Volume 23, Issue 21 e202200374
Research Article

Bicyclic Caged Morpholino Oligonucleotides for Optical Gene Silencing**

Dr. Sankha Pattanayak

Dr. Sankha Pattanayak

Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305 USA

Present Address, Creyon Bio, Inc., San Diego, CA 92121 USA

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Dr. Bhagyesh R. Sarode

Dr. Bhagyesh R. Sarode

Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305 USA

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Prof. Dr. Alexander Deiters

Prof. Dr. Alexander Deiters

Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260 USA

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Prof. Dr. James K. Chen

Corresponding Author

Prof. Dr. James K. Chen

Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305 USA

Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305 USA

Department of Chemistry, Stanford University, Stanford, CA 94305 USA

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First published: 06 September 2022
Citations: 4
**

A previous version of this manuscript has been deposited on a preprint server (https://doi.org/10.26434/chemrxiv-2022-z6shp).

Graphical Abstract

Caged morpholino oligonucleotides allow light-dependent gene silencing in whole organisms. In this study, a new type of caged morpholino with a bicyclic geometry was developed. Ultraviolet light linearizes the bicyclic structure through self-immolative linker cleavage, leading to targeted RNA silencing in zebrafish embryos.

Abstract

Caged morpholino oligonucleotides (cMOs) are synthetic tools that allow light-inducible gene silencing in live organisms. Previously reported cMOs have utilized hairpin, duplex, and cyclic structures, as well as caged nucleobases. While these antisense technologies enable efficient optical control of RNA splicing and translation, they can have limited dynamic range. A new caging strategy was developed where the two MO termini are conjugated to an internal position through a self-immolative trifunctional linker, thereby generating a bicyclic cMO that is conformationally resistant to RNA binding. The efficacy of this alternative cMO design has been demonstrated in zebrafish embryos and compared to linear MOs and monocyclic constructs.

Conflict of interest

The authors declare no conflict of interest.

Data Availability Statement

The data that support the findings of this study are available from the corresponding author upon reasonable request.