Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

The structure-based design of zinc finger nucleases can facilitate genomic editing

20.05.2011
A recent study of significant research value carried out at the State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China-Research, and published in the May 2011 issue of Science China Life Sciences (Issue 54) described a novel method using FoldX force field based protein modeling that can be applied in zinc finger nucleases design.

Zinc finger nucleases (ZFNs) can actively introduce a double-strand break (DSB) at target loci in eukaryotic genomes and this can improve the efficiency of gene knock-out or knock-in by several orders of magnitude. Therefore, ZFN is becoming a promising novel tool for genomic editing.

However, most current strategies for developing zinc finger nucleases with customized sequence specificities require the construction of numerous tandem arrays of zinc finger proteins (ZFPs), and the subsequent large-scale in vitro validation of their DNA binding affinities and specificities using bacterial selection. The labor and expertise required in this complex process limits the broad adoption of the ZFN technology.

In this work, an effective computational assisted design strategy was introduced to lower the complexity of the production of a pair of functional ZFNs. Dr. He and Prof. Chen used the FoldX force field to build 3D models of 420 ZFP-DNA complexes based on zinc finger arrays developed by the Zinc Finger Consortium using OPEN (oligomerized pool engineering). Using nonlinear and linear regression analysis, they found that the calculated protein-DNA binding energy in a modeled ZFP-DNA complex strongly correlates to the failure rate of the zinc finger array to show significant ZFN activity in human cells. In their models, less than 5% of the three-finger arrays with calculated protein-DNA binding energies lower than -13.132 kcal mol−1 failed to form active ZFNs in human cells. By contrast, for arrays with calculated protein-DNA binding energies higher than -5 kcal mol−1, as many as 40% of them lacked ZFN activity in human cells. Therefore, the FoldX force field based ZFN design strategy can be effectively used to reduce the failure rate and to increase efficiency in producing customized ZFNs.

"This is a novel strategy for designing customized ZFN pairs. It enables us to predict whether a candidate ZFN can function well in mammalian cells by calculating the protein-DNA binding energy within the modeled complex." was the opinion of one journal reviewer. "The authors tried a new method based on the FlodX force field to overcome the complex screening process in ZFN design. It appeared to be helpful to the rapid developed ZFN technology." commented another reviewer.

The authors are affiliated to The State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China. The group mainly focuses on unraveling the genetic basis of economic traits and disease resistant capabilities in swine using comprehensive strategies that include the generation of transgenic or gene knock-out pig models.

Funding for the project was provided by the National Natural Science Foundation of China (Grant No. 30901018) and the China Postdoctoral Science Foundation (Grant No. 201003388).

Reference: He Z Y, Mei G, Zhao C P, et al. Potential application of FoldX force field based protein modeling in zinc finger nucleases design. Sci China Life Sci, 2011, 54: 1-8, doi: 10.1007/s11427-011-4159-9

ZuYong He | EurekAlert!
Further information:
http://zh.scichina.com/english/

More articles from Studies and Analyses:

nachricht The importance of biodiversity in forests could increase due to climate change
17.11.2017 | Deutsches Zentrum für integrative Biodiversitätsforschung (iDiv) Halle-Jena-Leipzig

nachricht Win-win strategies for climate and food security
02.10.2017 | International Institute for Applied Systems Analysis (IIASA)

All articles from Studies and Analyses >>>

The most recent press releases about innovation >>>

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

Im Focus: Nanoparticles help with malaria diagnosis – new rapid test in development

The WHO reports an estimated 429,000 malaria deaths each year. The disease mostly affects tropical and subtropical regions and in particular the African continent. The Fraunhofer Institute for Silicate Research ISC teamed up with the Fraunhofer Institute for Molecular Biology and Applied Ecology IME and the Institute of Tropical Medicine at the University of Tübingen for a new test method to detect malaria parasites in blood. The idea of the research project “NanoFRET” is to develop a highly sensitive and reliable rapid diagnostic test so that patient treatment can begin as early as possible.

Malaria is caused by parasites transmitted by mosquito bite. The most dangerous form of malaria is malaria tropica. Left untreated, it is fatal in most cases....

Im Focus: A “cosmic snake” reveals the structure of remote galaxies

The formation of stars in distant galaxies is still largely unexplored. For the first time, astron-omers at the University of Geneva have now been able to closely observe a star system six billion light-years away. In doing so, they are confirming earlier simulations made by the University of Zurich. One special effect is made possible by the multiple reflections of images that run through the cosmos like a snake.

Today, astronomers have a pretty accurate idea of how stars were formed in the recent cosmic past. But do these laws also apply to older galaxies? For around a...

Im Focus: Visual intelligence is not the same as IQ

Just because someone is smart and well-motivated doesn't mean he or she can learn the visual skills needed to excel at tasks like matching fingerprints, interpreting medical X-rays, keeping track of aircraft on radar displays or forensic face matching.

That is the implication of a new study which shows for the first time that there is a broad range of differences in people's visual ability and that these...

Im Focus: Novel Nano-CT device creates high-resolution 3D-X-rays of tiny velvet worm legs

Computer Tomography (CT) is a standard procedure in hospitals, but so far, the technology has not been suitable for imaging extremely small objects. In PNAS, a team from the Technical University of Munich (TUM) describes a Nano-CT device that creates three-dimensional x-ray images at resolutions up to 100 nanometers. The first test application: Together with colleagues from the University of Kassel and Helmholtz-Zentrum Geesthacht the researchers analyzed the locomotory system of a velvet worm.

During a CT analysis, the object under investigation is x-rayed and a detector measures the respective amount of radiation absorbed from various angles....

Im Focus: Researchers Develop Data Bus for Quantum Computer

The quantum world is fragile; error correction codes are needed to protect the information stored in a quantum object from the deteriorating effects of noise. Quantum physicists in Innsbruck have developed a protocol to pass quantum information between differently encoded building blocks of a future quantum computer, such as processors and memories. Scientists may use this protocol in the future to build a data bus for quantum computers. The researchers have published their work in the journal Nature Communications.

Future quantum computers will be able to solve problems where conventional computers fail today. We are still far away from any large-scale implementation,...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Ecology Across Borders: International conference brings together 1,500 ecologists

15.11.2017 | Event News

Road into laboratory: Users discuss biaxial fatigue-testing for car and truck wheel

15.11.2017 | Event News

#Berlin5GWeek: The right network for Industry 4.0

30.10.2017 | Event News

 
Latest News

Corporate coworking as a driver of innovation

22.11.2017 | Business and Finance

PPPL scientists deliver new high-resolution diagnostic to national laser facility

22.11.2017 | Physics and Astronomy

Quantum optics allows us to abandon expensive lasers in spectroscopy

22.11.2017 | Physics and Astronomy

VideoLinks
B2B-VideoLinks
More VideoLinks >>>