Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

The geometry of RNA

30.10.2014

A new method simplifies the analysis of RNA structure

Messenger, transfer, ribosomal... there's more than one type of RNA. The difference lies not only in the sequence of the nucleotides, the "beads" that form the strand, but also in the three-dimensional structure that this long molecule takes on.


This image shows a three-dimensional distribution of nucleobases obtained from the crystal structure of a ribosomal RNA molecule. Different colours correspond to the different interaction types: Watson-Crick pairs in red/orange, non-canonical interactions in blue, stacked pairs in green.

Credit: SISSA

Computer models are often used to reveal this structure but these tend to be rather complex, and they vary depending on the field of application. A team of SISSA scientists used numerical techniques to develop a new "geometrical" model which has the advantage of being much simpler and faster than those traditionally used as well as having cross-sectional applications to different fields of study. The method proved to be effective and robust in the tests.

RNA, just like DNA, is a long chain composed of nucleotides, the building blocks that contain nucleobases, the "letters" that encode the information contained in these molecules. "It's relatively easy to discover the nucleotide sequence of an RNA molecule using standard experimental techniques", explains Giovanni Bussi, a professor at SISSA. "What's more difficult is to discover the shape of the molecule, but this is often crucial if we want to understand its function".

The method devised by Bussi and colleagues has the advantage of being based on very simple rules, and it has shown to be less cumbersome than the other computational methods currently used in laboratories. "Our technique looks at the relative position of nucleotides, their geometry, and, on this basis, it is able to classify the molecules according to their structure".

"We ran a series of tests on the method" comments Sandro Bottaro of SISSA and first author of the paper published in the scientific journal Nucleic Acid Research. "For example, we constructed a scoring function. In practice, having to compare different possible predictions of RNA structure, the scoring function provides a measure of the accuracy of each prediction. There are many ways to do this depending on the field of application. We assessed the reliability of our method, finding that it performed as well as and, in some cases, even better than conventional methods, which are, however, considerably more complex".

This means that, as well as being simpler than average, the method is also more versatile as it can be applied to a broad range of problems. In addition to Bussi and Bottaro, Francesco di Palma, a SISSA student, also took part in the study.

Federica Sgorbissa | EurekAlert!

More articles from Life Sciences:

nachricht A novel socio-ecological approach helps identifying suitable wolf habitats
17.02.2017 | Universität Zürich

nachricht New, ultra-flexible probes form reliable, scar-free integration with the brain
16.02.2017 | University of Texas at Austin

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: Breakthrough with a chain of gold atoms

In the field of nanoscience, an international team of physicists with participants from Konstanz has achieved a breakthrough in understanding heat transport

In the field of nanoscience, an international team of physicists with participants from Konstanz has achieved a breakthrough in understanding heat transport

Im Focus: DNA repair: a new letter in the cell alphabet

Results reveal how discoveries may be hidden in scientific “blind spots”

Cells need to repair damaged DNA in our genes to prevent the development of cancer and other diseases. Our cells therefore activate and send “repair-proteins”...

Im Focus: Dresdner scientists print tomorrow’s world

The Fraunhofer IWS Dresden and Technische Universität Dresden inaugurated their jointly operated Center for Additive Manufacturing Dresden (AMCD) with a festive ceremony on February 7, 2017. Scientists from various disciplines perform research on materials, additive manufacturing processes and innovative technologies, which build up components in a layer by layer process. This technology opens up new horizons for component design and combinations of functions. For example during fabrication, electrical conductors and sensors are already able to be additively manufactured into components. They provide information about stress conditions of a product during operation.

The 3D-printing technology, or additive manufacturing as it is often called, has long made the step out of scientific research laboratories into industrial...

Im Focus: Mimicking nature's cellular architectures via 3-D printing

Research offers new level of control over the structure of 3-D printed materials

Nature does amazing things with limited design materials. Grass, for example, can support its own weight, resist strong wind loads, and recover after being...

Im Focus: Three Magnetic States for Each Hole

Nanometer-scale magnetic perforated grids could create new possibilities for computing. Together with international colleagues, scientists from the Helmholtz Zentrum Dresden-Rossendorf (HZDR) have shown how a cobalt grid can be reliably programmed at room temperature. In addition they discovered that for every hole ("antidot") three magnetic states can be configured. The results have been published in the journal "Scientific Reports".

Physicist Dr. Rantej Bali from the HZDR, together with scientists from Singapore and Australia, designed a special grid structure in a thin layer of cobalt in...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Booth and panel discussion – The Lindau Nobel Laureate Meetings at the AAAS 2017 Annual Meeting

13.02.2017 | Event News

Complex Loading versus Hidden Reserves

10.02.2017 | Event News

International Conference on Crystal Growth in Freiburg

09.02.2017 | Event News

 
Latest News

Biocompatible 3-D tracking system has potential to improve robot-assisted surgery

17.02.2017 | Medical Engineering

Real-time MRI analysis powered by supercomputers

17.02.2017 | Medical Engineering

Antibiotic effective against drug-resistant bacteria in pediatric skin infections

17.02.2017 | Health and Medicine

VideoLinks
B2B-VideoLinks
More VideoLinks >>>