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loading RNA samples on denat. PAGE

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Old 01-21-2008, 10:55 AM
Simone Marker
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Default loading RNA samples on denat. PAGE


I have problems to get uniform bands when I load RNA samples on a denaturing
polyacryle amide gel:

My RNA samples are dissolved in formamide and my loading buffer is a
standard buffer with formamide, EDTA and bromphenole blue. Running buffer is
0,5x TBE.
I want to analyse samll RNA (23nt), so I have a 0,4mm thick 15% gel (like
sequencing gels, denaturing agent is 7 M urea). I load 10 microlitres on the
slots (its no problem to get uniform slots with adequate size).
The problem is, that the samples (at least the bromphenole blue) diffuse
into the gel bars between the slots immediatly after loading. Besides, when
I start the run the single samples enter the gel in different ways,
resulting in lanes of different width. After staining the gel I can still
see different width of the lanes and bands, although the slots were uniform.
Furthermore, the bands are not sharp enough.
I run the gel at ca 1800-2000V (ca 50-60W) and 50C.

Does anyone have an idea how to improve the running quality?

Thank you very much in advance,

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