CARBP Project

Overcoming the design, build, test (DBT) bottleneck for synthesis of nonrepetitive protein-RNA binding cassettes for RNA applications

CARBP

CARBP is a tool for the design of RNA cassettes containing multiple binding sites for RNA-binding proteins (RBPs). These cassettes can be used for many different applications, such as in vivo tagging of mRNAs [1], and scaffolding of enzymes for improved yield of enzymatic reactions [2].

Binding Sites Data

CARBP RNA Generator generates RNA cassettes for RNA-binding coat proteins of bacteriophages PP7, MS2, and Qbeta. The cassettes incorporate binding sites from two sources: sites that were evaluated experimentally, and sites identified algorithmically by applying machine learning (ML) to the experimental dataset. The experiment, ML, and scoring are described in our publication [3].

References

  1. In the right place at the right time: visualizing and understanding mRNA localization, Buxbaum, A., Haimovich, G. and Singer, R., Nat Rev Mol Cell Biol 16, 95–109 (2015)
  2. Organization of Intracellular Reactions with Rationally Designed RNA Assemblies, Delebecque, C. J., Lindner, A. B. , Silver P. A. and Aldaye, F. A., Science 333 (6041), 470-474 (2011)
  3. Overcoming the design, build, test (DBT) bottleneck for synthesis of nonrepetitive protein-RNA binding cassettes for RNA applications, Katz, N., Tripto, E., Goldberg, S., Atar, O., Yakhini, Z., Orenstein, Y. and Amit. R.

Project Funding

This project has received funding from the European Union's Horizon 2020 research and Innovation program under grant agreement 851065 (CARBP).

CARBP website was created by Avishay Bikowsky