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

[Stephen Montgomery-Smith <EMAIL:PROTECTED>]

Jonathan King wrote:
> 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. :-)

Of course computer magazines are no different ("15 ways to avoid getting 
your computer hacked").

> This DNA is then what you use (after a bit more processing I'll skip)
> on the microarray AKA gene chip AKA DNA chip.

So I've read a bit more of the Watson book, so I can take a bit more 
detail.  Do you make the DNA into a single strand?  Is the DNA still one 
long piece, or has it been chopped into small pieces?

>  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.

I'm trying to get an idea of what kind of statistical problems you might 
run into.  About how many pieces of DNA stick to one piece of probe? 
And are long pieces of similar probes next to each other, or are the 
adjacent probe pieces all totally different?  How many base pairs long 
is the typical probe, and how specific is it in how well it attaches to 
a piece of DNA (i.e. will it stick to a piece of DNA that gets 19 base 
pairs out of 20 correct)?

> 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.


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