title: Caged oligonucleotides for studying biological systems.
abstract: Light-activated ("caged") compounds have been widely employed for studying biological processes with high spatial and temporal control. In the past decade, several new approaches for caging the structure and function of DNA and RNA oligonucleotides have been developed. This review focuses on caged oligonucleotides that incorporate site-specifically one or two photocleavable linkers, whose photolysis yields oligonucleotides with dramatic structural and functional changes. This technique has been employed by our laboratory and others to photoregulate gene expression in cells and living organisms, typically using near UV-activated organic chromophores. To improve capabilities for in vivo studies, we harnessed the rich inorganic photochemistry of ruthenium bipyridyl complexes to synthesize Ru-caged morpholino antisense oligonucleotides that remain inactive in zebrafish embryos until uncaged with visible light. Expanding into new caged oligonucleotide applications, our lab has developed Transcriptome In Vivo Analysis (TIVA) technology, which provides the first noninvasive, unbiased method for isolating mRNA from single neurons in brain tissues. TIVA-isolated mRNA can be amplified and then analyzed using next-generation sequencing (RNA-seq).
authors: Department of Chemistry, University of Pennsylvania, 231S. 34th Street, Philadelphia, PA 19104, United States.
authors: Brittani K
authors: BK
authors: Ruble
authors: Department of Chemistry, University of Pennsylvania, 231S. 34th Street, Philadelphia, PA 19104, United States.
authors: Sean B
authors: SB
authors: Yeldell
authors: Department of Chemistry, University of Pennsylvania, 231S. 34th Street, Philadelphia, PA 19104, United States. Electronic address: ivandmo@sas.upenn.edu.
authors: Ivan J
authors: IJ
authors: Dmochowski
mesh_terms: D000818:Animals; D001921:Brain / Q000378:metabolism; D056831:Coordination Complexes / Q000737:chemistry* / Q000528:radiation effects; D004625:Embryo, Nonmammalian; D020869:Gene Expression Profiling; D006801:Humans; D008027:Light; D035683:MicroRNAs / Q000235:genetics / Q000528:radiation effects; D009690:Nucleic Acid Conformation; D009693:Nucleic Acid Hybridization; D016376:Oligonucleotides, Antisense / Q000235:genetics* / Q000528:radiation effects; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D012428:Ruthenium / Q000737:chemistry*; D015027:Zebrafish
chemical_list: D056831:Coordination Complexes; D035683:MicroRNAs; D016376:Oligonucleotides, Antisense; D012333:RNA, Messenger; D012428:Ruthenium
keywords: Caging chemistry; Light-activated oligonucleotides; Ruthenium photolinkers; Transcriptome In Vivo Analysis