Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Mathematical models reveal ’molten’ and ’glassy’ states of RNA

05.03.2003


Mathematical models have given physicists a new look at DNA’s chemical counterpart, RNA.



The models - showing that RNA behaves differently depending on the temperature of its environment - may help biologists better understand how life evolved on Earth.

The models suggest that high temperatures give twisted strands of RNA the flexibility to fold into many different shapes, while low temperatures cause it to collapse into a single shape.


Ralf Bundschuh, assistant professor of physics at Ohio State University, presented the results March 4 at the meeting of the American Physical Society in Austin, Texas.

RNA plays many different roles in a cell, such as the production of proteins that perform necessary functions, Bundschuh explained.

“People are probably more familiar with the genetic role of DNA, in which two strands of complementary base units bind to each other to create a double-helix structure. RNA behaves very much like a DNA molecule that has lost its complementary partner. In order for one strand of bases to form pairs, the strand must bend back onto itself -- it must fold,” he said.

The structure of folded RNA resembles a severely twisted rubber band, with the shape of loops and branches determining its biological function.

Exactly how RNA folds into any particular shape is a mystery. Other researchers have tried to tackle the problem with computer simulations, by calculating the possible formations that result from a certain number of base units coming together. But simulating very realistic RNA molecules -- that is, very long RNA strands with many base units -- is difficult.

Bundschuh and Terence Hwa of the University of California, San Diego, examined the problem differently. They have developed the first mathematical theory for the possible states of an RNA molecule.

In the past, scientists only knew for sure that RNA could fold into a given configuration, depending on its chemical makeup. Instead, these mathematical models show that high temperatures cause RNA to enter a flexible state in which it can take on a variety of configurations. The flexible state is known as the “molten” state. When temperatures fall too low, the RNA enters a tangled, or “glassy,” state.

“We know at high temperatures RNA is molten, and low temperatures, it is glassy. Somewhere in between, something has to happen to change its state from one to the other. We don’t know what that is, yet,” Bundschuh said.

Whether RNA forms a functional structure depends on the alignment of four base units -- adenine, guanine, cytosine and uracil -- a sequence of which resembles a strand of beads. When molten, the strand folds and unfolds with ease, and each base unit can connect with many different mates to form many possible overall shapes. In the glassy state, the strand “freezes” in a random pattern.

The results hold implications for the study of the related “protein folding problem.” Researchers are working to understand the issues nature has to overcome to design new RNA sequences, because someday researchers may be able to design sequences themselves, for drugs or other disease therapies.

“One does not want to end up with a sequence that gets stuck in some random structure, or cannot decide which structure to fold into,” Bundschuh said.

The work also has broader relevance for evolutionary biology, where experts have speculated that early life might have relied exclusively upon RNA.

“RNA could in fact be a stepping-stone to today’s world of DNA. DNA cannot replicate without proteins, and proteins cannot be produced without RNA,” Bundschuh said. “You could say we’re characterizing what evolution is up against.”

With five years’ effort, Bundschuh and Hwa have only just begun to be able to model simple RNA activities that occur in less than a second, countless times every day.

“Now we can better appreciate what biology has to do to create a functional RNA molecule,” he said.

Ohio State physics doctoral student Tsunglin Liu is working with Bundschuh to estimate how many base units would be required for computer simulations of more realistic RNA models, in order to observe the molten or glassy state. Liu has found that more than 8,000 units are necessary -- a computational task well beyond the reach of current studies, which are based on as few as 2,000 units.


Contact: Ralf Bundschuh, (614) 688-3978; Bundschuh.2@osu.edu

Written by Pam Frost Gorder, (614) 292-9475; Gorder.1@osu.edu

Pam Frost Gorder | EurekAlert!

More articles from Physics and Astronomy:

nachricht First direct observation and measurement of ultra-fast moving vortices in superconductors
20.07.2017 | The Hebrew University of Jerusalem

nachricht Manipulating Electron Spins Without Loss of Information
19.07.2017 | Universität Basel

All articles from Physics and Astronomy >>>

The most recent press releases about innovation >>>

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

Im Focus: Manipulating Electron Spins Without Loss of Information

Physicists have developed a new technique that uses electrical voltages to control the electron spin on a chip. The newly-developed method provides protection from spin decay, meaning that the contained information can be maintained and transmitted over comparatively large distances, as has been demonstrated by a team from the University of Basel’s Department of Physics and the Swiss Nanoscience Institute. The results have been published in Physical Review X.

For several years, researchers have been trying to use the spin of an electron to store and transmit information. The spin of each electron is always coupled...

Im Focus: The proton precisely weighted

What is the mass of a proton? Scientists from Germany and Japan successfully did an important step towards the most exact knowledge of this fundamental constant. By means of precision measurements on a single proton, they could improve the precision by a factor of three and also correct the existing value.

To determine the mass of a single proton still more accurate – a group of physicists led by Klaus Blaum and Sven Sturm of the Max Planck Institute for Nuclear...

Im Focus: On the way to a biological alternative

A bacterial enzyme enables reactions that open up alternatives to key industrial chemical processes

The research team of Prof. Dr. Oliver Einsle at the University of Freiburg's Institute of Biochemistry has long been exploring the functioning of nitrogenase....

Im Focus: The 1 trillion tonne iceberg

Larsen C Ice Shelf rift finally breaks through

A one trillion tonne iceberg - one of the biggest ever recorded -- has calved away from the Larsen C Ice Shelf in Antarctica, after a rift in the ice,...

Im Focus: Laser-cooled ions contribute to better understanding of friction

Physics supports biology: Researchers from PTB have developed a model system to investigate friction phenomena with atomic precision

Friction: what you want from car brakes, otherwise rather a nuisance. In any case, it is useful to know as precisely as possible how friction phenomena arise –...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

»We are bringing Additive Manufacturing to SMEs«

19.07.2017 | Event News

The technology with a feel for feelings

12.07.2017 | Event News

Leipzig HTP-Forum discusses "hydrothermal processes" as a key technology for a biobased economy

12.07.2017 | Event News

 
Latest News

Researchers create new technique for manipulating polarization of terahertz radiation

20.07.2017 | Information Technology

High-tech sensing illuminates concrete stress testing

20.07.2017 | Materials Sciences

First direct observation and measurement of ultra-fast moving vortices in superconductors

20.07.2017 | Physics and Astronomy

VideoLinks
B2B-VideoLinks
More VideoLinks >>>