

Unzipping Your DNA

by William Rozycki

DNA, the carrier of the genetic code in all living things, is ordinarily found as a tightly wound helical structure in every cell. The helix is made up of two long strands, each with amino acids ranged along it. The two strands are folded together in a complex embrace, and that structure itself is then wound around a large molecular configuration. But tightly wound as it is, the structure is not everlasting.

“During replication and translation, DNA unfolds from its complicated pattern, and the two strands separate,” explains Kyle Forinash, professor of physics at IU Southeast. “Despite its importance in the reproduction of living things, this dynamic mechanical process is not well understood. Why does it fold and unfold into certain shapes and not into others?”

Kyle Forinash is professor of physics at Indiana University Southeast. Photo Katherine Sears.

Forinash figures that some of the answers are chemical, distinct to each gene sequence. But other parts of the dynamic are mechanical, and those aspects motivate Forinash’s research.

“We are investigating generic features of all structures with the general mechanical characteristics of DNA,” Forinash says. “Our models are still pretty theoretical, but they do give a picture of how these processes might proceed.”

To understand the energy balance involved in DNA “unzipping,” Forinash starts with the assumption that because the energy moving through the complex structure of DNA is not randomized (i.e., it does not spread out over all the atoms of the structure and thereby become random thermal motion), the energy may be transferred by means of a nonlinear mechanism. This has led Forinash to computer modeling of solitons in discrete systems.

“Solitons,” he explains, “are wave-like solutions to specific nonlinear differential equations. In discrete systems (in contrast to continuum systems like water waves), where there are series of separate entities such as atoms or molecules that carry the wave, extremely narrow versions of these waves can exist.”

Forinash theorizes that solitons can be dynamic and oscillating in nature, allowing energy to be preserved as it moves through a complex system. This is one of the best answers to the question of why the energy of DNA unzipping does not dissipate: a specific type of nonlinear wave is at work.

The research Forinash is doing may shed light not only on energy transfer in DNA, but also on fundamental problems in solid-state physics.

“The general concept of solitary waves moving along discrete or continuous chains has a venerable history,” Forinash says. “Implications of this research could extend to models explaining properties of solids such as phase transitions, magnetic domain boundaries, and fiber-optic cable transmission.”

As the sole full-time physics professor on his campus, Forinash has taught up to fifteen hours per semester, but he does not see conflict between his teaching and his research. Forinash firmly believes that teaching and research are bound together, and he welcomes heightened research expectations for faculty at IU’s regional campuses.

“Knowledge is a community project; it takes more than one or even several persons,” he asserts. Forinash has involved numerous students in his research—seven of his students, all but one of them undergraduates, have appeared as his co-authors in peer-reviewed publications.

“Even after twenty-five years of teaching introductory physics, I still get questions in class that cause me to rethink and better understand the subject,” Forinash says. “Unless there is dialogue, there can be no genuine learning. We learn best when we teach others.”

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