Re: RNA: Possible Building Blocks For Nanomachines.

From: Phillip Thorne (thorne_at_underbase.org)
Date: 09/07/04 

Date: 7 Sep 2004 03:22:14 GMT

On 13 Aug 2004, Kadamose <Kada@myway.com> wrote:
>http://www.sciencedaily.com/releases/2004/08/040812052109.htm

(Phil reads the article.)

>What's truly interesting about the article is that they address the
>'weakness' of RNA - which is that it tends to degrade biologically
>over time. They claim that they are working on ways to make the RNA
>more resistant to degradation - the main question is,
>[how to do so,] the technical aspects behind it.

Well, RNA is a biopolymer, and has the same vulnerabilities as protein
chains: heat will cause its 3D structure to unravel; appropriate
enzymes will chop it apart (at the phosphate-ribose backbone).
High-temperature proteins are stabilized by cysteine disulfide
bridges, but AFAIK, RNA has only hydrogen bonding to produce secondary
(helices, sheets), tertiary and quaternary (multi-chain) structures.

Question not addressed by the release: in what chemical context is Guo
trying to stabilize the RNA, and for how long? On a gold substrate,
in vitro (test-tube), in vivo (a cell)? For minutes, days or months?

On occasion, researchers have created DNA with exotic bases -- ones
other than A, T, G and C. In DNA, these exhibit either two or three
hydrogen bonds. Perhaps exotic bases could have four? Or maybe
they're just designing the strands to have a greater number of
cross-links.

(IIRC, the amount of heat needed to split a double-stranded DNA
molecule is a good measure of its length, assuming an average of 2.5
H-bonds per base-pair.)

That's parallel to exotic amino acids in protein engineering, but
DNA/RNA is a lot easier to synthesize without enzymes. (I think. I
know that building entirely new tRNAs and transferases to handle
exotic amino acids within a bacterium was a big challenge, but is
there a "mechanical" way to synthesize large proteins? Continued
interest in recombinant engineering for pharmaceuticals, include
"pharm" animals for proteins too large for bacteria to produce,
implies not.)

Peixuan Guo works at the Birck Nanotechnology Center at Purdue
University. Cripes, that's an ugly URL:

http://discoverypark.e-enterprise.purdue.edu/wps/portal/.cmd/cs/.ce/155/.s/4271/_s.155/4271

Well, supposedly he does -- the Birck site's Staff Search doesn't list
him, and I can't guess which of the 17 research groups he's a member
of.

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