Breakthrough study unveils mechanics of DNA unwinding

For the first time, scientists have witnessed the very moment DNA begins to unravel, revealing a necessary molecular event for DNA to be the molecule that codes all life. A new study from King Abdullah University of Science and Technology (KAUST), published in Nature, captures the moment DNA begins to unwind, allowing for all the events that follow in DNA replication. This direct observation sheds light on the fundamental mechanisms that allow cells to faithfully duplicate their genetic material, a cornerstone for growth and reproduction. 

Using cryo-electron microscopy and deep learning to observe the helicase Simian Virus 40 Large Tumor Antigen interacting with DNA, the laboratories of KAUST Assistant Professor Alfredo De Biasio and Professor Samir Hamdan provide the most detailed description yet of the very first steps of DNA replication: 15 atomic states that describe how the enzyme helicase forces the unwinding of DNA. The achievement is not only a milestone in helicase research, but also a milestone in observing the dynamics of any enzyme at atomic resolution. 

While scientists have long known the importance of helicase in DNA replication, "they did not know how DNA, helicases and ATP work together in a coordinated cycle to drive DNA unwinding," De Biasio said. 

When Watson and Crick reported the double helix in 1953, they gave the scientific community a breakthrough understanding of how genetic information is stored and copied. For DNA to replicate, the helix must first unwind and break the DNA from a double strand into two single strands. 

Upon binding, helicases melt the DNA, breaking the chemicals bonds holding the double helix together. They then pull the two strands apart, allowing other enzymes to complete the replication. Without this first step, no DNA can be replicated. In this way, helicases are machines or, because of their size, nanomachines. 

If helicases are nanomachines, then 'ATP', or adenosine trisphosphate, is the fuel. Much like how burning gas drives the pistons of a car engine, burning ATP, the same fuel used to flex your muscles, causes the six pistons of a helicase to unwind DNA. The study found that as ATP is consumed, it reduces physical constraints that allow the helicase to proceed along the DNA, unwinding more and more of the double strand. Thus, ATP consumption acts a switch that increases the amount of entropy – or disorder – in the system, freeing the helicase to move along the DNA. 

The helicase uses ATP not to pry DNA apart in one motion, but to cycle through conformational changes that progressively destabilize and separate the strands. ATP burning, or hydrolysis, functions like the spring in a mouse trap, snapping the helicase forward and pulling the DNA strands apart."

Alfredo De Biasio, KAUST Assistant Professor

Among the many discoveries made by the KAUST scientists was that two helicases melt the DNA at two sites at the same time to initiate the unwinding. The chemistry of DNA is such that nanomachines move along a single DNA strand in one direction only. By binding at two sites simultaneously, the helicases coordinate so that the winding can happen in both directions with an energy efficiency unique to natural nanomachines. 

That efficiency, explains De Biasio, makes the study of DNA replication more than an attempt to answer the most fundamental scientific questions about life, it also makes helicases models for the design of new nanotechnology. 

"From a design perspective, helicases exemplify energy-efficient mechanical systems. Engineered nanomachines using entropy switches could harness similar energy-efficient mechanisms to perform complex, force-driven tasks," he said.