RNA marker doesn't show up on formaldehyde gel

Jun-Zhi Wei jwei at sfu.ca
Tue Mar 17 20:46:42 EST 1998

I got a problem on the formaldehyde RNA gel electrophoresis.
The RNA marker (from Novagene), which is visible on regular agarose gel,
doesn=D5t show up on my formaldehyde agarose gel and my RNA samples are
faint and a little blurred.  I am wondering if I did something wrong in
the denature agarose gel electrophoresis. =20

I did like this: Add 15.5 ul of sample buffer (2 ul 10x MOPs, 3.5 ul
formaldehyde and 10 ul formamide) to 2 ul of RNA sample (10 ug) or 2 ul o=
RNA marker. Heat them at 65 C for 15 min. Before loading, add 2.5 ul of
loading buffer with EB (47.5 ul 10x RNA loading buffer + 2.5 ul  10 mg/ml
EB). Run the gel (1x MOPS, 2.2 M formaldehyde) for 3 hours.  10x MOPs
includes 0.2 M MOPS, 0.05 M NaAc, and 0.01 EDTA.  Formamide and
formaldehyde are deionized and stored at -20C, and the pH is around 6.

Any advice and suggestion? Thanks in advance.


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