Number 627, March 7, 2003
by Phillip F. Schewe, Ben Stein, and James Riordon
Microfluidics
Microfluidics is a traffic control system for sampling, sorting,
and mixing mesocopic objects. The objects are often biological---cells,
proteins, chromosomes in a solvent---and the platform is often a lithographically
patterned chip on which fluids are urged through microchannels using volts,
heat, or even peristaltic pressure. Microfluidics was a large topic at
this week's March
Meeting of the American Physical Society (APS) in Austin, Texas. Here
are some highlights.
Carl Hansen (Caltech) described a device with the largest degree of
integration yet achieved: a chip with 1000 250-picoliter chambers with
attendant valves for controlling flow and mixing (see also Science,
18 October 2002). Another device in the Caltech lab of Stephen Quake
allows the careful metering of reagents in order to facilitate protein
crystallization under a variety of conditions (pH, viscosity, surface
tension, 48 different solvents, etc.) on a huge scale (144 parallel
reactions can take place) and with a minimum of means---only 10 nl of
precious protein samples are needed, 100 times less than with usual
methods (see also Proc. Natl. Acad. Sci.,
24 Dec 2002). In this way, many proteins have been turned into crystals,
often in the space of hours rather than days. Indeed some protein species
were crystallized for the first time. The crystals can then be bombarded
with x rays in order to determine molecular structure.
David Grier (Univ. Chicago) reported on a method called holographic
optical tweezers, in which a beam of laser light, sent into a hologram,
is divided into a myriad of sub-beams which can independently suspend
and manipulate numerous tiny objects for possible transportation, mixing,
or reacting. Grier showed movies of ensembles of micro-spheres moved
into patterns and even set to spinning by the holographically sculpted
light fields. Applied to fluid samples of biomolecules, the holographic
multiplexing produces what Grier calls "optical fractionation,"
an optical equivalent of gel electrophoresis, in which electric fields
are used differentially to drive and separate macromolecules. In the
flexible Chicago approach, there is no viscous gel, and a deft change
in the computer-generated hologram or the laser wavelength can quickly
bring about sorting of objects ranging from the 100-nm size (viruses)
up to the 100-micron size scale.
Meanwhile, Jochen Guck (Univ. Leipzig) subjects fluid-borne cells to
a pair of laser beams which stretch the cells and probe their elasticity.
In general sick cells are softer (by a factor of 2 to 10) than healthy
cells. In this way, Guck's "optical stretcher" can "feel"
the difference between normal and abnormal at a rate of hundreds of
cells per hour, compared to typical rates of 10 cells per day using
other elasticity-measuring methods, thus reducing the need for biopsies
requiring larger tissue samples. The Leipzig device might even be able
to tell the difference between ordinary cancerous cells from the even
softer metastasizing-capable cells.
The Search for an RNA "Eve"
The Search for an RNA "Eve," a hypothetical ancestor of some
or all of the types of RNA now known, might be possible using a technique
pioneered by scientists at MIT's Whitehead Institute. Just as DNA samples
are used by paleo-anthropologists to study the spread of humans to different
part of the world, and by evolutionary biologists to study connections
among various lineages on the tree of living organisms, so too there
might be ways of studying the origins of RNA, or at least the relation
between RNA foldedness and biochemical function. Unlike DNA, its double-stranded
cousin, RNA starts out single-stranded, but can at many places along
its length double over on itself to arrive at complicated, twisted shapes.
Speaking at the APS March Meeting, Erik
Schultes (MIT-Whitehead) reported on an experiment in which a particular
sequence of RNA bases could, by altering one base at a time, take on
rather quickly the identity of either of two very different ribozymes
(RNA molecules that can catalyze reactions) with two very different
functions, one for cleavage and one for ligation. Continuing to substitute
different bases in a clever way, the researchers noticed that they could
retain the functionality of the two RNA species (that is, the ribozymes
went on performing their cleavage or ligation jobs) even though the
two were getting progressively further apart in "sequence space."
At the end one could look at the two contrasting ribozymes, with different
function and very different sequences, and hardly suspect that they
had a common origin. Schultes compared this to transforming the word
cat into the word dog through a sequence of single-letter "mutations,"
each one of which resulted in a legitimate word: cat-cot-cog-dog (for
background see Science, 21
July 2000).
At the same RNA session Ranjan
Mukhopadhyay reported that he and his colleagues at NEC Laboratories
in New Jersey have found that a typical RNA sequence with its 4-base
chemical code folds more predictably and stably than would hypothetical
RNA sequences based on a two-base or six-base "alphabet. Both 4-base
and 6-base RNA proved to be more stable than 2-base RNA. Furthermore,
4-base RNA possessed more stable, foldable structures than 6-base RNA
(just as it is easier to form 4-letter Scrabble words than it is to
form 6-letter words).
In other theoretical work, Ralf
Bundschuh of Ohio State and Terence Hwa of UC-San Diego have showed
that RNA could exhibit several different "phases," just as
water can exist on a pressure-versus-temperature phase diagram in the
solid, gaseous, or liquid forms. In the case of RNA, Bundschuh showed
mathematically, RNA could exist in a normal, glassy, molten, or denatured
phase. At low temperatures, for instance, in the "glassy"
phase, a given RNA sequence can get stuck in a random structure. At
higher temperatures, RNA can assume a more flexible molten state, in
which it is free to fold into a variety of different shapes.