E.coli genome on a chip?

David Alexander dalex at NEXUS.MICROIMM.MCGILL.CA
Fri Feb 13 09:28:38 EST 1998

Hi netters!

I recently attended a seminar which highlighted the potential
of using oligonucleotide microarrays (aka DNA chips)
for Southern and Northern style hybridization - and more!.
Apparently chips for some yeast and a couple of pathogenic
prokaryotes have been prepared (or are in preparation).
What I would like is a chip of the entire E.coli genome.
Apparently such a thing is possible.
It would involve affixing overlapping 500-mers
to a 100 x 100 microarray grid.

So, if you've pulled a promising clone from an E.coli library,
all you need to do is PCR out the insert, label it with
a fluorescent tag, and hybridize it to the chip. 
Identify the microarry co-ordinant(s) that it binds to 
et voila, you know the sequence of your insert.
Since these chips are apparently reusable, you can repeat the
process for each of your promising clones
(or do several clones at once if you label with
different fluorophores). It sounds as if it should be 
more efficient that having to sequence every single insert
the old way...
This can apparently be adapted for differential-display
type analysis too! Just label control cDNA with one fluorophore
and cDNA from cells exposed to your experimental conditions
with a second fluorophore. Hybridize to the chip and
look for co-ordinates that light up differently.

My lab doesn't have the technology to produce such a chip,
but if somebody out there has the know how.
I'd really like to get one!


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