The Biodesign Institute’s Marcia Levitus has been named the recipient of a $568,000 National Science Foundation CAREER award, given to a very select group of young scientists deemed to be leaders in their respective fields. With the prestigious award, Levitus will develop a finely detailed picture of how genes are controlled.
“Our current understanding of how genes are turned on and off is very hazy,” said Levitus. “I believe that medicine will not be able to provide answers to how cellular processes lead to disease until we understand the most fundamental questions regarding how DNA is packed in our cells at the molecular level. But to get there, we still need to resolve many open puzzles regarding how DNA bends and wraps around proteins. We are reaching an exciting quantitative era in biology where it is possible to address these questions with tools traditionally used in the physical sciences.”
A nucleosome is the fundamental unit of DNA packaging. In a single nucleosome, 147 letters of the DNA code (red) wrap once around a core octet of proteins, called histones.
Typically, an organism’s complete genetic information, or genome, contains anywhere from 10 million to 100 billion DNA letters spaced out along chromosomes. If all of the DNA were stretched out from end to end, it would be up to 6 feet long. Somehow, the threads of DNA must be finely spooled and stuffed into the cell’s nucleus, a space about 10 times smaller than the width of a human hair.
“Understanding how DNA is packed inside the nucleus of the cell is necessary to decipher fundamental processes in cell physiology,” said Levitus. “This knowledge will improve our very limited understanding of how genes work, which will aid the understanding of biological processes including aging and cancer.”
The core DNA packaging unit is called a nucleosome, which acts like a protective armor for the DNA code. It can only take a single nick, misplaced or lost letter in the DNA code to cause the development of diseases such as cancer. But nucleosomes also must fill the role of a genetic conductor, helping to orchestrate all of the DNA information in a cell to be copied, read and turned on and off at precisely the right tempo.
Levitus, a researcher in the institute’s Center for Single Molecule Biophysics and assistant professor of chemistry and biochemistry and physics, is attempting to create a quantitative model of the first triggering events in this cascade. Her research focuses on the smallest unit of DNA packaging –a single nucleosome–where 147 letters of the DNA code are wrapped twice around a core octet of proteins.
The energetics of this process requires a cellular feat of strength. Levitus explains that DNA is a very stiff material, with a physical strength similar to a thin cylinder made of plexiglass. “The physics of DNA bending around the nucleosome is not that well understood, but I am trying to understand the physics of how the DNA sequence influences the ability of DNA to bend around the nucleosome.”
To help reach her research milestones, Levitus is collaborating with Northwestern University researcher Jonathan Widom, whose recent groundbreaking work has shown that nucleosomes seem to prefer to assemble at preferred positions within the DNA sequence, the first important steps to uncovering a nucleosome positioning code that may be hidden within every genome.
In FRET analysis, Biodesign Institute researcher Marcia Levitus measures the difference between two different color emitting compounds (red and green stars) to understanding the dynamics of DNA bending (black) around the nucleosome proteins.
Levitus’ research grant is also important for its social commitment. A native of Buenos Aires, Argentina, she is particularly interested in increasing participation of women and Hispanic students into the sciences.
“There are not too many women in the physical sciences, and as the scientific field becomes more quantitative, the number of women goes down,” said Levitus. “It’s a very sad fact and I think it’s terrible that more women don’t go into this field. I also realize from talking with Hispanic undergraduates that they often feel like they don’t belong in science.” To overcome these barriers, Levitus works one on one in the classroom as both a role model and mentor to encourage more minority women participation in the physical sciences.
In addition, many students with interests in biochemistry and the life sciences can struggle with the math and basic numerical skills that have become increasingly indispensable for today’s interdisciplinary and large team approach to solving science problems.
“My research exemplifies the increasing demand for quantitative reasoning in today’s biochemical and biological research, and shows the importance of applying concepts from the physical sciences to address basic questions involving biological systems,” said Levitus. “My background allows me to teach biochemistry students to think in quantitative terms and make them appreciate the importance of learning math and physics. I want them to realize that otherwise they will not be able to face the challenges found in some of the most exciting problems of today’s biochemical research.”
Levitus will focus on new delivery methods including visual demos, podcasts and lesson plans to help improve students’ math skills in the life sciences.
A spotlight on DNA
Levitus’ experimental data must allow her research team to develop a comprehensive understanding of what is happening on scales–a single DNA molecule–they can’t directly see. But working with a single DNA molecule in solution can be a daunting task. Just a tiny, pinpoint drop of DNA might contain a hundred times more molecules (about 600 billion) than people on the Earth.
“If you study billions of molecules, which is what people who routinely work with DNA at the bench do everyday, you don’t see anything,” said Levitus. “To make progress, you need to study a biological molecule individually and see what is happening in real time, because in biochemistry you are looking at processes that are not synchronized.”
Levitus compares the problem to a theater audience trying to follow the movements of 100 ballet dancers on stage. Without a spotlight, it would be difficult to focus on a single pirouette. “I needed to develop techniques so that I can visualize processes that would otherwise be hidden in the average.”
To create her DNA single molecule spotlight, Levitus’ techniques uses fluorescent compounds, or fluorophores. When a fluorophore is excited by a laser beam, it emits a signal to provide researchers ultrafast snapshots of the DNA as it ravels and unravels from the core nucleosome proteins.
In a typical experiment, the measurements take advantages of pairs of fluorophores that generate different color intensities. The compounds are physically attached to the DNA and nucleosome proteins.
“The idea is to use fluorescence to probe the distance between the DNA and one of the histone proteins,” said Levitus. “In this way, we will be able to measure how often the DNA unwraps from the protein core, and how long it remains unwrapped until wrapping back again. To do this, we put a fluorophore on the DNA and another one on the histone protein. These fluorophores interact in a distance-dependent fashion, so the intensities of the two colors allow us to calculate their relative distance.”
Utilizing customized instrumentation and homemade optics to obtain her measurements, Levitus can begin to understand how the DNA sequence, flexibility and energy dynamics contribute to the snaking of DNA around the protein core of the nucleosome.
Each month, innovative research from the Biodesign Institute appears in the world’s premier scientific journals. Many such studies have graced the covers of these journals, showcasing Biodesign research ranging from water remediation to nanometer-scale structures built from DNA.
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