DNA purification from agarose gels

Paul N Hengen pnh at fcsparc6.ncifcrf.gov
Thu Jun 29 13:13:03 EST 1995

Eric Anderson (anderson at pharmdec.wustl.edu) writes:

: The easiest and cheapest method I think is "Gene Clean". You just need 6M
: NaI and glasmilk to get pure and good DNA for cloning experiments.

| my biggest complaint with the GeneClean protocol is it's inability to
| recover small fragments.  when we need to get fragments <400bp we go for
| either the QiaQuick or the Qiaex (Qiagen's answer to Glassmilk/Silica
| particles) which claims recovery of 50bp fragments and larger.
| ...there was an article in the June "Biotechniques" about getting better
| small fragment performance from silica particles by incubating the DNA
| and silica at elevated temperatures (protcol reccomends 4 degrees).


I've read the paper in BioTechniques, and it really makes no sense to me at
all. The original BIO101 Geneclean protocol clearly states that the binding
should be done at 45 to 55 C, yet the paper claims that the new kit
instructions say 4 C. Elution was always to be done at 45-55 C.  The paper
proves that binding at 55 C gave better recovery of a 200 bp fragment than
binding at 4 C. What's so astonishing? I think perhaps the new kit instructions
had a typo. That's all. What's all the fuss about recovery of small fragments
using GeneClean? I've cloned a 27 bp promoter using it! I just eluted it
at 60 C for 10 minutes.

author = "L. S. Smith
     and T. L. Lewis
     and S. M. Matsui",
title = "Increased yield of small {DNA}
fragments purified by silica binding",
journal = "BioTechniques",
volume = "18",
number = "6",
pages = "970-975",
month = "jun",    
comment = "heating to 55 C inproves DNA recovery",
year = "1995"}

* 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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