| CPC C12Q 1/6804 (2013.01) | 15 Claims |
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1. A method for detecting one or more non-canonical features of RNA in a plurality of target nucleic acids, the method comprising:
(a) contacting the target nucleic acids with a nucleic acid-binding molecule comprising:
a binding domain, and
an adapter,
wherein the binding domain binds specifically to a non-canonical feature of an RNA; and
wherein the adapter comprises a nucleic acid barcode sequence unique to the non-canonical feature bound specifically by the binding domain;
(b) transferring the nucleic acid barcode of the adapter to the target nucleic acids to generate barcoded target nucleic acids, in an environment that substantially prevents off-target generation of barcoded nucleic acids; and
(c) sequencing the barcoded target nucleic acids,
wherein the nucleic acid-binding molecule is coupled to a surface of a substrate and is spatially separated from other nucleic acid-binding molecules, such that each target nucleic acid can only contact one nucleic acid-binding molecule, or wherein the target nucleic acids are coupled to the surface of the substrate and each coupled target nucleic acid is spatially separated from other target nucleic acids, such that each coupled target nucleic acid can only contact one nucleic acid-binding molecule, and
wherein the nucleic acid barcode is transferred to the target nucleic acid enzymatically by single stranded ligation, splint ligation, primer extension, reverse transcription, or double-stranded ligation.
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