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gel shifting assay

Zhixiang Chen zchen at UIDAHO.EDU
Wed Feb 28 13:18:03 EST 1996

I would appreciate receiving advice from anyone on runing gel retardation
assays.  For our purpose, we need to run protein/DNA shifting gels with a
relatively high resolution.  But we constantly obtain gels that have very
steep "V" shaped free DNA probe bands (i.e., high background of free DNA
probes on both edges of wells). The DNA probe we use is a 55 bp oligo and
we use nuclear extracts for binding assays.  We typically do biinding assay
at the room temperature and run the gel at 4C in 4% (20:1) polyacrylamide
gel using 0.5X TBE as runing buffer.  Any advice for helping us solve or
minimize our problem would be greatly appreciated.

Zhixiang Chen
Department of MMBB
University of Idaho

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