Mechanical engineers use magnets, nanobeads to measure DNA torque

Schematic of Magnetic Nano-rod
DNA fiber attached to magnetic nano-rod bead can be wound and unwound using magnetic “tweezers“ shown above as blue (north) and red (south) magnets. Credit: Sun Lab/JHU

Torque measures the tendency of a force to rotate something around an axis—think of a tether ball on a string. Torque also comes into play when the enzymes that read genetic code travel along a length of DNA. The segment behind the enzyme unwinds, while the portion ahead becomes more coiled and compact. Researchers from Johns Hopkins Institute for NanoBioTechnology have developed a method that uses magnets and a nanobead to measure, for the first time, single molecule rotational forces involved in the winding and unwinding of DNA fibers within the chromosome. Understanding these forces could help scientists predict gene regulation and provide important information on molecular targets for the development of disease-fighting drugs.

Mechanical engineering doctoral student Alfredo Celedon observed the torque of a 1-micron length of chromatin fiber. In this instance, torque is a measure of the rotational force required to twist the end of the fiber. Chromatin is the protein-rich protective structure that stuffs nearly six-feet of DNA into a package small enough to fit inside cells. DNA spools around proteins called histones within the chromatin fiber.

Celedon collaborated with principal investigator Sean X. Sun, associate professor of Mechanical Engineering and INBT affiliated faculty member. The team attached one end of the chromatin fiber to a glass slide. [See illustration.] The other end of the chromatin was attached to a 200-nanometer diameter rod coupled to a magnetic bead. This end of the fiber was pulled upward by weak forces exerted on the bead by the magnet tweezers positioned above the slide.

When the researchers rotated the magnetic tweezers, the nanorod-bead spun introducing twists but adding very little vertical pulling force on the fiber. As the chromatin fiber twisted clockwise or counter clockwise, Celedon obtained torque from the change in the angle of the nano-rod bead from its resting position. This work was published in the March 20, 2009 issue of Nano Letters.

“Because the forces pulling upward on the nanorod-bead are so small, we are able to measure chromatin torque without unraveling the structure of the fiber or melting DNA, something that has not been done before,“ says Sun. Applying low vertical pulling forces is physiologically relevant, Sun adds, because that state mimics what might be found in a living cell.

The researchers compared the torque of chromatin fibers with that of bare DNA strands, and found that DNA packed in the chromatin structure was able to absorb more twists with lower torque than bare DNA.

“This makes sense,“ Celedon says. “Because the histones act like springs and absorb rotational forces.“

The chromatin used in these experiments was reconstituted in vitro, Celedon added. “The next step is to study the effects on chromatin torque of modifications to the structure associated with different levels of gene expression This will allow us to understand how chromatin structure regulates transcription.“

Other contributors to this research include Ilana Nodelman, research scientist in Biophysics; Bridget Wildt, doctoral student in Materials Science; Rohit Dewan, junior in Chemical and Biomolecular Engineering; Peter Searson, Reynolds Professor of Materials Science and Engineering and INBT director; Denis Wirtz, professor of Chemical and Biomolecular Engineering and associate director of INBT; and Gregory Bowman, assistant professor of Biophysics. Celedon’s research was funded by the National Science Foundation and the Howard Hughes Medical Institute Graduate Training Program at the Johns Hopkins Institute for NanoBioTechnology. Bowman, Searson, Wirtz, and Sun are affiliated faculty members of INBT.

Links

Magnetic Tweezers Measurement of Single Molecule Torque, Alfredo Celedon, Ilana M. Nodelman, Bridget Wildt, Rohit Dewan, Peter Searson, Denis Wirtz, Gregory D. Bowman, Sean X. Sun, Nano Letters 2009 9 (4), 1720-1725.

Sean Sun’s INBT page

Greg Bowman’s INBT page

Story by Mary Spiro

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