Abstract: An RNA probe containing RNA functional structural units is prepared by the following steps: (1) recognizing one or more stem structures contained in the RNA based on RNA sequence information; (2) extracting a motif region with reference to the one or more recognized stem structures; (3) adding an assistive stem region to the extracted motif region; and (4) adding a barcode region, which represents a complementary sequence to a DNA barcode sequence, to the assistive stem region. Also provided is a method for detecting a protein-binding RNA by using an RNA probe containing RNA functional structural units.

Abstract: Provided is a method for analyzing a higher-order structure of RNA, the method comprising the steps of: (a) preparing one or a plurality of RNA probes, each comprising an RNA to be analyzed attached to a barcode sequence; (b) contacting the RNA probes and an RNA modification reagent; and (c) detecting a position and a frequency of modified nucleotides in a sequence of the RNA probe obtained in step (b), wherein each of the barcode sequences has a structure that has a reduced reactivity with the RNA modification reagent. The method improves the accuracy of detecting mutations, insertions, and deletions, etc., of a base introduced when carrying out mutation profiling using an RNA library.

Abstract: The present disclosure provides a technique for efficiently detecting a wider variety of RNA higher-order structures including non-Watson-Crick base pair-type higher order structures. The method for analyzing the RNA higher-order structure according to the present disclosure comprises the steps of providing a compound in which a target-binding moiety Sm and an RNA-modifying moiety Y are linked by a linker L; contacting the compound and one or a plurality of RNAs; determining a nucleotide sequence of the RNA after contacting with the compound; and determining a position and/or a region on the RNA that interacts with the target binding moiety of the compound, based on the nucleotide sequence.

Abstract: An RNA probe containing RNA functional structural units is prepared by the following steps: (1) recognizing one or more stem structures contained in the RNA based on RNA sequence information; (2) extracting a motif region with reference to the one or more recognized stem structures; (3) adding an assistive stem region to the extracted motif region; and (4) adding a barcode region, which represents a complementary sequence to a DNA barcode sequence, to the assistive stem region. Also provided is a method for detecting a protein-binding RNA by using an RNA probe containing RNA functional structural units.