Proposal: Light-dependent RNA polymerase
Bryan Bishop
Proposal: Light-dependent RNA polymerase
http://sphere.chronosempire.org.uk/~HEx/tmp/prop.pdf
Also, Tom extracts Sonic the Hedgehog music :3
http://sphere.chronosempire.org.uk/~HEx/sonic/
Marc Juul
> Here's another one from September 2011.
>
> Proposal: Light-dependent RNA polymerasehttp://sphere.chronosempire.org.uk/~HEx/tmp/prop.pdf
template to add repeats of six nucleotides to the 3' end of DNA. Not
template-independent, but the template is part of the enzyme complex.
--
Marc Juul
Cathal Garvey
up somewhere detailing research into this, where they messed around with
the templating region in telomerase template RNA to see how it worked.
Turns out that, once you account for secondary structures at the
boundary of the template (which define the "start" and "finish" of the
template region, in effect), everything else is exactly as you'd expect.
If the template can bind loose 3' DNA, the rest of the template is written.
Assuming there's no minimum length to the template, you could have a set
of telomerases with different minimal templates, maybe 3n long; 2n for
reading the prior two nucleotides, and 1n for templating the next
addition. For synthesis of DNA with this system, you'd therefore need
4^3 enzymes; 64.
Think we could work with a 64-ink printer? :)
--
www.indiebiotech.com
twitter.com/onetruecathal
joindiaspora.com/u/cathalgarvey
PGP Public Key: http://bit.ly/CathalGKey
Marc Juul
> Importantly, the template is hackable. I have a bunch of papers zipped
> up somewhere detailing research into this, where they messed around with
> the templating region in telomerase template RNA to see how it worked.
> Turns out that, once you account for secondary structures at the
> boundary of the template (which define the "start" and "finish" of the
> template region, in effect), everything else is exactly as you'd expect.
> If the template can bind loose 3' DNA, the rest of the template is written.
>
> Assuming there's no minimum length to the template, you could have a set
> of telomerases with different minimal templates, maybe 3n long; 2n for
> reading the prior two nucleotides, and 1n for templating the next
> addition. For synthesis of DNA with this system, you'd therefore need
> 4^3 enzymes; 64.
>
> Think we could work with a 64-ink printer? :)
Hehe. The binding may be too weak with so few nucleotides. One way to
fix that, at least to some degree, could be to use Locked Nucleic Acid
(unfortunately patented) instead of the normal RNA template.
--
Marc Juul
Bryan Bishop
> Importantly, the template is hackable. I have a bunch of papers zipped
> up somewhere detailing research into this, where they messed around with
> the templating region in telomerase template RNA to see how it worked.
Hey wait, that's not fair.. you gotta provide the actual zip, or a few
citations, or something.
Dan Bolser
> On Fri, Feb 24, 2012 at 6:39 PM, Cathal Garvey wrote:
>> Importantly, the template is hackable. I have a bunch of papers zipped
>> up somewhere detailing research into this, where they messed around with
>> the templating region in telomerase template RNA to see how it worked.
>
> Hey wait, that's not fair.. you gotta provide the actual zip, or a few
> citations, or something.
++ to that, sounds great!
Cathal Garvey
didn't have a chance to reliable SSH home!
Here's a bunch of papers I grabbed ages ago on Telomerase-hacking, which
I was researching for a far more ambitious (and for now entirely out of
reach) goal: In-vivo DNA synthesis.
Here's batch 1..
Cathal Garvey
Essentially, what the research boiled down to is some study into the
minimum template/recognition area, which was somewhat flawed for the
below reason, and loads of research into replacing the
template/recognition area.
It's all somewhat suffering from a lack of vision, because most of the
work was pure reverse genetics in the narrowest sense; someone might
edit the template to a different sort of template, or might create an
asymmetric template/recognition domain, just to prove that they have to
be symmetric.
Nobody seemed (when I first researched this) to have bothered with the
idea of targeted gene editing with modified telomerases, but their work
suggests that it's entirely possible, both in vitro and in vivo.
Your biggest problem in-vivo is that you're working with a loose 3' end
of DNA, which is rarely stable, certainly not stable for long enough to
edit with sequential gene activation/suppression, the cycles of which
can take hours.
In vitro, there's no such problem; you can afford to wait a while and
wash telomerase+NTP over your growing 3' end repeatedly. Your problem
becomes; what's the minimum recognition/template domain?
Sadly, that's not a question that even the paper dealing exclusively
with it answered adequately. They edited one end of the domain without
editing the other, which I feel is a little silly, especially because if
they cut out even one "G"-templating residue then the crucial
g-quadroplexes that make up telomeres may have suffered (I must check
again and see for sure). It may be an answer to "how short can
telomerase template be if you want functional telomeres", but it doesn't
answer "How low can the enzyme go?"
My gut instinct is "pretty damned low", because I don't think the RNA is
"taught" within the active site, and if it is there's research showing
that the "boundary" of the template/recognition domain is simply dsRNA;
you could extend the dsRNA flanks to account for reduced
template/recognition domain length.
Bonus: because you can use the same telomerase protein and only change
the telomerase RNAs between prototypes, your cost-per-prototype drops
dramatically after the first revision. Just have a plasmid encoding the
telomerase and a convenient cassette injection point for the RNA
template gene.
On 25/02/12 13:56, Dan Bolser wrote: