Molecular scaffolding is ubiquitous in biology. Scaffolding facilitates enzymatic or physical reactions by tethering reactants in close proximity. Theoretically, molecular scaffolding enables complex chemical cascades that may not occur if a standard 3D search for reactants is required. Despite the pervasiveness of scaffolding in natural biological systems, scaffolding had been thus far underutilized in synthetic biology due to an insufficient understanding of the modular parts, which limits our ability to assemble these parts into functional units.
In recent years, we have studied RNA molecular scaffolds. Unlike DNA, RNA can provide a structurally flexible programmable scaffold. In order learn how to reliably construct functional molecular scaffolds, a systematic characterization of the sequence-structure-function relationship encoded within scaffold modules is needed. We take advantage of modern DNA synthesis technology and in vivo transcription to generate large libraries of RNA sequence variants, and to simultaneously explore many different structural variants.
Overcoming the design, build, test bottleneck for synthesis of nonrepetitive protein-RNA cassettes
Noa Katz, Eitamar Tripto, Naor Granik, Sarah Goldberg, Orna Atar, Zohar Yakhini, Yaron Orenstein and Roee Amit. Nature Communications (2021).
Synthetic 5’ UTRs can either up- or down-regulate expression upon RBP binding
Katz, Noa, Roni Cohen, Oz Solomon, Beate Kaufmann, Orna Atar, Zohar Yakhini, Sarah Goldberg, and Roee Amit. Cell Systems (2019).
An in Vivo Binding Assay for RNA-Binding Proteins Based on Repression of a Reporter Gene
Katz, Noa, Roni Cohen, Oz Solomon, Beate Kaufmann, Orna Atar, Zohar Yakhini, Sarah Goldberg, and Roee Amit. ACS Synthetic Biology (2018).