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.
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!
Ion treatments for cardiac arrhythmia — Non-invasive alternative to catheter-based surgery
20.01.2017 | GSI Helmholtzzentrum für Schwerionenforschung GmbH
Seeking structure with metagenome sequences
20.01.2017 | DOE/Joint Genome Institute
An important step towards a completely new experimental access to quantum physics has been made at University of Konstanz. The team of scientists headed by...
Yersiniae cause severe intestinal infections. Studies using Yersinia pseudotuberculosis as a model organism aim to elucidate the infection mechanisms of these...
Researchers from the University of Hamburg in Germany, in collaboration with colleagues from the University of Aarhus in Denmark, have synthesized a new superconducting material by growing a few layers of an antiferromagnetic transition-metal chalcogenide on a bismuth-based topological insulator, both being non-superconducting materials.
While superconductivity and magnetism are generally believed to be mutually exclusive, surprisingly, in this new material, superconducting correlations...
Laser-driving of semimetals allows creating novel quasiparticle states within condensed matter systems and switching between different states on ultrafast time scales
Studying properties of fundamental particles in condensed matter systems is a promising approach to quantum field theory. Quasiparticles offer the opportunity...
Among the general public, solar thermal energy is currently associated with dark blue, rectangular collectors on building roofs. Technologies are needed for aesthetically high quality architecture which offer the architect more room for manoeuvre when it comes to low- and plus-energy buildings. With the “ArKol” project, researchers at Fraunhofer ISE together with partners are currently developing two façade collectors for solar thermal energy generation, which permit a high degree of design flexibility: a strip collector for opaque façade sections and a solar thermal blind for transparent sections. The current state of the two developments will be presented at the BAU 2017 trade fair.
As part of the “ArKol – development of architecturally highly integrated façade collectors with heat pipes” project, Fraunhofer ISE together with its partners...
19.01.2017 | Event News
10.01.2017 | Event News
09.01.2017 | Event News
20.01.2017 | Awards Funding
20.01.2017 | Materials Sciences
20.01.2017 | Life Sciences