Abstract: Provided are methods of adding a polymer of non-canonical nucleotides to the 3? end of a ribonucleic acid (RNA). In certain embodiments, the methods comprise combining an RNA, a polynucleotide-3? nucleotidyl transferase, and non-canonical nucleotides, in a reaction mixture under conditions in which the polynucleotide-3? nucleotidyl transferase adds a polymer of the non-canonical nucleotides to the 3? end of the RNA. Such methods may further include analyzing the RNA using a nanopore. According to some embodiments, the methods include identifying the polymer of non-canonical nucleotides added to the 3? end of the RNA, and determining the junction between the 3? end of the RNA and the polymer of non-canonical nucleotides to identify the 3? end of the RNA. Kits that find use, e.g., in practicing the methods of the present disclosure are also provided.

Abstract: Provided are methods of adding a polymer of non-canonical nucleotides to the 3? end of a ribonucleic acid (RNA). In certain embodiments, the methods comprise combining an RNA, a polynucleotide-3? nucleotidyl transferase, and non-canonical nucleotides, in a reaction mixture under conditions in which the polynucleotide-3? nucleotidyl transferase adds a polymer of the non-canonical nucleotides to the 3? end of the RNA. Such methods may further include analyzing the RNA using a nanopore. According to some embodiments, the methods include identifying the polymer of non-canonical nucleotides added to the 3? end of the RNA, and determining the junction between the 3? end of the RNA and the polymer of non-canonical nucleotides to identify the 3? end of the RNA. Kits that find use, e.g., in practicing the methods of the present disclosure are also provided.

Abstract: The invention features an array comprising at least one set of nucleic acid probes for detection of gene products that are produced by mRNA splicing of a selected gene, wherein each probe set is specific for a selected gene, and wherein the probe set minimally comprises a splice junction probe and either an intron probe or an exon probe. The splice junction probe hybridizes specifically to a sequence corresponding to a preselected, non-genomic sequence present in a product of mRNA splicing, while the intron probe hybridizes specifically to a sequence corresponding to an intronic sequence present in unspliced mRNA. The exon probe hybridizes specifically to a sequence corresponding to an exonic sequence of the gene. The intron probe and the exon probe may each serve as an internal control. The invention also features methods of using the array to analyze mRNA splice products in a sample.

Abstract: The invention features an array comprising at least one set of nucleic acid probes for detection of gene products that are produced by mRNA splicing of a selected gene, wherein each probe set is specific for a selected gene, and wherein the probe set minimally comprises a splice junction probe and either an intron probe or an exon probe. The splice junction probe hybridizes specifically to a sequence corresponding to a preselected, non-genomic sequence present in a product of mRNA splicing, while the intron probe hybridizes specifically to a sequence corresponding to an intronic sequence present in unspliced mRNA. The exon probe hybridizes specifically to a sequence corresponding to an exonic sequence of the gene. The intron probe and the exon probe may each serve as an internal control. The invention also features methods of using the array to analyze mRNA splice products in a sample.

Abstract: A prototype RNA cyclase ribozyme that allows efficient production of circular RNA. Methods for modifying the prototype to produce a wide variety of custom circular RNA are detailed. The method utilizes a new plasmid which enables production of a wide variety of imaginable RNA sequences in a covalent, circular form free from intron sequences in vitro. At a particular site in the plasmid, a sequence coding for the desired circular RNA is inserted to create a new RNA cyclase ribozyme gene. RNA transcribed from RNA cyclase ribozyme genes autocatalytically converts the desired RNA sequence it contains into circular form. RNA cyclase genes may be placed into appropriate expression vectors for synthesis of circular RNA in vivo as part of ribozyme or antisense gene regulation approaches to genetic engineering.