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A publication of the Foresight Institute
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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
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.
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.