Researchers at Northwestern University have unveiled findings that challenge traditional biochemical practices regarding DNA strand separation. The study, led by Professor John Marko and post-doctoral researcher Parth Desai, indicates that more mechanical force is required for DNA strand separation in living cells than previously thought.
In most biochemistry labs, DNA is isolated in a water-based solution where it can be manipulated without interference from other molecules. Traditionally, heat is used to separate DNA strands, reaching temperatures of over 150 degrees Fahrenheit. However, in living cells, DNA exists in a crowded environment with proteins mechanically unwinding the double helix.
Professor Marko explained the significance of their findings: “The interior of the cell is super crowded with molecules, and most biochemistry experiments are super uncrowded. You can think of extra molecules as billiard balls. They’re pounding against the DNA double helix and keeping it from opening.”
The research involved using microscopic magnetic tweezers to separate DNA strands and introduce three types of molecules to mimic cellular proteins. These interactions were studied to understand how they affect DNA stability.
Desai noted the importance of this approach: “We wanted to have a wide variety of molecules where some cause dehydration, destabilizing DNA mechanically, and then others that stabilize DNA.” He suggested that similar effects could occur within cells due to competing proteins.
Marko emphasized the broader implications: “If this affects DNA strand separation, all protein interactions with DNA are also going to be affected.” This includes protein binding specificity and process control on DNA.
The study's results will be published in the Biophysical Journal on June 17. The work was supported by grants from the National Institutes of Health and a subcontract to the University of Massachusetts Center for 3D Structure and Physics of the Genome.