Nav: Home

RNA in stop-motion

April 18, 2016

You are an animator (a specialist who creates cartoons) who works in stop-motion. This technique involves patiently lining up many pictures of a subject that changes slightly position in each picture, so as to have a coherent and continuous sequence of frames. For those who know him, Pingu, the mischievous and adventurous penguin, is an example of stop-motion. In the case of RNA, though, rather than plasticine figures you have a huge database of general images, something like Flickr. You need to create an animation of a smile, from the time the mouth is in neutral position to when the smile reaches its maximum extent. You extract from the database all the images containing a human face and you isolate the mouth from them. The fact that each frame depicts a different person will only make your animation more creative. All you have to do is arrange your images into the right sequence, but as the number of images to be included increases, the more time-consuming and laborious this task becomes. And what if a program existed that was capable of arranging them automatically based on their "similarity"? That is what some scientists actually did although, instead of a smile and Flickr, they used RNA and a huge international database of crystallographic images, the Protein Data Bank (PDB).

Giovanni Bussi, SISSA professor, and his colleagues are studying RNA dynamics, that is, the way this molecule takes on different forms in three-dimensional space. RNA is a molecule made up of a long chain of nucleotides (in fact, sometimes in the form of a double helix of paired strands, like DNA), which is very important in many cell processes, including gene transcription and regulation. RNA is found in many conformations, with varying dimensions and functions. Some typical, recurring structures are especially important, which is why scientists are studying them, in part in an attempt to understand how the molecule passes from one form to another. One important structure is the tetraloop, a small piece of RNA consisting of 4 nucleotides folded over to form a loop. Bussi, who coordinated the work of the first author, Sandro Bottaro, SISSA research scientist, and Alejandro Gil-Ley, SISSA student, decided to adopt a really clever technique, based on a sort of molecular stop-motion.

"We usually work with computer simulations, but in this case we started from experimental data to get a real image of the molecule", explains Bussi. "So we went through the PDB, which contains crystallographic images of a huge number of molecules. A crystallographic image is a kind of 3D image of a molecule". Bussi and colleagues searched this huge database for images of RNA and in particular for images of certain sequences formed by 4 specific nucleotides. "In general, the 'photos' depict a much larger molecule" (a bit like the case of the smile, which is generally a part of a larger portrait), explains Bottaro. "Once all the pictures had been isolated, we had the problem of sorting them". Bussi and colleagues had an ace up their sleeve. "Some time ago we devised a measure able to provide an estimate of similarity between RNA conformations" says Bussi. The results of this work had been published in a previous paper. "So it was thanks to this algorithm that we were able to arrange the images into coherent sequences".

That way, the researchers obtained animations showing the transition of the strands from an elongated conformation to a tetraloop. "The important thing is that we did it using images of observed, hence real and possible, conformations", concludes Bussi. The technique is naturally "transferable" in the sense that it can be applied to other, different RNA structures as well as to other proteins and molecules, provided that one has a sufficiently large database of images.

International School of Advanced Studies (SISSA)

Related Rna Articles:

New kind of CRISPR technology to target RNA, including RNA viruses like coronavirus
Researchers in the lab of Neville Sanjana, PhD, at the New York Genome Center and New York University have developed a new kind of CRISPR screen technology to target RNA.
Discovery of entirely new class of RNA caps in bacteria
The group of Dr. Hana Cahová of the Institute of Organic Chemistry and Biochemistry of the CAS, in collaboration with scientists from the Institute of Microbiology of the CAS, has discovered an entirely new class of dinucleoside polyphosphate 5'RNA caps in bacteria and described the function of alarmones and their mechanism of function.
New RNA mapping technique shows how RNA interacts with chromatin in the genome
A group led by scientists from the RIKEN Center for Integrative Medical Sciences (IMS) in Japan have developed a new method, RADICL-seq, which allows scientists to better understand how RNA interacts with the genome through chromatin--the structure in which the genome is organized.
Characterising RNA alterations in cancer
The largest and most comprehensive catalogue of cancer-specific RNA alterations reveals new insights into the cancer genome.
A new approach to reveal the multiple structures of RNA
The key of the extraordinary functionality of ribonucleic acid, better known as RNA, is a highly flexible and dynamic structure.
RNA modification -- Methylation and mopping up
Ludwig-Maximilian-Universitaet (LMU) in Munich researchers have discovered a novel type of chemical modification in bacterial RNAs.
New RNA molecules may play a role in aging
Using a new sequencing method, this class of previously invisible RNA molecules were found to be abundantly expressed.
AI reveals nature of RNA-protein interactions
A deep learning tool could help in structure-based drug discovery.
Uncovering the principles behind RNA folding
Using high-throughput next-generation sequencing technology, Professor Julius Lucks found similarities in the folding tendencies among a family of RNA molecules called riboswitches, which play a pivotal role in gene expression.
A new, unified pathway for prebiotic RNA synthesis
Adding to support for the RNA world hypothesis, Sidney Becker and colleagues have presented what's not been shown before -- a single chemical pathway that could generate both the purine and pyrimidine nucleosides, the key building blocks of RNA.
More RNA News and RNA Current Events

Trending Science News

Current Coronavirus (COVID-19) News

Top Science Podcasts

We have hand picked the top science podcasts of 2020.
Now Playing: TED Radio Hour

Teaching For Better Humans 2.0
More than test scores or good grades–what do kids need for the future? This hour, TED speakers explore how to help children grow into better humans, both during and after this time of crisis. Guests include educators Richard Culatta and Liz Kleinrock, psychologist Thomas Curran, and writer Jacqueline Woodson.
Now Playing: Science for the People

#556 The Power of Friendship
It's 2020 and times are tough. Maybe some of us are learning about social distancing the hard way. Maybe we just are all a little anxious. No matter what, we could probably use a friend. But what is a friend, exactly? And why do we need them so much? This week host Bethany Brookshire speaks with Lydia Denworth, author of the new book "Friendship: The Evolution, Biology, and Extraordinary Power of Life's Fundamental Bond". This episode is hosted by Bethany Brookshire, science writer from Science News.
Now Playing: Radiolab

One of the most consistent questions we get at the show is from parents who want to know which episodes are kid-friendly and which aren't. So today, we're releasing a separate feed, Radiolab for Kids. To kick it off, we're rerunning an all-time favorite episode: Space. In the 60's, space exploration was an American obsession. This hour, we chart the path from romance to increasing cynicism. We begin with Ann Druyan, widow of Carl Sagan, with a story about the Voyager expedition, true love, and a golden record that travels through space. And astrophysicist Neil de Grasse Tyson explains the Coepernican Principle, and just how insignificant we are. Support Radiolab today at