controlling an enzyme, interfacing nano to macro/TTL, MEMS modules

[Nathan McCorkle]

controlling an enzyme,
i think terminal transferase and optogenetics are the best place to
start... engineer one of those opto-isomerization groups onto the
right place (we can find this by random trials) such that it kinks the
enzyme in the off state, and in the on state its unkinked to allow
addition of a nucleotide (which we had previously washed in)

interfacing nano to macro/TTL,
optics? DNA has some conductive properties

MEMS modules:
pumps and optical waveguides, as well as standard electrode traces for
capacitance and electro poration and phoresis.

[Marc Juul]

On Feb 20, 9:29 pm, Nathan McCorkle <nmz...@gmail.com> wrote:
> controlling an enzyme,
> i think terminal transferase and optogenetics are the best place to
> start... engineer one of those opto-isomerization groups onto the
> right place (we can find this by random trials) such that it kinks the
> enzyme in the off state, and in the on state its unkinked to allow
> addition of a nucleotide (which we had previously washed in)

What about attaching opto-isomerization groups to the nucleotides?
Attach a different group for each of the four nucleotides so each
responds to a different wavelength of light and see if we can make
them control whether the nucleotide is available to the DNA
polymerase. If that works, then no washing will be needed. We still
need to be able to "clock" the polymerase, as polymerase activity is
otherwise stochastic and we may end up adding an unknown number of the
currently available nucleotide, but if we can figure out how to
effectively tell the polymerase "attach exactly one nucleotide now"
then the required non-biological equipment would basically be some
diodes with a USB interface.

--
Marc Juul

[Cory Tobin]

> i think terminal transferase and optogenetics are the best place to
> start... engineer one of those opto-isomerization groups onto the
> right place (we can find this by random trials) such that it kinks the
> enzyme in the off state, and in the on state its unkinked to allow
> addition of a nucleotide (which we had previously washed in)

Getting the opto-isomerization domain into the right place shouldn't
be too difficult if we have a structure for the enzyme. You could
make a couple of good guesses and probably get a functioning light-
activated polymerase.

> interfacing nano to macro/TTL,
> optics? DNA has some conductive properties

Better than DNA, there's a number of different conducting polymers
( http://en.wikipedia.org/wiki/Conducting_polymer ). The ends of the
polymers can be functionalized so you might be able to covalently link
the enzyme to a solid substrate.


-cory