JUN 13, 2017 4:51 PM PDT

Within Cells, DNA can Move Molecules

WRITTEN BY: Carmen Leitch

While DNA is portrayed as a beautiful double helix, in live cells it’s a clump of tangles that seems impenetrable. However, there are lots of important molecules that need to get to the right parts of specific areas of DNA, and scientists wondered how they could do that in such a dense cluster. New work published in Biophysical Journal by researchers at the Georgia Institute of Technology has indicated that DNA is not immobile but has dynamic properties that allow it to push those critical molecules to the right places at the right times.

Transcription factors work to express the proper genes, and they are very large molecules. It’s long been a mystery as to how they got where they needed to be in the dense thicket that is natural DNA. In the video above, the green ball represents a transcription factor within grey DNA strands.

"If the thicket is so thick, and on top of that doesn't move, then it should be impenetrable. So, how do you get stuff through to the right site?" queried Jeffrey Skolnick, a Professor at Georgia Tech's School of Biological Sciences.

Skolnick collaborated with a computer scientist that specializes in algorithms for scientific inquiries, Edmond Chow. They challenged the idea that DNA is a rigid structure, and instead simulated DNA as a moveable molecule that can twist and turn moving itself and the stuff around it. 

"The DNA motion is far and away the dominant force moving molecules through its thicket," Skolnick explained. "DNA is a bully."

For this work the investigators used the well-known transcription factor LacI (moedled in the videos as the green ball) from the bacterium Esherichia coli for their study. In the computer simulations, strands of DNA could move out of the way of LacI and also propel the LacI forward to the next space. This could help explain why transcription factors seem to move so slow in simulations that use DNA that does not flex. When the DNA wiggles, the LacI can speed along.

Transcription factors are known to be able to hop on and off, clicking into the right spot on DNA when needed. "But the sliding and hopping combined still don't account for the speed of diffusion," Chow noted. However, the DNA can flick the transcription factor as it hops, propelling it ahead and increasing their diffusion rate.

The revelations in this work were made possible by massive computational power. "These simulations are unique to this problem because of their enormity and the advanced computing techniques used. Very efficient algorithms ran in parallel on powerful computers, and, still, it took three weeks for the simulations to complete," Chow commented.

It still required some trimming of real-life conditions in order to be able to run the entire simulation. Scientists are still working to develop models that can account for the entire framework of the cell. "The ultimate goal is to put a whole cell on a computer. Let it live. Let it divide, and understand the processes," Skolnick said. "Maybe even let the cell mutate and evolve."

"When the size of a problem grows, the computing costs to solve it can grow disproportionately," Chow noted. "You have to build algorithms that can run efficiently even when you scale up the problem size."

Naturally occurring DNA is in constant motion, researchers hypothesize, and transports large transcription factors (depicted in green) through its tangles until they reach sites where they bind and carry out their activity. Here a still image from a very large, unique simulation. / Credit: Georgia Tech / Edmond Chow / Jeff Skolnick

Sources: AAAS/Eurekalert! via Georgia Institute of Technology, Biophysical Journal

About the Author
  • Experienced research scientist and technical expert with authorships on over 30 peer-reviewed publications, traveler to over 70 countries, published photographer and internationally-exhibited painter, volunteer trained in disaster-response, CPR and DV counseling.
You May Also Like
MAR 28, 2021
Cell & Molecular Biology
Understanding How Cold-Induced Tooth Pain Happens
MAR 28, 2021
Understanding How Cold-Induced Tooth Pain Happens
Our teeth do a lot of work, and they may become sensitive to cold as the gums erode due to aging or because they have an ...
MAR 31, 2021
Microbiology
Deep-Sea Microbes Are 'Invisible' to the Human Immune System
MAR 31, 2021
Deep-Sea Microbes Are 'Invisible' to the Human Immune System
Scientists took an exploratory journey to a place in the central Pacific Ocean in Kirbati called the Phoenix Islands Pro ...
APR 13, 2021
Genetics & Genomics
Skull Fossil Yields One of the Oldest Modern Human Genomes
APR 13, 2021
Skull Fossil Yields One of the Oldest Modern Human Genomes
DNA from a very old skull is changing what we know about when and where early humans lived.
APR 29, 2021
Cell & Molecular Biology
Cancer Cell Fate Influenced by Dietary Amino Acid
APR 29, 2021
Cancer Cell Fate Influenced by Dietary Amino Acid
This work could one day open up dietary therapeutic options for cancer.
MAY 04, 2021
Cell & Molecular Biology
A Potential Weakness in SARS-CoV-2 is Caught on Video
MAY 04, 2021
A Potential Weakness in SARS-CoV-2 is Caught on Video
You can see the spike protein of the virus in action in this video.
MAY 14, 2021
Coronavirus
How COVID-19 Patients Lose Their Sense of Smell
MAY 14, 2021
How COVID-19 Patients Lose Their Sense of Smell
The loss of the sense of smell is a well-known symptom of COVID-19, and was common even in people that did not have many ...
Loading Comments...