Palindromic & repeated DNA

metzler at mbcl.rutgers.edu metzler at mbcl.rutgers.edu
Tue Mar 31 17:52:22 EST 1992

I have a molecular biology problem that is not strictly an evolutionary problem,
but this seemed like the best group to post this to.
I have a piece of bacterial DNA about which I know only that many copies
of it exist on the bacterial chromosome, although I originally isolated this
DNA fragment from a plasmid. In the process of trying to determine if it
contained any sequences indicating that it might be a transposon or inser-
tion sequence, I used the GCG program "gap" to align the sequence to its 
reverse complement. I found a region of just over 300 base pairs which is
palindromic, with 40% identity. The palendrome is perfect, you can find an
axis of symmetry from which you can produce a mirror image for all of the
matched positions (which must be true in order for the thing to be a palindrome)
But as I said, the match is not even close to 100%.
I decided that this must be some kind of artifact, or else a coincidence - 
something that looks odd, but based on the laws of probability is not actually
that unusual. So for a comparison, I took what I know is a sequence which
codes for a gene (a malate dehydrogenase from maize), and I did the same thing
to it. I did this just to see whether something like this would happen by
chance on another piece of DNA. To my surprise I found a similar region of
about 100 base pairs, and this time the level of identity was 65%. I thought
perhaps this was some kind of transcriptional or translational control region,
but it turned out to be in the signal peptide of the protein!
I would appreciate suggestions as to whether this is artifactual, coincidental,
or maybe something someone else has seen before. Just to show you what I am
talking about (I find it hard to explain these things in words) here is a
sample of the sequence from maize - this is the core region, with the axis
of symmetry between the unmatched AG & GC in the upper line:
||  |||||| |  ||    ||  | ||||||  ||
Thanks in advance for any suggestions or comments that you might have.
Mary Metzler
Mary C. Metzler				|Bionet: Metzler at Biovax.Rutgers.edu
Department of Plant Pathology		|Bitnet: Metzler at BioVax
Cook College, Rutgers University
New Brunswick, NJ 08901

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