Foresight Update 8
page 4
A publication of the Foresight Institute
 Recent
Progress: Steps Toward Nanotechnology
by Russell Mills
New tools for observation
The past few years have brought important advances in our
ability to study the structure and dynamics of molecules--the
scanning tunneling microscope and its relatives, new kinds of
nuclear magnetic resonance analysis, and femtosecond-resolution
laser chemistry, to name three. More recently, the pace has
quickened: hardly a month now passes without some remarkable new
technique being reported. Let us look at a few of these.
J.M.R. Weaver and colleagues at IBM have developed a method that,
in effect, images materials at optical wavelengths but at 1
nanometer resolution. Impossible, you say? Not if you cast light
on the sample, and detect the light's effects on individual
molecules with a scanning tunneling microscope (STM). In
practice, the sample is illuminated with monochromatic light of a
desired wavelength; some of the light is absorbed by particular
atoms or groups of atoms, where it changes the shapes and
positions of the electron clouds surrounding them; these changes
are detected by the STM. The arrival of this technique is like
the arrival of a lamp in a darkened room where formerly objects
had to be studied by touch. Among its many potential applications
is the sequencing of DNA: a judicious choice of wavelength should
permit the different nucleotides to be distinguished by color.
[Nature 342:783-785,14Dec89]
Another new approach to subwavelength optical imaging is called
molecular exciton imaging (MEM). Developed by K. Lieberman at the
Hebrew University in Jerusalem and others, the technique makes
use of crystals that store light energy as excitons--bound pairs
of electrons and "holes." A crystal of anthracene is
grown in the tip of a micropipette less than 100 nanometers in
diameter. When illuminated from inside the pipette, the crystal
concentrates the light energy and then emits it from the tip of
the pipette as a very compact beam of photons. If a sample is
brought to within a few nanometers of the pipette tip, a photon
of suitable wavelength will be absorbed with almost 100%
probability--an increase of about 109 as compared with
ordinary light sources. When combined with high resolution
scanning, MEM may lead to optical microscopes capable of
resolving molecules. Furthermore, the technology promises to be
very inexpensive.
[Science 247:59-61,5Jan90]
A very different imaging technology has been developed by Z.
Vager at the Weizmann Institute of Science, and others. Called
"coulomb explosion imaging" (CEI), it has already
elucidated the structures of molecules resistant to other
analytical methods. The sample to be analyzed is accelerated to
about 2% of the speed of light and made to pass through a plastic
film 3 nanometers thick. The film strips all of the bonding
electrons from the molecule, leaving the individual atoms
positively charged. These atoms now repel each other as they
continue to travel toward a detector where their positions and
arrival times are recorded. Roughly speaking, the effect is to
magnify the configuration of the molecule at t0, the
moment of passage through the film. Working backward from the
recorded data, one can determine the precise arrangement of the
atoms in the molecule at t0; even the vibrational and
rotational displacements are accurately represented. Since the
sample consists of many molecules caught in different phases of
motion at t0, the recorded data contains not just the
geometry of one particular molecule but a full representation of
the possible configurations for the molecular species being
studied.
[Science 244:426-431,28Apr89]
It remains to be seen whether CEI can be used to study the
structure of large molecules like enzymes, but even if it can't
it promises to revolutionize our understanding of smaller ones,
particularly molecular ions and molecules in excited states.
Who would have thought that detailed structural information could
be gleaned from the pieces that fly out of a surface after an ion
crashes into it? Nicholas Winograd of Penn State thought so, and
he was right. The technique is called "secondary ion mass
spectroscopy" (SIMS), and consists of directing a beam of
ions at the surface of interest, then measuring the angles and
energies of the particles that emerge. Although it is not
possible to use these measurements to compute backward to
determine the original state of the surface, one can compare the
measurements to the results calculated from various theoretical
models and then reject the models that give the wrong answers.
SIMS is expected to reveal details of chemical reactions taking
place on surfaces; catalysis is of particular interest.
[Science 246:995-997,24Nov89]
Just think of it: four new techniques... how might they affect
progress toward nanotechnology? The first--STM imaging of
photon-stimulated materials--should greatly simplify the task of
identifying molecules and parts of molecules. In combination with
MEM, it may become an efficient optical probe for doing
spectroscopic studies on local regions within molecules. Such a
probe might even enable researchers to make and break specific
bonds: STM information would be used to steer the MEM probe to
the desired target, where the probe would release one or more
photons having energies appropriate for controlling the desired
reaction.
CEI promises to bring rapid understanding of the structure and
dynamics of small molecules and molecular fragments--just the
sort of understanding that is needed if the design and
construction of nanomachines is to become more than a hit-or-miss
affair.
SIMS should help to elucidate the structure of surfaces,
making possible the rational design of moving parts for
nanomachinery.
Nanomachinery
Molecular motors and flagella are in the news again:
J. Howard at the Univ. of Calif. at San Francisco, and others,
have been studying the kinesin motor proteins that move
organelles along microtubules inside cells (see Update
No. 7, Progress). They are developing methods for measuring the
force exerted on a microtubule by a single kinesin motor, and the
amount by which the motor moves along a microtubule during each
stroke.
[Nature 342:154-158,9Nov89]
Bacteria swim by using rotary motors to turn helical filaments
extending from their surfaces. These filaments, called
"flagella," are composed of repeating subunits of the
protein "flagellin." A map of a flagellar filament has
now been made at 20 Å resolution by Keiichi Namba and others of
ERATO in Japan. Flagellin molecules, it appears, form a flagellum
by stacking in a helical pattern with approximately 11 subunits
per two turns of the helix. The center of the filament is a hole
60 Å in diameter--thought to be the channel through which
pre-folded flagellin molecules travel during flagellar assembly.
The researchers plan to investigate the mechanisms by which
bacterial flagella change shape in response to chemical and
physical changes such as pH, ionic strength, or the direction of
motor rotation.
[Nature 342:648-654,7Dec89]
What might we want to do with flagella? Use them to drill
holes? Let them pull loads along some microscopic byway? Attach
special molecules to their tips and use them as robot arms? Since
flagella have evolved as bacterial propellors, they will likely
not have all the right characteristics for doing any of these
things. But recent work with enzymes has shown that it can be
surprisingly easy to re-engineer existing proteins, radically
improving them for given tasks. Bacterial flagella have a lot to
offer as starting points for molecular engineering: they
self-assemble, they are equipped with motors, and their helical
parameters can be controlled by external stimuli.
Electronics
The road to nanometer-sized diodes appears to be open. At
IBM's T.J. Watson Research Center, In-Whan Lyo and colleagues
have demonstrated negative differential resistance (NDR) in sites
this small on treated silicon surfaces. NDR is the essential
property that allows fast switching in quantum-well devices and
Esaki diodes. The investigators used a scanning tunneling
microscope to create a tunneling current between the STM tip and
a silicon surface containing isolated boron atoms as defects. NDR
appeared when the tip was located over such defects.
[Science 245:1369-1371,22Sep89]
The (truly) new biology
One of the great themes of the 21st Century, in my opinion,
will be the generalizing of traditional biological motifs. We are
already seeing the early harbingers: artificial hearts, mice with
human immune systems, bacteria that can produce plastic, cotton
with bacterial genes for insect resistance. But in the
laboratory, more fundamental generalizations are already
underway. Let us look now at three exciting examples.
An enzyme is a molecule (or molecular complex) that accelerates a
chemical reaction by binding the reactant(s) into positions and
circumstances that make the reaction more probable. Biological
enzymes are generally proteins, but nonprotein enzymes can (and
have) been made that are much smaller and simpler; until now
these have been designed for reactions involving only one
reactant. T. Ross Kelly and others at Boston College have now
constructed a rudimentary nonprotein enzyme that binds two
reactants, fosters the formation of an amide bond between them,
then releases the product back into solution. The binding is
accomplished by patterns of hydrogen bonds between groups on the
enzyme and matching groups on the intended substrate molecules.
Having established that the enzyme works, Kelly's group now
intends to alter the reaction rate by fiddling with the geometry
of the system and to design enzymes for other kinds of reactions.
[J. Am. Chem. Soc. 111(10):3744-3745,1989]
About 20 kinds of amino acids make up the vast array of
traditional proteins that play so many roles in the biological
world. Why only 20? Because every cell must either contain the
machinery for making each such amino acid or have a 100% reliable
source of it. So there is an advantage in keeping the number low,
even though a larger number might be much better from an
engineering point of view. Human technology, however, is under no
such constraints. Hence, we find that Christopher J. Noren and
his colleagues at the Univ. of Calif. at Berkeley have developed
a general method for getting bacteria to make proteins that
include nonstandard amino acids. Their strategy makes use of the
codon TAG--a triplet of DNA bases that normally stops protein
synthesis when encountered by a cell during the translation of
DNA, because it corresponds to no amino acid. Noren's group
prepared a special transfer-RNA molecule by attaching an amino
acid of their own choosing to a transfer-RNA bearing a
recognition site for the TAG codon. They also prepared a mutant
DNA gene for the protein they wanted to make by putting the codon
TAG at a place in the DNA corresponding to the place in the
protein chain where they wanted their special amino acid to be.
When this DNA was used as the program for protein synthesis, the
desired protein was produced.
[Science 244:182-188,14Apr89]
Nonstandard proteins should be of great use in studies of
protein structure and function. The method's principal limitation
stems from its dependence on traditionally unused codons--since
there are only three of these, and one is needed as a stop
signal, only two novel amino acid type can be used in a given
protein.
The traditional "genetic alphabet" of DNA has only 4
"letters"--A, T, C, and G--representing the four
nucleotides from which DNA molecules are composed. Joseph A.
Piccirilli and others at Zurich's Laboratory for Organic
Chemistry have now added at least two new letters: kappa and pi.
Starting with a larger collection of candidate base-pairs, the
researchers subjected each to tests of stability and
acceptability to DNA and RNA polymerases (the biological proteins
responsible for replication). Kappa and pi emerged as
winners--they pair with each other and not with A, T, C, or G;
and they are recognized and dealt with by DNA polymerases almost
as well as are A, T, C, and G.
[Nature 343:33-37,4Jan90]
A genetic code like Earth's leads to a Rube-Goldberg
biosphere--most of the active machinery (proteins) has to be
built from only a few types of components (amino acids). An amino
acid is specified by a triplet of letters taken from a 4-letter
alphabet; thus, Earth's genetic code is limited to specifying at
most 64 kinds of amino acids (actually 63, since one triplet is
needed as a stop signal). In practice, the need for redundancy
has reduced this number to 20.
|
| We would have at least 48 new amino
acids to work with in a given organism |
|
A 6-letter genetic code would increase the theoretical
number of amino acids to 216 (i.e., 63);
the useable number would be about 68 if present levels of
redundancy are retained. Assuming that the existing 4-letter code
is kept as a subset for "upward compatibility," we
would have at least 48 new amino acids to work with in each
organism.
Effective use of an extended genetic code requires the
development of a set of transfer-RNAs to specify the translation
of the new triplets, and a set of synthetases to load these
transfer-RNAs with the new amino acids. This is a major
undertaking and will not be accomplished overnight.
The most obvious application of an extended genetic code would
be to simplify existing proteins by replacing sections of their
protein chains by shorter chains containing nonstandard amino
acids. Similarly, one might improve the stability, specificity,
or activity of enzymes. Carrying this strategy a little further
might lead to endowing proteins with novel properties not
achievable with standard amino acids. Such improved proteins
would be developed as industrial catalysts, new materials,
research tools, and the like.
Another interesting application would be in ensuring the
safety of engineered, self-replicating organisms. An organism
that meets the following three criteria could not survive without
being fed by its employer: (1) some of the organism's essential
proteins require nonstandard amino acids; (2) the organism lacks
the apparatus needed to synthesize these amino acids; (3) these
amino acids are not found in the environment. See Engines
of Creation for discussion of an analogous concept for
nanoreplicators.
If an era of multiple, mutually incompatible genetic codes
lies ahead then there are profound philosophical and historical
implications to be discussed.... but not in this column.
Dr. Mills's background is in biophysics; he is currently a
businessman and a volunteer at the Foresight Institute.
Conference
Comments
The Foresight Institute has received many comments on the First Foresight
Conference on Nanotechnology. Herewith some excerpts:
John Chiplin of Biosym: "The Conference brought together a
fascinating collection of people. The presentations relevant to
the molecular CAD field actively represented the current
state-of-play and also the future challenges that lie ahead for
us--particularly in the protein/structure field. I look forward
to future meetings."
Michael Ward of Du Pont: "In addition to being the most well
organized meeting I have attended, I found it to be one of the
most stimulating as well."
Prof. Josef Michl of University of Texas at Austin, Dept. of
Chemistry: "It was marvelous to have an opportunity to meet
people in related fields and to listen to what they have to
say."
A sample of the comments from the conference evaluation forms:
Best aspect of the meeting: "Broad,
high-quality technical presentations, superb organization."
"The quality of the attendees." "Outstanding
speakers and coherence among subjects." "Broad range of
areas described by leaders in the field." "Cast of
stars--so many top people." "Interdisciplinary
contact." "Informal discussions."
"Heterogeneity of participants." "Open
discussion--informality." "Diversity."
"Breadth of coverage." "Good mix of
scientific/technical disciplines." "Caliber of speakers
and guests." "The speakers acknowledged the diversity
of backgrounds and started from basics." "Extensive
opportunities to interact informally." "Very thought
provoking" "Success in bringing together people of
different disciplines for serious discussion of
nanotechnology." "Clearly a meeting of quality people
who wouldn't otherwise meet each other easily." "Small
enough to mix and mingle." "Good overview. Emphasis of
interdisciplinary aspects." "Legitimized, for me, the
field of nanotechnology."
Worst aspect of the meeting: "Need better
meeting rooms." "Visibility of screen from side
seating." "Inadequate time for informal discussion
toward the end of the meeting." "Program too
long." "Too short!" "Expensive!" "I
ate too much. The food was too good."
From Foresight Update 8, originally
published 15 March 1990.
Foresight thanks Dave Kilbridge for converting Update 8 to
html for this web page.
|