From: keithl@klic.rain.com (Keith Lofstrom)
Newsgroups: sci.nanotech
Subject: photoribosome
Date: 2 Sep 92 20:52:02 GMT

I am of course posting this just before leaving on vacation, so mail replies
are encouraged.

My rudimentary understanding of ribosomes is that they are little beasties
that read RNAs at one end and write protein at the other.  Change the read
sequence, and you change the protein they write.   Rhodopsin is a molecule
that occurs in the rod cells of the eye, and generates the chemical signals
when exposed to light.  I believe it has a long carbon chain that acts as
an "antenna".


The following is wild speculation.  As near as I can tell, I haven't read it
anywhere, and may be completely bogus.  I am posting it, not for comparison
to revealed truth, but as a jump off point for further amplification or
speculation.


What if one bonded a relatively small molecule on the end of a rhodopsin, and
bolted the whole thing onto the read end of a ribosome?  The little molecule
has sites that resemble to a ribosome the different bases it sees when it reads
an RNA, with the sites arranged in a ring.   The little molecule also has some
sort of mechanism to start and stop the ribosome from travelling down it.  It
has two simple commands - rotate (select) to the next site, and activate
ribosome to read that site.  These commands are received optically.

The rhodopsin ( or rhodopsins ) with the sequence molecule is tuned to three
different colors of light, and colors of photons do the following:

red  blue   - allow ribosome to read the next base
green blue  - select the next base type
red green   - select next base, if not reset position (go to reset)
red  red    - do not change state
green green - do not change state
blue blue   - do not change state

The biotechnologist simply shines colored lights at this little ribosome,
allowing enough time to make sure the little fellow gets at least one
photon of the appropriate color to do something.  Many photons of the same
color have the same effect as one - since statistics are involved, the 
little machine can't be made to respond efficiently, but it can be made
to respond surely.

A typical sequence might be:

red green red green red green ... red green //  Move to reset position
green blue green blue green blue            //  Move to 3rd RNA base, skipping
					    //  the two between
red blue                                    //  allow ribosome to add to
                                            //  protein under construction

I can imagine that this setup could be used to put together proteins at very
high rates, limited only by the ability of the solution to dissipate heat from
all the wasted photons.  The pieces of the modified ribosome could be
laboriously put together with traditional wet chemistry and biological
techniques;  in most cases we are working with "found" materials.

This little beast could be optically programmed to build "second stage"
ribosomes - modified ribosomes with the functionality built in rather than
mixed together.  THOSE ribosomes could, in turn, be used to crank out 
assemblers.  This is all predicated on a lot of protein design computation
by macroscopic computers which we don't know how to do yet, of course.  In
a very hand-waving way, this could be a path to implementation - once we learn
what to implement.

Well folks?  Whaddaya think?

Keith
-- 
Keith Lofstrom         keithl@klic.rain.com       Voice (503)-520-1993
KLIC --- Keith Lofstrom Integrated Circuits --- "Your Ideas in Silicon"
Design Contracting in Bipolar and CMOS - Analog, Digital, and Power ICs