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 Oxygen can wake up dormant bacteria for antibiotic attacks
08.12.2016 | Penn State

nachricht NTU scientists build new ultrasound device using 3-D printing technology
07.12.2016 | Nanyang Technological University

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: Significantly more productivity in USP lasers

In recent years, lasers with ultrashort pulses (USP) down to the femtosecond range have become established on an industrial scale. They could advance some applications with the much-lauded “cold ablation” – if that meant they would then achieve more throughput. A new generation of process engineering that will address this issue in particular will be discussed at the “4th UKP Workshop – Ultrafast Laser Technology” in April 2017.

Even back in the 1990s, scientists were comparing materials processing with nanosecond, picosecond and femtosesecond pulses. The result was surprising:...

Im Focus: Shape matters when light meets atom

Mapping the interaction of a single atom with a single photon may inform design of quantum devices

Have you ever wondered how you see the world? Vision is about photons of light, which are packets of energy, interacting with the atoms or molecules in what...

Im Focus: Novel silicon etching technique crafts 3-D gradient refractive index micro-optics

A multi-institutional research collaboration has created a novel approach for fabricating three-dimensional micro-optics through the shape-defined formation of porous silicon (PSi), with broad impacts in integrated optoelectronics, imaging, and photovoltaics.

Working with colleagues at Stanford and The Dow Chemical Company, researchers at the University of Illinois at Urbana-Champaign fabricated 3-D birefringent...

Im Focus: Quantum Particles Form Droplets

In experiments with magnetic atoms conducted at extremely low temperatures, scientists have demonstrated a unique phase of matter: The atoms form a new type of quantum liquid or quantum droplet state. These so called quantum droplets may preserve their form in absence of external confinement because of quantum effects. The joint team of experimental physicists from Innsbruck and theoretical physicists from Hannover report on their findings in the journal Physical Review X.

“Our Quantum droplets are in the gas phase but they still drop like a rock,” explains experimental physicist Francesca Ferlaino when talking about the...

Im Focus: MADMAX: Max Planck Institute for Physics takes up axion research

The Max Planck Institute for Physics (MPP) is opening up a new research field. A workshop from November 21 - 22, 2016 will mark the start of activities for an innovative axion experiment. Axions are still only purely hypothetical particles. Their detection could solve two fundamental problems in particle physics: What dark matter consists of and why it has not yet been possible to directly observe a CP violation for the strong interaction.

The “MADMAX” project is the MPP’s commitment to axion research. Axions are so far only a theoretical prediction and are difficult to detect: on the one hand,...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

ICTM Conference 2017: Production technology for turbomachine manufacturing of the future

16.11.2016 | Event News

Innovation Day Laser Technology – Laser Additive Manufacturing

01.11.2016 | Event News

#IC2S2: When Social Science meets Computer Science - GESIS will host the IC2S2 conference 2017

14.10.2016 | Event News

 
Latest News

Closing the carbon loop

08.12.2016 | Life Sciences

Applicability of dynamic facilitation theory to binary hard disk systems

08.12.2016 | Physics and Astronomy

Scientists track chemical and structural evolution of catalytic nanoparticles in 3-D

08.12.2016 | Materials Sciences

VideoLinks
B2B-VideoLinks
More VideoLinks >>>