Bioinformatics, Vol 15, 687-703, Copyright © 1999 by Oxford University Press
MP Ponomarenko, JV Ponomarenko, AS Frolov, NL Podkolodny, LK Savinkova, NA Kolchanov and GC Overton
MOTIVATION: The commonly accepted statistical mechanical theory is now
multiply confirmed by using the weight matrix methods successfully
recognizing DNA sites binding regulatory proteins in prokaryotes.
Nevertheless, the recent evaluation of weight matrix methods application
for transcription factor binding site recognition in eukaryotes has
unexpectedly revealed that the matrix scores correlate better to each other
than to the activity of DNA sites interacting with proteins. This
observation points out that molecular mechanisms of DNA/protein recognition
are more complicated in eukaryotes than in prokaryotes. As the extra events
in eukaryotes, the following processes may be considered: (i) competition
between the proteins and nucleosome core particle for DNA sites binding
these proteins and (ii) interaction between two synergetic/antagonist
proteins recognizing a composed element compiled from two DNA sites binding
these proteins. That is why identification of the sequence-dependent DNA
features correlating with affinity magnitudes of DNA sites interacting with
a protein can pinpoint the molecular event limiting this protein/DNA
recognition machinery. RESULTS: An approach for predicting site activity
based on its primary nucleotide sequence has been developed. The approach
is realized in the computer system ACTIVITY, containing the databases on
site activity and on conformational and physicochemical DNA/RNA parameters.
By using the system ACTIVITY, an analysis of some sites was provided and
the methods for predicting site activity were constructed. The methods
developed are in good agreement with the experimental data. AVAILABILITY:
The database ACTIVITY is available at
http://wwwmgs.bionet.nsc.ru/systems/Activity/ and the mirror site,
http://www.cbil.upenn.edu/mgs/systems/acti vity/.
ARTICLES
Identification of sequence-dependent DNA features correlating to activity of DNA sites interacting with proteins
Laboratory of Theoretical Genetics, Institute of Cytology & Genetics, 10 Lavrentyev Avenue, Novosibirsk, 630090, Russia. pon@bionet.nsc.ru
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