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Agarose gel electroforesis buffer

Paul N Hengen pnh at ncifcrf.gov
Wed Nov 8 15:03:01 EST 1995

Yap Yun Kiam wrote:

: We have been using Tris-Acetate-EDTA (TAE) buffer for 
: occured in which our 1kb DNA marker bands either appeared as smear ( as 
: if degraded) or there are a lot of stray bands. First, we check the 1kb 
: marker and found that it is okay (let another lab try it). We tried to 
: trace out the culprit, and finally we change all the TAE buffer (TAE is 
: prepared in 10x stock and diluted before used). we suspect something went 
: wrong with the buffer but we can't tell what went wrong. Recently, this 
: problem re-occured, the 10x TAE buffer is not a newly prepared one, half 
: of it has been used without any problem. We thought that it could be the 
: deionize water that is used to dilute the 10xTAE, so we change all the 
: deionize water in the lab and collect some fresh one (from the same 
: deionize machine) but the problem still persist.
: Can someone suggest what the culprit is? How it can be solved?

Does the buffer glow blue under UV? If so, read this article for the
answer, then make up a fresh batch of concentrated buffer in a clean
bottle and test it again. You probably have a microorganism growing
in your 10x buffer.

author = "P. N. Hengen",
title = "Methods and reagents - Glowing blue gels and nuked nucleases",
journal = "Trends in Biochemical Sciences", 
volume = "19", 
number = "12", 
pages = "556-557", 
month = "dec", 
year = "1994"}

* Paul N. Hengen, Ph.D.                           /--------------------------/*
* National Cancer Institute                       |Internet: pnh at ncifcrf.gov |*
* Laboratory of Mathematical Biology              |   Phone: (301) 846-5581  |*
* Frederick Cancer Research and Development Center|     FAX: (301) 846-5598  |*
* Frederick, Maryland 21702-1201 USA              /--------------------------/*
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