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 Correct connections are crucial
26.06.2017 | Charité - Universitätsmedizin Berlin

nachricht One gene closer to regenerative therapy for muscular disorders
01.06.2017 | Cincinnati Children's Hospital Medical Center

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: Can we see monkeys from space? Emerging technologies to map biodiversity

An international team of scientists has proposed a new multi-disciplinary approach in which an array of new technologies will allow us to map biodiversity and the risks that wildlife is facing at the scale of whole landscapes. The findings are published in Nature Ecology and Evolution. This international research is led by the Kunming Institute of Zoology from China, University of East Anglia, University of Leicester and the Leibniz Institute for Zoo and Wildlife Research.

Using a combination of satellite and ground data, the team proposes that it is now possible to map biodiversity with an accuracy that has not been previously...

Im Focus: Climate satellite: Tracking methane with robust laser technology

Heatwaves in the Arctic, longer periods of vegetation in Europe, severe floods in West Africa – starting in 2021, scientists want to explore the emissions of the greenhouse gas methane with the German-French satellite MERLIN. This is made possible by a new robust laser system of the Fraunhofer Institute for Laser Technology ILT in Aachen, which achieves unprecedented measurement accuracy.

Methane is primarily the result of the decomposition of organic matter. The gas has a 25 times greater warming potential than carbon dioxide, but is not as...

Im Focus: How protons move through a fuel cell

Hydrogen is regarded as the energy source of the future: It is produced with solar power and can be used to generate heat and electricity in fuel cells. Empa researchers have now succeeded in decoding the movement of hydrogen ions in crystals – a key step towards more efficient energy conversion in the hydrogen industry of tomorrow.

As charge carriers, electrons and ions play the leading role in electrochemical energy storage devices and converters such as batteries and fuel cells. Proton...

Im Focus: A unique data centre for cosmological simulations

Scientists from the Excellence Cluster Universe at the Ludwig-Maximilians-Universität Munich have establised "Cosmowebportal", a unique data centre for cosmological simulations located at the Leibniz Supercomputing Centre (LRZ) of the Bavarian Academy of Sciences. The complete results of a series of large hydrodynamical cosmological simulations are available, with data volumes typically exceeding several hundred terabytes. Scientists worldwide can interactively explore these complex simulations via a web interface and directly access the results.

With current telescopes, scientists can observe our Universe’s galaxies and galaxy clusters and their distribution along an invisible cosmic web. From the...

Im Focus: Scientists develop molecular thermometer for contactless measurement using infrared light

Temperature measurements possible even on the smallest scale / Molecular ruby for use in material sciences, biology, and medicine

Chemists at Johannes Gutenberg University Mainz (JGU) in cooperation with researchers of the German Federal Institute for Materials Research and Testing (BAM)...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Plants are networkers

19.06.2017 | Event News

Digital Survival Training for Executives

13.06.2017 | Event News

Global Learning Council Summit 2017

13.06.2017 | Event News

 
Latest News

Study shines light on brain cells that coordinate movement

26.06.2017 | Life Sciences

Smooth propagation of spin waves using gold

26.06.2017 | Physics and Astronomy

Switchable DNA mini-machines store information

26.06.2017 | Information Technology

VideoLinks
B2B-VideoLinks
More VideoLinks >>>