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 BigH1 -- The key histone for male fertility
14.12.2017 | Institute for Research in Biomedicine (IRB Barcelona)

nachricht Guardians of the Gate
14.12.2017 | Max-Planck-Institut für Biochemie

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

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

Im Focus: Long-lived storage of a photonic qubit for worldwide teleportation

MPQ scientists achieve long storage times for photonic quantum bits which break the lower bound for direct teleportation in a global quantum network.

Concerning the development of quantum memories for the realization of global quantum networks, scientists of the Quantum Dynamics Division led by Professor...

Im Focus: Electromagnetic water cloak eliminates drag and wake

Detailed calculations show water cloaks are feasible with today's technology

Researchers have developed a water cloaking concept based on electromagnetic forces that could eliminate an object's wake, greatly reducing its drag while...

Im Focus: Scientists channel graphene to understand filtration and ion transport into cells

Tiny pores at a cell's entryway act as miniature bouncers, letting in some electrically charged atoms--ions--but blocking others. Operating as exquisitely sensitive filters, these "ion channels" play a critical role in biological functions such as muscle contraction and the firing of brain cells.

To rapidly transport the right ions through the cell membrane, the tiny channels rely on a complex interplay between the ions and surrounding molecules,...

Im Focus: Towards data storage at the single molecule level

The miniaturization of the current technology of storage media is hindered by fundamental limits of quantum mechanics. A new approach consists in using so-called spin-crossover molecules as the smallest possible storage unit. Similar to normal hard drives, these special molecules can save information via their magnetic state. A research team from Kiel University has now managed to successfully place a new class of spin-crossover molecules onto a surface and to improve the molecule’s storage capacity. The storage density of conventional hard drives could therefore theoretically be increased by more than one hundred fold. The study has been published in the scientific journal Nano Letters.

Over the past few years, the building blocks of storage media have gotten ever smaller. But further miniaturization of the current technology is hindered by...

Im Focus: Successful Mechanical Testing of Nanowires

With innovative experiments, researchers at the Helmholtz-Zentrums Geesthacht and the Technical University Hamburg unravel why tiny metallic structures are extremely strong

Light-weight and simultaneously strong – porous metallic nanomaterials promise interesting applications as, for instance, for future aeroplanes with enhanced...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

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

AKL’18: The opportunities and challenges of digitalization in the laser industry

07.12.2017 | Event News

 
Latest News

Plasmonic biosensors enable development of new easy-to-use health tests

14.12.2017 | Health and Medicine

New type of smart windows use liquid to switch from clear to reflective

14.12.2017 | Physics and Astronomy

BigH1 -- The key histone for male fertility

14.12.2017 | Life Sciences

VideoLinks
B2B-VideoLinks
More VideoLinks >>>