Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

New tools speed drug discovery and disease research

13.03.2003


To study the genetic components of disease, researchers rely on mice or other research models in which particular genes are silenced, or turned off. In recent years, researchers discovered that they can selectively silence genes using small pieces of RNA called siRNA (short interfering RNA).



Unfortunately, sorting out which siRNA sequences block expression of which genes has proven to be truly daunting. Researchers at Whitehead Institute, however, recently released for public use a new computational tool that will vastly improve this process, streamlining drug discovery and disease research efforts.

A Needle in a Haystack


To harness the power of siRNA, researchers need predictive tools to narrow down the search for siRNA molecules that are most likely to affect a gene in a desired way without affecting the function of other genes. Until now, hunting for siRNA candidates has been like looking for a needle in haystack. Given a gene of 3000 nucleotides, there are 2980 possible siRNA candidates that might affect how the gene functions. (siRNA sequences are approximately 21 nucleotide bases long).

The Biocomputing Group at Whitehead has greatly simplified this process by devising and publishing a web-based tool that can quickly narrow down siRNA candidates.

"Scientists routinely came to Biocomputing asking how they could more efficiently predict siRNA targets," says Lewitter. "Unfortunately, without suitable prediction tools, scientists had to randomly select siRNA strands from a pool of thousands of possibilities and hope that they would be successful in studying a gene of interest."

Faced with scientists’ mounting frustration, Biocomputing took on the challenge to develop an easy and efficient tool to predict which siRNA molecules will be effective in a particular experiment. "Using this tool, researchers can narrow down the possibilities of potential siRNAs to a small handful that are likely to be effective for studying a particular gene," says Lewitter.

To jumpstart the process, Lewitter initiated a collaboration with Tom Tuschl, a former Whitehead postdoc who had studied siRNA in David Bartel’s lab. Tuschl, who has further developed his characterization of siRNA, first at the Max Planck Institute and now at Rockefeller University, provided Biocomputing with a set of rules for determining candidate siRNAs devised from looking at many siRNA samples. These rules were based on qualities such as the size of the siRNA, its two-dimensional structure, and the components that start and stop the strands.

Using Tuschl’s rules, Bingbing Yuan of the Biocomputing Group wrote a series of computer programs that made these rules available to researchers through a simple web form. Users can enter the human or mouse genes that they are studying and specify certain criteria, and the program selects and displays potential siRNA sequences that can be used to generate a desired genetic effect. When the researcher selects a candidate, the program searches further. An email shortly appears in the user’s inbox with a weblink that shows a refined siRNA target sequence based on the candidate.

Taking it to the Bench

The web-based tool has proven to be a great resource for Whitehead scientists. For researcher David Sabatini, the web tool has streamlined his lab’s efforts to study genes that control cell growth. "Until recently, the process by which we identified siRNA candidates was arbitrary. We now have a tool that enables us to make more precise selections, which saves time, energy, and money," says Sabatini.

Responding to the growing interest in siRNA from both academic and industry scientists, the Biocomputing Group has made their technology available to the public at http://jura.wi.mit.edu/bioc/siRNA/home.php. Based solely on word of mouth, groups in Europe and Asia, as well as throughout the United States, are already flocking to the site.

But, stresses Lewitter, this is just the tip of the iceberg. "Scientists face tremendous challenges in making use of today’s new technologies," she says. "We’re trying to eliminate some of these hurdles by developing computational tools that make sense out of an otherwise overwhelming sea of data. Although we’ve made some great strides, it’s clear that we’ve only just begun."

And so the work continues. Biocomputing’s current set of siRNA web tools will be followed by improvements based on examining all known siRNA experiments. The Biocomputing group is also collaborating with Carl Novina, a postdoc in Phillip Sharp’s lab in the Biology Department at MIT, who has developed an alternative method of predicting siRNA. Based on these contributions, Biocomputing intends to improve the predictive accuracy of the tool and provide a scoring system that will rank the efficacy of possible hits.

Kelli Whitlock | EurekAlert!
Further information:
http://www.wi.mit.edu/home.html

More articles from Health and Medicine:

nachricht Norovirus evades immune system by hiding out in rare gut cells
12.10.2017 | University of Pennsylvania School of Medicine

nachricht Flexible sensors can detect movement in GI tract
11.10.2017 | Massachusetts Institute of Technology

All articles from Health and Medicine >>>

The most recent press releases about innovation >>>

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

Im Focus: Breaking: the first light from two neutron stars merging

Seven new papers describe the first-ever detection of light from a gravitational wave source. The event, caused by two neutron stars colliding and merging together, was dubbed GW170817 because it sent ripples through space-time that reached Earth on 2017 August 17. Around the world, hundreds of excited astronomers mobilized quickly and were able to observe the event using numerous telescopes, providing a wealth of new data.

Previous detections of gravitational waves have all involved the merger of two black holes, a feat that won the 2017 Nobel Prize in Physics earlier this month....

Im Focus: Smart sensors for efficient processes

Material defects in end products can quickly result in failures in many areas of industry, and have a massive impact on the safe use of their products. This is why, in the field of quality assurance, intelligent, nondestructive sensor systems play a key role. They allow testing components and parts in a rapid and cost-efficient manner without destroying the actual product or changing its surface. Experts from the Fraunhofer IZFP in Saarbrücken will be presenting two exhibits at the Blechexpo in Stuttgart from 7–10 November 2017 that allow fast, reliable, and automated characterization of materials and detection of defects (Hall 5, Booth 5306).

When quality testing uses time-consuming destructive test methods, it can result in enormous costs due to damaging or destroying the products. And given that...

Im Focus: Cold molecules on collision course

Using a new cooling technique MPQ scientists succeed at observing collisions in a dense beam of cold and slow dipolar molecules.

How do chemical reactions proceed at extremely low temperatures? The answer requires the investigation of molecular samples that are cold, dense, and slow at...

Im Focus: Shrinking the proton again!

Scientists from the Max Planck Institute of Quantum Optics, using high precision laser spectroscopy of atomic hydrogen, confirm the surprisingly small value of the proton radius determined from muonic hydrogen.

It was one of the breakthroughs of the year 2010: Laser spectroscopy of muonic hydrogen resulted in a value for the proton charge radius that was significantly...

Im Focus: New nanomaterial can extract hydrogen fuel from seawater

Hybrid material converts more sunlight and can weather seawater's harsh conditions

It's possible to produce hydrogen to power fuel cells by extracting the gas from seawater, but the electricity required to do it makes the process costly. UCF...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

ASEAN Member States discuss the future role of renewable energy

17.10.2017 | Event News

World Health Summit 2017: International experts set the course for the future of Global Health

10.10.2017 | Event News

Climate Engineering Conference 2017 Opens in Berlin

10.10.2017 | Event News

 
Latest News

Plant escape from waterlogging

17.10.2017 | Life Sciences

Study suggests oysters offer hot spot for reducing nutrient pollution

17.10.2017 | Life Sciences

Breaking: the first light from two neutron stars merging

17.10.2017 | Physics and Astronomy

VideoLinks
B2B-VideoLinks
More VideoLinks >>>