Nat Kolber

All Publications

• Sequence-Independent RNA Sensing in Living Mammalian Cells. bioRxiv : the preprint server for biology Kolber, N. S., Kaseniit, K. E., Lanz, T. V., Robinson, W. H., Gao, X. J. 2025

  Abstract

  Recently, several groups described sensors in living cells that take advantage of adenosine deaminases acting on RNA (ADARs) to link the presence of an RNA (a "target transcript") to the translation of a payload from a second, exogenously introduced mRNA. These sensors share the key mechanism of editing a stop codon opposite a specific sequence motif in the target transcript, where this motif requirement is dictated by ADAR's strong sequence preference. This constrains sensor design and precludes the sensing of short sequences that lack such motifs, often essential for key applications such as sensing viral RNAs and differentiating splice isoforms. Here we address this limitation with modular RNA sensors using adenosine deaminases acting on RNA ("modulADAR"). ModulADAR features two key elements that mirror the modularity of ADARs: regions that hybridize with the target transcript to recruit ADAR's dsRNA-binding domains, and a stem-loop for stop-codon editing by ADAR's catalytic domain. We optimize modulADAR and apply it to detect short subsequences that cannot be sensed by prior-generation sensors. We anticipate that modulADAR will empower broader basic science and therapeutic applications, especially those that will uniquely benefit from programmable RNA detection in living cells.

  View details for DOI 10.1101/2025.09.18.677213

  View details for PubMedID 41000785

  View details for PubMedCentralID PMC12458216

• Cell-Type Specific In Vivo Delivery Using RNA Sensors Kolber, N., Kaseniit, E., Katz, N., Wolfsberg, E., Zhang, M., Gao, X. CELL PRESS. 2024: 889

  View details for Web of Science ID 001332783403328

• Author Correction: Modular, programmable RNA sensing using ADAR editing in living cells. Nature biotechnology Kaseniit, K. E., Katz, N., Kolber, N. S., Call, C. C., Wengier, D. L., Cody, W. B., Sattely, E. S., Gao, X. J. 2022

  View details for DOI 10.1038/s41587-022-01617-3

  View details for PubMedID 36418591

• Modular, programmable RNA sensing using ADAR editing in living cells. Nature biotechnology Kaseniit, K. E., Katz, N., Kolber, N. S., Call, C. C., Wengier, D. L., Cody, W. B., Sattely, E. S., Gao, X. J. 2022

  Abstract

  With the increasing availability of single-cell transcriptomes, RNA signatures offer a promising basis for targeting living cells. Molecular RNA sensors would enable the study of and therapeutic interventions for specific cell types/states in diverse contexts, particularly in human patients and non-model organisms. Here we describe a modular, programmable system for live RNA sensing using adenosine deaminases acting on RNA (RADAR). We validate, and then expand, our basic design, characterize its performance, and analyze its compatibility with human and mouse transcriptomes. We identify strategies to boost output levels and improve the dynamic range. Additionally, we show that RADAR enables compact AND logic. In addition to responding to transcript levels, RADAR can distinguish disease-relevant sequence alterations of transcript identities, such as point mutations and fusions. Finally, we demonstrate that RADAR is a self-contained system with the potential to function in diverse organisms.

  View details for DOI 10.1038/s41587-022-01493-x

  View details for PubMedID 36198772

• Orthogonal translation enables heterologous ribosome engineering in E. coli. Nature communications Kolber, N. S., Fattal, R., Bratulic, S., Carver, G. D., Badran, A. H. 2021; 12 (1): 599

  Abstract

  The ribosome represents a promising avenue for synthetic biology, but its complexity and essentiality have hindered significant engineering efforts. Heterologous ribosomes, comprising rRNAs and r-proteins derived from different microorganisms, may offer opportunities for novel translational functions. Such heterologous ribosomes have previously been evaluated in E. coli via complementation of a genomic ribosome deficiency, but this method fails to guide the engineering of refractory ribosomes. Here, we implement orthogonal ribosome binding site (RBS):antiRBS pairs, in which engineered ribosomes are directed to researcher-defined transcripts, to inform requirements for heterologous ribosome functionality. We discover that optimized rRNA processing and supplementation with cognate r-proteins enhances heterologous ribosome function for rRNAs derived from organisms with ≥76.1% 16S rRNA identity to E. coli. Additionally, some heterologous ribosomes undergo reduced subunit exchange with E. coli-derived subunits. Cumulatively, this work provides a general framework for heterologous ribosome engineering in living cells.

  View details for DOI 10.1038/s41467-020-20759-z

  View details for PubMedID 33500394