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 Two dimensional circuit with magnetic quasi-particles
22.01.2018 | Technische Universität Kaiserslautern

nachricht Meteoritic stardust unlocks timing of supernova dust formation
19.01.2018 | Carnegie Institution for Science

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: Artificial agent designs quantum experiments

On the way to an intelligent laboratory, physicists from Innsbruck and Vienna present an artificial agent that autonomously designs quantum experiments. In initial experiments, the system has independently (re)discovered experimental techniques that are nowadays standard in modern quantum optical laboratories. This shows how machines could play a more creative role in research in the future.

We carry smartphones in our pockets, the streets are dotted with semi-autonomous cars, but in the research laboratory experiments are still being designed by...

Im Focus: Scientists decipher key principle behind reaction of metalloenzymes

So-called pre-distorted states accelerate photochemical reactions too

What enables electrons to be transferred swiftly, for example during photosynthesis? An interdisciplinary team of researchers has worked out the details of how...

Im Focus: The first precise measurement of a single molecule's effective charge

For the first time, scientists have precisely measured the effective electrical charge of a single molecule in solution. This fundamental insight of an SNSF Professor could also pave the way for future medical diagnostics.

Electrical charge is one of the key properties that allows molecules to interact. Life itself depends on this phenomenon: many biological processes involve...

Im Focus: Paradigm shift in Paris: Encouraging an holistic view of laser machining

At the JEC World Composite Show in Paris in March 2018, the Fraunhofer Institute for Laser Technology ILT will be focusing on the latest trends and innovations in laser machining of composites. Among other things, researchers at the booth shared with the Aachen Center for Integrative Lightweight Production (AZL) will demonstrate how lasers can be used for joining, structuring, cutting and drilling composite materials.

No other industry has attracted as much public attention to composite materials as the automotive industry, which along with the aerospace industry is a driver...

Im Focus: Room-temperature multiferroic thin films and their properties

Scientists at Tokyo Institute of Technology (Tokyo Tech) and Tohoku University have developed high-quality GFO epitaxial films and systematically investigated their ferroelectric and ferromagnetic properties. They also demonstrated the room-temperature magnetocapacitance effects of these GFO thin films.

Multiferroic materials show magnetically driven ferroelectricity. They are attracting increasing attention because of their fascinating properties such as...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

10th International Symposium: “Advanced Battery Power – Kraftwerk Batterie” Münster, 10-11 April 2018

08.01.2018 | Event News

See, understand and experience the work of the future

11.12.2017 | Event News

Innovative strategies to tackle parasitic worms

08.12.2017 | Event News

 
Latest News

Multifunctional Platform for the Delivery of Gene Therapeutics

22.01.2018 | Life Sciences

The world's most powerful acoustic tractor beam could pave the way for levitating humans

22.01.2018 | Power and Electrical Engineering

Siberian scientists learned how to reduce harmful emissions from HPPs

22.01.2018 | Power and Electrical Engineering

VideoLinks