Number 633, April 16, 2003
by Phillip F. Schewe, Ben Stein, and James Riordon
The First Single-Molecule, Single-Base-Resolution
DNA Sequencing
The first single-molecule, single-base-resolution DNA sequencing has
been carried out by a Caltech group. In this new approach, the bases
forming the backbone of the typical DNA molecule are viewed one by one
in the act of replicating. To be more exact, a DNA polymerase molecule,
acting as a genetic xerox machine, copies a single strand of DNA by
adding complementary base units to it; the "fuel" for this
process, the base molecules being added, were fluorescently labeled
beforehand (by attaching site-specific, light-producing fluorophore
molecules), so the DNA sequence could be observed by microscope observations
(schematic setup figure).
Sequencing single-molecule DNA strands is intrinsically difficult because
of the high linear data storage density: the bases are only about 3.4
angstroms apart along the DNA helix. Past efforts to sequence bases
through their fluorescence have been complicated by background noise,
a problem avoided by the Caltech scientists through careful use of two
laser pulses, one for producing pinpoint fluorescence and another for
nulling or "bleaching" the fluorescence in order to prepare
for the next base identification.
Stephen Quake and his colleagues
can currently identify no more than about 6 bases in a row, so this
research is still at the proof-of-principle stage. However, within about
two years or so, Quake believes, his process should be a factor of ten
faster than standard gel-electrophoresis techniques used to sequence
DNA molecules on a wholesale level, and several orders of magnitude
cheaper. (Braslavsky
et al., Proc. Natl. Acad. Sci., 1 April 2003.)
Charge Symmetry Breaking
Charge symmetry breaking has been observed in two experiments reported
at the recent American Physical Society meeting in Philadelphia. In
the 1930s, physicist Werner Heisenberg proposed that the neutron and
proton are simply slightly different manifestations of the same particle,
called the "nucleon." Modern nuclear physics endorses this
view: plenty of nuclear reactions proceed exactly the same way if a
proton takes the place of a neutron, or vice versa. However, this close
similarity breaks down in some cases, leading to a situation known as
"charge symmetry breaking" (CSB). In separate experiments
at the Indiana University Cyclotron Facility (IUCF) and the TRIUMF cyclotron
in Canada, researchers have made groundbreaking new measurements of
CSB (which, incidentally, is a nuclear-physics phenomenon completely
different from charge [C] conjugation in particle physics). Such CSB
measurements can provide deep insights into why nature gave the neutron
and proton slightly different masses. At an even more fundamental level,
the CSB measurements can potentially yield more precise values of the
mass difference between the up and down quarks that make up protons
and neutrons. Nuclear theorists are busily analyzing these new experimental
results to put tighter constraints on the up-down mass difference.
At the APS meeting, Ed
Stephenson of Indiana University announced the first unambiguous
identification of a rare process: the fusion of two nuclei of heavy
hydrogen to form a nucleus of helium and an uncharged pion, one of the
subatomic particles responsible for the strong force that binds nuclei
together. This process would not exist at all were it not that nature
allowed a small violation of charge symmetry. Over a two-month period,
researchers observed this rare reaction several dozen times, giving
physicists enough data to test theories of charge-symmetry breaking.
Representing a collaboration at TRIUMF, Allena
Opper of Ohio University discussed the detection of CSB in another
nuclear reaction: the fusion of a proton and neutron, which produces
a charged pion as one of its products. Viewed from a perspective or
("reference frame") at which the proton and neutron meet at the center,
the reaction, repeated man times, produces a small excess of pions (0.17%)
in a preferred direction. Such an asymmetry is a hallmark of CSB. Taken
together, these new CSB results promise a wealth of information on such
things as the slightly different electromagnetic fields inside each
nucleon. As it turns out, such fields may contribute to the proton-neutron
mass difference, as they carry energy which convert into a small amount
of mass.
Tunable Photonic Crystals
Photonic crystals affect the flow of photons in much the same way
that electronic devices affect the flow of electrons. Most photonic
crystals, however, have specific properties that cannot be varied once
the crystals are made. A few types of photonic crystals, such as fluid
suspensions of colloidal silica, can be modified on the fly, but the
time required to change configurations is inconveniently long. Researchers
at Brown University have now made photonic crystals that can be modified
in milliseconds. The tunable photonic crystals consist of a class of
materials known as holographic-polymer dispersed liquid crystals (H-PDLCs).
Complex structures are defined in the material by exposing it to an
interference pattern produced by a set of four laser beams. Liquid crystal
droplets form in regions where the laser light interferes coherently;
these droplets constitute a photonic crystal. An electric field applied
to the suspension of liquid crystals modifies the refraction index of
the droplets, which changes the spectrum of light that the photonic
crystals transmits. The new photonic crystals are easily constructed
on a wide range of scales, which allows them to affect a wide spectrum
of light, and can replicate sophisticated structures including diamond
lattices as well as anisotropic lattices that affect light differently
depending on the direction of propagation through the crystal. Potential
applications of the tunable photonic crystals include filters to selectively
block certain light frequencies. With further improvement, they may
also lead other optical devices such as to novel lasers and optical
waveguides. Jun Qi of Brown University
(401-863-3078) described the tunable photonic crystals in a paper he
presented recently at the Optical
Fiber and Communication Conference in Atlanta.