Conditionally Activated (Caged) Oligonucleotides

Conditionally activated (caged) oligonucleotides provide useful spatiotemporal control for studying dynamic biological processes, e.g., regulating in vivo gene expression or probing specific oligonucleotide targets. This review summarizes recent advances in caging strategies, which involve different stimuli in the activation step. Oligo cyclization is a particularly attractive caging strategy, which simplifies the probe design and affords oligo stabilization. Our laboratory developed an efficient synthesis for circular caged oligos, and a circular caged antisense DNA oligo was successfully applied in gene regulation. A second technology is Transcriptome In Vivo Analysis (TIVA), where caged oligos enable mRNA isolation from single cells in living tissue. We highlight our development of TIVA probes with improved caging stability. Finally, we illustrate the first protease-activated oligo probe, which was designed for caspase-3. This expands the toolkit for investigating the transcriptome under a specific physiologic condition (e.g., apoptosis), particularly in specimens where light activation is impractical.

Automated summary

This review presents recent advances in caging strategies for oligonucleotides, with a focus on oligo cyclization as an attractive approach. It also discusses the application of circular caged oligos in gene regulation and in Transcriptome In Vivo Analysis (TIVA) for mRNA isolation. Additionally, it introduces a protease-activated oligo probe designed for caspase-3, expanding the toolkit for studying the transcriptome under specific physiologic conditions.