[Hplusroadmap] A partial STM DNA sequencer and the $0 genomics project

[Eugen Leitl]

On Sun, Feb 10, 2008 at 04:31:47PM -0600, Bryan Bishop wrote:
> 
> So, I took a look at DNA sequencing techniques, such as Sanger or the 

Ever thought about going into biosciences?

> Maxam protocol, and I looked at how long it takes to sequence a few 
> hundred thousand base pairs, and honestly I disliked what I saw. So I 
> came up with my own method of doing DNA sequencing via scanning 

Speculations on direct reading techniques are not new. Actual
results are rare thought, and you might like 
http://www.sciencedaily.com/releases/2008/01/080128113219.htm

> tunneling microscopes to measure the voltage difference between the 
> probe tip (tungsten), the nucleotide, and some charged background 
> surface. Now, typically STM machines are in UHVs (ultra-high vacuums), 
> and if they aren't, then there accumulates this layer of water, dust 
> and muck in general and it becomes unclean, which interferes if you 
> want to look for a smooth surface. This means noise in the viewport, 
> but if you're able to identify where your DNA is, then you're basically 
> okay as long as you can continue to follow it -- maybe by assuming the 
> molecule is completely straight (see molecular combing techniques).*
> 
> Notes are on the wiki at:
> http://biohack.sourceforge.net/wiki/index.php/DNA_sequencer#Scanning_Tunneling_Microscopy_.28STM.29_DNA_sequencing
> 
> Other individuals have been able to construct STM machines for under 
> $100, there's even a high schooler out there that was able to do 10 nm 

The scanning microscope alone gives you jack.

> resolution (on a bumpy surface due to lack of vacuum, no less). So the 
> technology is definitely doable and proven, and on the wiki I include a 
> link to a ppt presentation from a group that was figuring out whether 
> or not DNA sequencing is possible with STM, and their results say yes, 
> but they didn't bother to try decoding a few bp -- this is peculiar. 
> The work remaining for this DNA sequencer is basically assembling all 
> of the resources on making an STM and repeating the results of the 
> Washington group and beginning to write the software to use the piezo 
> electric tip to follow the DNA molecule, plus the software to assemble 
> the nucleotide information, and hey, maybe we can submit the 
> first 'open source' sequence of data to GenBank or the other genome 
> projects just for the hell of it.

-- 
Eugen* Leitl <a href="http://leitl.org">leitl</a> http://leitl.org
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