Agarose for SSLPs

John M. McDowell johnmcd at vt.edu
Sun Feb 18 13:36:07 EST 2001


Hi Everyone,
A couple of weeks ago I posted a request for accounts of successes or
difficulties in scoring SSLP markers with various brands of agarose.  The
responses are posted below (7 total).  Metaphor and Nusieve from FMC were
the most popular brands.
Many thanks to all who responded, and good luck with your mapping!
-John McDowell

*****

We use 4% gels prepared with a high-resolution agarose blend (agarose
3:1) from Amresco (Solon, OH; www.amresco-inc.com; catalog# E776) and
1X TBE as running buffer (3 Vcm-1 for 3-5 hours). Also see
http://plantbiology.stanford.edu/methods/ppsuppl.html
Dr. Wolf Scheible

*****

We use Gibco BRL ultyre PURE Agarose (ref 15510-027) at 4% (w/v).
This is to identify differences in size bands superior to 15 bp
in the 80 - 300 bp range.
Yours,
Dr. Pierre BERTHOMIEU

*****

We use metaphor agarose from FMC. It is a good choice to
separate and distinguish bands with 4 bp differences and higher.
Ton Peeters

*****

I have used FMC Nusieve 3:1 (4-4.5% conc) to separate upto 4 bp difference
consistently. Also, the gel thickness matters a lot. Thinner the gel and
thinner the well , better the separation. I tried BRL, but didn't get a
good separation and hard to cast the gel.
Sendil K Devadas

*****

Hi I am using BMA metaphor agarose, cat # 50180. It works very well
at 2%, but pouring the gels is a project.
Naomi Ori

*****

I use 2% Agarose (Gibco BRL) + 2% NuSieve GTG (FMC) in 1XTAE.  I am happy
with the resolution in most cases. I think a 3bp difference for products
180-250bp is not detectable using agarose gel electrophoresis.
Scott E. Sattler

*****

Regaring your newsgroup query: We have used Metaphor agarose (FMC) for all
our SSLP and many CAPS markers. We usually use 4% gels.  Unfortunately,
Metaphor is very expensive.  We have tried cheaper alternatives (such as
AgarGel L/F from Continental Lab Products), but have not been satisfied
with the results.
Stephen Chisholm

*****

John M. McDowell
Assistant Professor
Dept. of Plant Pathology, Physiology, and Weed Science
Fralin Biotechnology Center (0346)
Virginia Tech
Blacksburg, VA 24061-0346

email johnmcd at vt.edu
phone 540-231-2388
fax 540-231-7126



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