April 11, 2006
PHOTOS BY AARON HANDELSMAN/Daily
Rackham student Mark Ditzler working at a microscope in
Chemistry Prof. Nils Walter's laboratory
Scientists are using
the new frontiers of
By A. J. Hogg
Daily Science Writer
Imagine grabbing a strand of
protein with tweezers made from a
beam of light and extracting it from
the surface of a cell the same way
you would pull a loose thread from
a sweater. That's just one technique
used by University researchers to
learn about the structure and func-
tion of proteins in single-molecule
Chemistry Prof. Nils Walter is
attempting to set up a center at the
University to encourage this kind of
single-molecule research. His goal is
to bring people who have experience
in using single-molecule technology
together with people whose research
would benefit from that technology.
They include researchers from engi-
neering, the sciences and the medi-
No other university has a single-
molecule center with this kind of
range under one roof. Walter said
that the University is good at fos-
tering collaboration, but the cen-
ter would stimulate further joint
research. In order to drum up inter-
est, he is organizing a Single Mol-
ecule Symposium, to be held at the
Alumni Center May 18 to 20.
Walter's research focuses on ribo-
nucleic acid, or RNA, which regu-
lates the proteins made in a cell.
Scientists have a good understand-
ing of how DNA makes RNA, which
in turn makes a protein, but by look-
ing at individual RNA molecules, it
turns out RNA itself can be biologi-
Walter uses nanotechnology in
order to study RNA in his research.
Looking at a single molecule
To watch what a.single RNA mol-
ecule does, Walter uses single-mol-
ecule fluorescence spectroscopy.
He attaches two fluorophores, or
organic dyes, to specific locations
on the molecule. When exposed to
one particular frequency of light,
fluorophores emit a different fre-
quency, making them detectable: In
Walter's research, he uses one fluo-
rophore that gives off green light and
a second that emits red light. When
the two fluorophores are far apart,
the green emits light more intensely,
but when they are close together, the
green dims as energy is transferred
from the green fluorophore to the
red one; and more red light is emit-
ted. By measuring the color of the
light coming from the molecule, he
determines how close the two parts
of the molecule are, which tells him
how the molecule is folding.
Proper folding is vital for pro-
teins to function. A wrong fold
changes the shape of the protein,
which can alter how it interacts with
other molecules. If the folding goes
wrong, the protein can stop work-
ing, or worse, act in harmful way.
Alzheimer's disease is caused by a
Scientists use fluorophores with
proteins as well as with RNA to
determine how protein folding
changes over time.
Many times, the protein is able
to fold from one configuration to
another, and may spend only a small
amount of time in a particular con-
"It can flip-flop," Walter said.
When looking at many molecules
at once, you can only see the average
configuration, but the advantage of
looking at individual molecules is
that you can see the unusual fold.
"One hundred times one thing
happens, once or twice another
thing happens," he explained. Wal-
ter said it is these rare occurrences
that scientists are just now learning
about through current research.
In addition to observing the pro-
tein, researchers can introduce muta-
tions and observe changes in the
folding properties of the protein.
Once researchers introduce a
known change in a protein, they can
observe the effects of a new "ver-
sion" of the protein.
Walter said the real question is,
"How likely is it for this particular ver-
sion to become biologically active?"
Another single-molecule research
technique is optical tweezers - a
way to manipulate individual mol-
ecules without touching them. By
focusing a laser onto a small, one-
micron diameter clear plastic sphere,
researchers can trap it within the
beam. If the sphere moves out of the
beam, the diffractive index - how
the beam bends as it passes through
the sphere -- changes and light,
behaving like a particle, moves the
sphere back into place.
"You get a recoil," Walter said.
By stringing a protein between
two spheres - one end trapped by a
laser in the optical tweezers, and the
other held still - you can measure
the required force to displace the
protein. Imagine a spring, with one
end bound to a wall and the other
held in a person's hand. If the spring
contracts, it pulls toward the wall,
and the person can feel the force
exerted by the spring.
Scientists can do this at the molecu-
lar level. For example, rather than a
spring, scientists can use a strand of
DNA. Because single-stranded DNA
is more folded and more coiled than
double-stranded, scientists can mea-
sure how fast an enzyme chews up one
strand of the double-stranded DNA.
This technique works with any
enzymes that can move on a given tar-
get that can be tethered on the spheres.
"Then you learn something about
the forces these enzymes can exert
on their substrates," Walter said.
Atomic force microscopy
A third way of looking at single
molecules is a technique called
atomic force microscopy. Using this
method, researchers set a cantilever
with a very fine point (similar to a
very small version of the needle on
a record turntable) to measure the
surface of a cluster of molecules.
The top of the cantilever is reflec-
tive. When a laser reflects off the
cantilever, a photodiode measures
how much and in which direction the
cantilever moves. The measurement
is accurate to one nanometer.
The cantilever moves over the sur-
face in meanders, scanning it to give
an image of the surface topography.
Individual molecules can also be
pulled from the surface with the
tip. Sometimes a molecule sticks to
the cantilever and gets pulled out of
the surface. By measuring the force
it takes to pull the molecule off,
researchers can learn about how the
molecule is folded or threaded in
'U' researcher studies
hormone's role in stomach
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' Gastrin, a hormone
found in the stomach,
may have dual purpose
By Brittany Davis and
Daily Staff Reporters
You've just finished dining at the
local burger joint, and you feel the
need to check into the Heartburn
Heartburn and acid reflux are
caused primarily by the overpro-
duction of gastrin, a hormone that
initiates stomach acid produc-
tion. Sometimes too much gastrin
is produced during the digestive
process, resulting in that familiar
But research conducted by Medical
School Prof. Juanita Merchant, indi-
cates that gastrin may also play a vital
role in the immune system.
Scientists are studying gastrin to
better understand how the gastric
system is regulated. In essence, the
same hormone that aids in digest-
ing those greasy fries you just
consumed for lunch may also be
protecting you from harmful bac-
The hormone gastrin appears to
be one of the initial respondents
in the innate immune system, the
body's first line of defense against
harmful bacteria. It tells the stom-
ach cells to start producing acid,
which, in addition to Gastrin's
digestive responsibilities, can also
destroy foreign microbes.
Some trickier bacteria, such as
Nelinhnmtr nlr bs aante
ra like these. Leading brands,
including Prilosec and Prevacid,
are available by prescription.
These drugs essentially stop the
production of stomach acid. Mer-
chant said the drugs effectively
relieve gastric conditions such as
heartburn or ulcers, but has some
concerns regarding their extend-
ed use. Long-term suppression
of acid production could weaken
the immune system response.
Many bacteria would have a better
chance of surviving in weakened
acidic conditions. Merchant sug-
gested that the best way to deter-
mine long-term effects is to "keep
an eye on pediatric patients."
Merchant used "knock-out"
mice in her study to test the effects
of suppressing gastrin production.
These mice, created by another
Medical School Prof. Linda Samu-
elson, were genetically engineered
so that they could not produce gas-
According to Samuelson, the use
of such mice is quite common.
"(The mice) have really given
us an insight into many fields of
mammalian biology," Samuelson
The University has a Transgenic
Animal Model Core that creates
genetically engineered mice for
researchers. Merchant's lab used
mice that were already being stud-
ied by Samuelson in her own lab.
Although scientists have yet
to see the long-term implica-
tions of stopping acid production
in humans, Merchant's research
revealed that the mice that had
be enenetic-allengneered not to
Fast facts about
During digestion, a
hormone called gastrin
initiates the production
of stomach acid.
Too much gastrin
can cause too much
stomach acid to be pro-
duced. This can cause
heartburn or acid reflux.
Gastrin could also be
responsible for defend-
ing against harmful
bacteria, by triggering
the production of stom-
ach acid that can break
down food and kill harm-
Helicobacter pylori is
a type of bacteria that
has adapted to survive
in highly acidic environ-
ments. If a person is
infected with this kind
of bacteria, it can cause
the body to increase its
acid production, in order
to eliminate the bacte-