresis temperature (run gel in cold room); reduce or eliminate competing nucleic acid |
Binding occurred but complexes dissociated in the well prior to electrophoresis | Minimize interval that sample is in well before electrophoresis. Complexes may be destabilized by component(s) of running buffer. If so, they may be more stable in gel and running buffers that more closely resemble the composition of binding buffer | |
Binding occurred but complexes dissociated in the well during electrophoresis | To minimize gel ‘dead time,’ use smallest sample volume possible; conduct electrophoresis at high voltage (approximately 50 V cm–1) until samples enter the gel, then reduce to approximately 10 V cm–1 | |
Binding occurred but samples containing protein are too salty | Reduce salt concentration in protein stock and/or in binding buffer | |
Free band is sharp, complex band(s) are broad and indistinct | Heterogeneous protein | Multiple species may be due to post-translational modification or to partial degradation without loss of binding activity |
Complex and free bands are broad and indistinct | Sample zone is too large (measured from top of sample to bottom of well) at the start of electrophoresis | Reduce sample volume. Increase density of sample (e.g., increase glycerol concentration) to facilitate gel loading. Minimize time between loading and electrophoresis |
Electrophoresis period too long | Reduce run-time | |
Nucleic acid degradation | Verify that nucleic acid is intact. If nuclease activity is suspected, treat extracts and buffers with diethyl pyrocarbonate. Exclude divalent cations wherever possible. Use RNase and phosphatase inhibitors | |
Nucleic acid stuck in well, no free species visible | Protein/nucleic acid ratio is too high | Reduce the concentration of protein or increase the concentration of unlabeled nonspecific competitor |
Protein is aggregated | Change binding conditions to improve protein solubility. Possible modifications: add solutes that stabilize folded (compact) forms of proteins (e.g., glycerol); keep protein stocks and binding reactions at ice temperature; avoid freeze–thaw cycles with protein stocks; include non-ionic detergents in protein storage buffer and/or binding buffer | |
Free nucleic acid and complexes are too large for gel system | Try lower percentage polyacrylamide or reduce the acrylamide/bisacrylamide ratio. Test agarose gel as alternative to polyacrylamid |