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Interactive web-based tool for the design of multi-RNA binding protein binding site cassettes

Project description

Novel multi-RNA binding tool to boost synthetic biology research

In a lock-and-key fashion, RNA-binding proteins bind RNA at one or more RNA-binding domains to modulate gene expression by altering RNA processing and translation. Hundreds of 'keys' have been discovered over the years and recent studies have revealed even more. Characterising their interaction and subsequent biological implications is a huge area of research expected to reveal previously unidentified structures and functions for numerous applications. CARBP is supporting that effort with software to quickly and intelligently design RNA-binding domains and create synthetic DNA libraries. The software will be part of a suite of web-based tools that could tremendously increase the rate of discovery, depth of understanding and ultimate utility of novel molecules involved in gene expression.


DNA synthesis technology has greatly developed over recent years, serving a growing multi-billion synthetic DNA market. Synthetic DNA is used in projects that optimize reagents, chemicals, crops and other organisms, in projects seeking to increase the manufacturing efficiency for the above, as well as in studies of molecular regulation and other cellular processes. The latter is the focus of the MRG-GRammar H2020 FET project.
As the market and application range for synthetic DNA expand a need arises to test and quality control raw synthetic nucleic acids as well as products built upon such reagents. We have developed a prototype software tool for assessing quality parameters in synthetic DNA libraries and used it in several projects in the framework of MRG-GRammar
We propose to productize this prototype into a stable version that will be availed to a broader synthetic biology community. Our proposed product, CARBP, is a software system that enables design of RNA binding protein binding sites cassettes for various applications in biological imaging and synthetic biology. Requested funding will be used to improve usability and user interface, to expand the implementation of analysis and statistical tools, to produce a stable version available to the scientific community and to commercial entities and, finally, to investigate potential sustainable mechanisms for supporting continued service, including commercial or service models. CARBP will form part of a suite of interactive web-based tools whose purpose will be to accelerate the development of the nascent synthetic biology industry sector, by making advanced molecular technologies available to various users at a push of a button.

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Net EU contribution
€ 68 750,00
Senate building technion city
32000 Haifa

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Activity type
Higher or Secondary Education Establishments
Other funding
€ 0,00

Participants (1)