Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:


Cells' springy coils pump bursts of RNA


Rice University model quantifies basic processes of transcription

In your cells, it's almost always spring. Or at least springy.

Models by Rice University chemists calculate the chemical and mechanical energies involved in "bursty" RNA production in cells. Their models show how RNA polymerases create supercoils of DNA that allow production of RNA that goes on to produce proteins.

Credit: Alena Klindziuk/Rice University

Bioscientists have known for some time that chromosomes tend to express their protein products in bursts, rather than in a steady manner. A new theoretical study by Rice University scientists, detailed in the Biophysical Journal, aims to better explain the process that combines chemical reactions and mechanical forces.

Rice chemist Anatoly Kolomeisky and applied physics graduate student and lead author Alena Klindziuk built the first simplified analytical model of "bursting" to show how pressure from a RNA polymerase enzyme triggers the rush of RNA production, but only to the degree that it can push a coil of DNA.

... more about:
»Cells »DNA »RNA »RNA polymerase »enzyme »proteins

As it compresses like a spring, that DNA "supercoil" continues to express RNA -- which goes on to make the proteins themselves -- until the enzyme can push no more. It isn't until another enzyme, a gyrase, comes along to release the tension that production can start anew.

"With advances in experimental techniques, people are able to measure how much RNA you are producing, and so it was a naive expectation that the speed of production was more or less constant," said Kolomeisky, a chemist by title whose group has long been interested in how biochemical reactions work to power biological mechanisms, and vice versa.

"It was surprising when we found it actually doesn't work this way," he said. "A lot of RNA is produced and then there's a period of silence. RNA is produced in a very bursty behavior, but the molecular details have been lacking."

He said the way RNA polymerase aligns with the double-helical DNA coils it in the process. "It rotates, putting mechanical constraints on DNA," Kolomeisky said. "A spring is an excellent example. The more you push a spring, the harder it becomes to push.

"We think the RNA polymerase coils DNA to start RNA production," he said. "At the beginning of the process, you get a burst, but the process slows down as it squeezes the spring. Then gyrases come in; they untangle this supercoil so that normal production can begin again." At the same time, he said gyrases also relieve negative stress created on the other side of the polymerase.

"Essentially, we created the first quantitative energetic model that explains this burstiness," Kolomeisky said. "We are able to interpret the experimental data (gathered in experiments on bacteria) and found this supercoil exists."

He said the calculations show the DNA "spring" is relatively weak. "That has biological significance because it means we can more easily regulate the process by regulating gyrases," he said.

Klindziuk noted there are many other players in the process that ultimately need to be accounted for. "We could have added many effects, like transcriptional and other epigenetic factors," she said. "We want to make a model where there are multiple polymerases on DNA. In this model, we only had one, but in reality, there are many polymerases. There might be effects from polymerase traffic, like they're bumping into each other and stopping and resuming their activity."

"This is an example of advanced experimentation that led us to seek a significant theoretical solution," Kolomeisky said. "It usually happens in the opposite direction, but this time experiments were able to visualize the process, and that led us to think about and start to explain it."


Visiting undergraduate student Billie Meadowcroft is a co-author of the paper. Kolomeisky is a professor of chemistry and of chemical and biomolecular engineering and chair of Rice's Department of Chemistry.

The Welch Foundation, the National Science Foundation and Rice's Center for Theoretical Biological Physics supported the research.


Read the abstract at

This news release can be found online at

Follow Rice News and Media Relations via Twitter @RiceUNews.

Related materials:

Kolomeisky Research Group:

Department of Chemistry:

Wiess School of Natural Sciences:

Images for download:

Models by Rice University chemists calculate the chemical and mechanical energies involved in "bursty" RNA production in cells. Their models show how RNA polymerases create supercoils of DNA that allow production of RNA that goes on to produce proteins. (Credit: Alena Klindziuk/Rice University)

CAPTION: Alena Klindziuk. (Credit: Jeff Fitlow/Rice University)

CAPTION: Anatoly Kolomeisky. (Credit: Jeff Fitlow/Rice University)

Located on a 300-acre forested campus in Houston, Rice University is consistently ranked among the nation's top 20 universities by U.S. News & World Report. Rice has highly respected schools of Architecture, Business, Continuing Studies, Engineering, Humanities, Music, Natural Sciences and Social Sciences and is home to the Baker Institute for Public Policy. With 3,962 undergraduates and 3,027 graduate students, Rice's undergraduate student-to-faculty ratio is just under 6-to-1. Its residential college system builds close-knit communities and lifelong friendships, just one reason why Rice is ranked No. 1 for lots of race/class interaction and No. 4 for quality of life by the Princeton Review. Rice is also rated as a best value among private universities by Kiplinger's Personal Finance.

Media Contact

Jeff Falk

Mike Williams

Jeff Falk | EurekAlert!
Further information:

Further reports about: Cells DNA RNA RNA polymerase enzyme proteins

More articles from Life Sciences:

nachricht Gold nanoclusters: new frontier for developing medication for treatment of Alzheimer's disease
17.02.2020 | Science China Press

nachricht Catalyst deposition on fragile chips
17.02.2020 | Ruhr-University Bochum

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Freiburg researcher investigate the origins of surface texture

Most natural and artificial surfaces are rough: metals and even glasses that appear smooth to the naked eye can look like jagged mountain ranges under the microscope. There is currently no uniform theory about the origin of this roughness despite it being observed on all scales, from the atomic to the tectonic. Scientists suspect that the rough surface is formed by irreversible plastic deformation that occurs in many processes of mechanical machining of components such as milling.

Prof. Dr. Lars Pastewka from the Simulation group at the Department of Microsystems Engineering at the University of Freiburg and his team have simulated such...

Im Focus: Skyrmions like it hot: Spin structures are controllable even at high temperatures

Investigation of the temperature dependence of the skyrmion Hall effect reveals further insights into possible new data storage devices

The joint research project of Johannes Gutenberg University Mainz (JGU) and the Massachusetts Institute of Technology (MIT) that had previously demonstrated...

Im Focus: Making the internet more energy efficient through systemic optimization

Researchers at Chalmers University of Technology, Sweden, recently completed a 5-year research project looking at how to make fibre optic communications systems more energy efficient. Among their proposals are smart, error-correcting data chip circuits, which they refined to be 10 times less energy consumptive. The project has yielded several scientific articles, in publications including Nature Communications.

Streaming films and music, scrolling through social media, and using cloud-based storage services are everyday activities now.

Im Focus: New synthesis methods enhance 3D chemical space for drug discovery

After helping develop a new approach for organic synthesis -- carbon-hydrogen functionalization -- scientists at Emory University are now showing how this approach may apply to drug discovery. Nature Catalysis published their most recent work -- a streamlined process for making a three-dimensional scaffold of keen interest to the pharmaceutical industry.

"Our tools open up whole new chemical space for potential drug targets," says Huw Davies, Emory professor of organic chemistry and senior author of the paper.

Im Focus: Quantum fluctuations sustain the record superconductor

Superconductivity approaching room temperature may be possible in hydrogen-rich compounds at much lower pressures than previously expected

Reaching room-temperature superconductivity is one of the biggest dreams in physics. Its discovery would bring a technological revolution by providing...

All Focus news of the innovation-report >>>



Industry & Economy
Event News

70th Lindau Nobel Laureate Meeting: Around 70 Laureates set to meet with young scientists from approx. 100 countries

12.02.2020 | Event News

11th Advanced Battery Power Conference, March 24-25, 2020 in Münster/Germany

16.01.2020 | Event News

Laser Colloquium Hydrogen LKH2: fast and reliable fuel cell manufacturing

15.01.2020 | Event News

Latest News

Gold nanoclusters: new frontier for developing medication for treatment of Alzheimer's disease

17.02.2020 | Life Sciences

Artificial intelligence is becoming sustainable!

17.02.2020 | Information Technology

Catalyst deposition on fragile chips

17.02.2020 | Life Sciences

Science & Research
Overview of more VideoLinks >>>