Re: [MLUG - DISCUSSION] these are the days of miracles and wonders: a radically new sequencing machine appears

[Jonathan King <EMAIL:PROTECTED>]

On 8/1/05, Stephen Montgomery-Smith <EMAIL:PROTECTED> wrote:
> Is this what they call "microarrays"?

No, but that's a logical guess. :-)
 
> I picked up a science magazine in Tucker Hall the other day.  On its
> cover was the lead in to one of its articles "4 ways to produce better
> microarrays" (just like "10 ways to get your man to love you more" that
> you find in grocery store check out line magazines).

Yeah, sad to say, biologists do fall for this kind of thing. :-)

What a microarray is a beautiful technique not to find out what the
genomic DNA sequence is, but how much of each gene is actually being
produced in some specific tissue type.  So, for example, tumors are
cells that have essentially gone crazy, and you might want to know
what genes are now being expressed in those cells compared to normal
cells.  The way you do this is you take the tissue sample, extract the
total *RNA* from it (since DNA is transcribed into RNA before being
translated), and then purify the true messenger RNA from that.  Then
you stir that up with some raw DNA bases, eye of newt, and reverse
transcriptase.  Reverse transcriptase is the enzyme that copies RNA
into DNA (no, this usually doesn't happen, but some viruses use
exactly this technique to sneak into your genome; HIV does this).

This DNA is then what you use (after a bit more processing I'll skip)
on the microarray AKA gene chip AKA DNA chip.  Basically, you take a
minute spot of this stuff and apply it to a specific tiny piece of the
chip that has been "printed" with a short stretch of DNA probe (a
complementary sequence) that some of your sample might stick to.  With
correct treatment and processing, you can then measure the amount of
sample that stuck to the probe, and compare it to what stuck to other
places on the chip that have different probes.

As you might now guess, you have cleverly chosen your probes to match
the unique parts of known or presumed mRNAs from different genes.  And
the probe dots are really, really small (essentially microscopic). 
This allows you to measure the *relative* expression pattern of
thousands of genes on one chip.  Needless to say, this is an
incredibly valuable thing to be able to do.  Unfortunately, it is a
very tricky technique, and there is a certain amount of "noise" in the
measurement system, and people are doing a lot of work on how to
improve the results you get.  (Hence the article Stephen saw on the
tabloid.)

Now, just to confuse matters one more time, you can actually use a DNA
chip to sequence some kinds of DNA some of the time.  In this
application, you start with the genomic DNA, dice it into a bunch of
little random pieces, and hybridize it to your chip, which might have
(say) every single possible probe that is 16 bp long.  IF your DNA
does not contain very highly repetitive stuff (e.g.,
cgcgcgcgcg....etc.), you can actually piece together uniquely the
sequences you "traped" on your chip inot a single unique sequence from
the overlaps.  In practice, this is not the way we usually do it,
although it might turn out to be a good method for certain
applications.

The real message is that molecular biology has really jumped on the
computers and sensors bandwagon, which promises advancements in our
capabilities that mirror the amazing advances we continue to see in
information processing technology.

jking

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