NIH Nanomedicine Center Draws On NYU School Of Medicine Expertise

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NIH Nanomedicine Center Draws On NYU School Of Medicine Expertise

http://www.medicalnewstoday.com/medicalnews.php?newsid=58421

As biomedical science progresses, physicians apply increasingly

refined tools to treat disease. Researchers hope it will eventually

be possible to use tools based on the emerging field of

nanomedicine. The idea is to repair the body on the tiny scale of

molecules-at the nano-scale or roughly one millionth the size of an

ant-to reach inside cells and fix what may be broken.

As part of a new National Institutes of Health (NIH) nanomedicine

grant, Roth, M.D., Ph.D., Chairman of the Department of

Pathology and the Irene Diamond Professor of Immunology, is

collaborating with colleagues at academic research institutions

around the country to set up a Nanomedicine Center for Nucleoprotein

Machines. The center will be headquartered at the Georgia Institute

of Technology, where it will be directed by Georgia Tech biomedical

engineer Gang Bao, Ph.D. and molecular biologist Dynan,

Ph.D. of the Medical College of Georgia.

The center's scientists will focus on the repair of damaged DNA, an

essential process that cells perform to preserve the integrity of

their genetic material. The first step in the research project is to

build tools and do experiments to observe, characterize, and track

various stages and types of DNA repair processes.

Just as athletes rely on key muscle groups to power their

performance, cells need their protein machines. " Lots of important

bodily processes are performed by protein machines that typically

contain a number of individual proteins assembled together much like

a sophisticated car engine, " explains Dr. Roth. " The machine we

elected to study in this project is the DNA repair machine, " he

says. " It contains many components and assembles dynamically: its

composition also changes with time as different stages of the repair

process are completed. "

The team has developed a customized instrument to study a special

kind of DNA break.

The nano-tool

The miniscule scale at which experiments must be performed is a

major challenge. After all, the cell's nucleoprotein machines-

composed of complexes of proteins and nucleic acids-are roughly 100

times smaller than the diameter of a human red blood cell.

To operate at this level, the team will be using a special tool that

Bernhard Schnurr, Ph.D. has built. Dr. Schnurr is a post-doctoral

fellow in Dr. Roth's lab, a physicist by training who says he

is " amazed by biological systems. " The instrument is a microscope

that lets scientists hold and handle a snippet of DNA. Like a yo-yo

in water, the DNA segment is suspended in a tiny vial of liquid. The

top end is attached to a glass slide and a tiny magnetic bead is

affixed to the bottom end.

In this setup, moving a magnet changes the force pulling on the

bead, which in turn tugs at the DNA strand. " You change the force by

moving the magnet up and down, " says Dr. Schnurr. " If you move the

magnet closer to the bead, you pull on it harder and if you rotate

the magnets the bead rotates too, much like a compass needle. " The

scientists can essentially grip the DNA with magnetic tweezers.

The repair machine

Using these tweezers, the researchers can set up their experiments

to observe a special kind of DNA break. Dr. Roth has long been

intrigued by a process during which certain cells-precursors to

immune cells called lymphocytes-purposefully break their own

chromosomal DNA and then repair the breaks. This purposeful break is

risky business for the cell. It has even been called " an accident

waiting to happen, " says Dr. Roth, since some lymphomas and

leukemias may arise when this process is faulty.

At the same time, this process is essential for lymphocyte

development, explains Dr. Roth. It helps these cells become a

population of superheroes, their bodies studded with special

equipment, namely receptor molecules able to recognize and attack

millions of invading pathogens.

The cells acquire these qualities in the course of their development

in the bone marrow and thymus gland. Not every cell makes it through

what appears to be a grueling and selective quality control

process. " The thymus and bone marrow are tough schools with a 97 -

99 percent failure rate, " says Dr. Roth. " The mature immune cells

that do emerge are stunningly diverse. "

The immune cells owe their diversity to the special way they are

made from their genetic blueprint. Following an intentional and

specific DNA break, a process called V(D)J recombination occurs. The

acronym stands for the V (variable), D (diversity) and J (joining)

gene segments that get shuffled around and put together in a variety

of combinations. The process is akin to building an architecturally

diverse city by taking elements of a blueprint for a single house

and recombining them with slight variations. The DNA molecule forms

a loop, enzymes cut it at that looped spot, and then hold the loop

in place. The gene segments at that location are then combined in

many differing ways, explains Dr. Roth.

This recombining step is one of the key events the team wants to

study in detail. It relies on a DNA repair pathway known as

nonhomologous DNA end-joining that is essential for the repair of

many kinds of chromosome breaks and about which little is known.

The proteins that orchestrate the DNA loop formation are

recombination-activating gene proteins called RAG1 and RAG2. In

their controlled experiment on DNA repair, the scientists plan to

watch these proteins, and the subsequent repair of the DNA breaks by

nonhomologous DNA end-joining, in action.

Tugging and watching

Using the instrument Dr. Schnurr built, the scientists can flow

proteins such as RAG1 and RAG2 into the vial containing the DNA. The

microscope is equipped with a camera to record what happens and

software that analyzes the observations. The bead and its motion are

all the microscope can actually record, explains Dr. Schnurr. The

DNA strand is not visible under the microscope. Movements of the DNA

strand are inferred from the bead's motion.

When a loop forms in the DNA, much like a loop in a string, the

strand of DNA shortens. Then, if the loop is pulled apart, the

strand is back to its original length. By recording how the strand's

length changes, scientists can watch stages of a cellular DNA repair

process. " Usually you don't know where chromosomes are going to

break, " says Dr. Roth. In this instance, though, the breaks are not

random. The researchers are using proteins with known

characteristics-they form loops in the DNA by grabbing it at

particular spots and cutting at precise locations. This background

knowledge gives the scientists an edge for their experiments. " Given

the V(D)J reaction you know exactly where the breaks are going to

happen and you can even control when they are going to happen, " says

Dr. Roth.

He and his team are looking forward to using this microscope as part

of the new nanomedicine venture. It will help them observe and

characterize the intricate steps of the DNA repair process as they

occur in real time.