Synthesis of unnatural nucleic acids (like GNA)

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Bryan Bishop

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May 29, 2009, 12:00:01 PM5/29/09
to diy...@googlegroups.com, kan...@gmail.com
Re: Gene Hacker's genome printer and how outrageously expensive it is
to synthesize DNA if you're not the son of Merck or Sigma-Aldrich, or
something--

Why not just use simplified nucleic acids and simplified
artificial/unnatural nucleotides for incorporation into an artificial
strand encoding your sequence? Then, amplify it with DNA polymerase.
The trick is to pick "unnatural simplified nucleotides" that correctly
hybridize with the correct complementary regular nucleotide (cytosine,
adenine, guanine, thymine, etc.). That way, polymerase just picks out
the correct nucleotide and synthesizes a complementary strand in the
correct, more complicated version that biology likes to use. But the
synthesis of the oligonucleotide only has to be glycerol nucleic acid,
or something even more simple, rather than the complicated steps of
phosphoramidite synthesis. What do you think? This may or may not be
compatible with the photolabile oligonucleotide synthesis methods. As
you said- the chemicals cost a lot, so making up cheap little hacks
like this should prove useful.

Replacing nucleobases in DNA with designer molecules
http://heybryan.org/books/papers/Replacing%20nucleobases%20in%20DNA%20with%20designer%20molecules%20-%202002.pdf

Synthesis of novel phosphoramidite building blocks from pentaerythritol
http://heybryan.org/books/papers/Synthesis%20of%20novel%20phosphoramidite%20building%20blocks%20from%20pentaerythritol.pdf

Atom economical solution for a functional nucleic acid backbone
http://heybryan.org/books/papers/Synthesis%20of%20glycol%20nucleic%20acids%20-%20atom%20economical%20solution%20for%20a%20functional%20nucleic%20acid%20backbone%20-%202006.pdf

GNA & polymerase study
http://heybryan.org/books/papers/Glycerol%20nucleoside%20triphosphates%20-%20synthesis%20and%20polymerase%20substrate%20activities.pdf

- Bryan
http://heybryan.org/
1 512 203 0507

4phl...@gmail.com

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May 29, 2009, 12:30:52 PM5/29/09
to Diybio
Very interesting. Can you think of a way to diy this though? A sample project?
Sent via BlackBerry by AT&T

-----Original Message-----
From: Bryan Bishop <kan...@gmail.com>

Date: Fri, 29 May 2009 11:00:01
To: <diy...@googlegroups.com>; <kan...@gmail.com>
Subject: Synthesis of unnatural nucleic acids (like GNA)

Bryan Bishop

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Jun 4, 2009, 9:43:26 PM6/4/09
to diy...@googlegroups.com, kan...@gmail.com, papers
On Fri, May 29, 2009 at 11:30 AM, <4phl...@gmail.com> wrote:
> Very interesting. Can you think of a way to diy this though? A sample project?

I suppose there's this, which helps out quite a bit:

Enzymatic synthesis of DNA on glycerol nucleic acid templates without
stable duplex formation between product and template (Szostak)
http://sata.serveftp.org/~bryan/papers/Enzymatic%20synthesis%20of%20DNA%20on%20glycerol%20nucleic%20acid%20templates%20without%20stable%20duplex%20formation%20between%20product%20and%20template%20-%20Szostak.pdf

"Glycerol nucleic acid (GNA) is an interesting alternative
base-pairing system based on an acyclic, glycerol-phosphate backbone
repeat unit. The question of whether DNA polymerases can catalyze
efficient template-dependent synthesis using GNA as the template is of
particular interest because GNA is unable to form a stable duplex with
DNA. In the present study, we screened a variety of DNA polymerases
for GNA-dependent DNA synthesis. We find that Bst DNA polymerase can
catalyze full-length DNA synthesis on a dodecamer GNA template. The
efficiency of DNA synthesis is increased by replacing adenine with
diaminopurine in both the GNA template and the DNA monomers and by the
presence of manganese ions. We suggest that the BstDNA polymerase
maintains a short, transient region of base-pairing between the DNA
product strand and the GNA template, but that stable duplex formation
between product and template strands is not required for
template-dependent polymerization. "

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