----------
From: Graham Dellaire <dellaire at odyssee.net
To: genstruc at net.bio.net
Subject: RE:Can you Predict Mars/sars from Sequence...Article by T.
Boulikas
Date: Monday, January 20, 1997 9:36 AM
Hello Laurent,
Although I don't think there are any publicly available programs to
determine MARS/Sars Teni Boulikas in a 1993 article in JCB gives you a
handy list of characteristics to look for:
ex. AT rich, replication origins, homeodomain binding regions,bent
(curved) dna tracts etc.
see: "Nature of DNA Sequences at the Attatchment Regions of Genes to the
Nuclear Matrix", (1993) Teni Boulikas, J. of Cell. Biochem. 52:14-22
In addition I believe that Sandor Pangor at ICGEB in Trieste
(see:http://base.icgeb.trieste.it/) is working on a (or may have
completed) a DNA bend determination program. This program is going to
be available on line and will enable you to determine DNA bends for a
given sequence you have isolated. The bending rules were developed by
Sandor and Ivan Brukner who now works with me in Montreal (Ivan has a
page at: Http://www.medcor.mcgill.ca/EXPMED/ivan/ivan.html).
The fact that MARS/SARS often correlate with bent DNA may enable you to
screen any sequences you isolate for intrinsic shape before you have to
run any 2D gels. But remember bent DNA is only one of Teni's 13 rules
for potential MARS!
Most Mars to date have been isolated by empirical methods... basically
any DNA retained in the Matrix fraction of isolated nuclei after LIS
treatment etc. or by reconstitution of sheared DNA with isolated
matrix.
Good Luck and I hope this helps.
Graham Dellaire
