Rna microarray for detecting interaction between protein and rna containing a higher-order structure

A method for detecting RNA which binds to a substance, comprising the following steps:

• (1) a step of bringing a multiplicity of RNA probes into contact with a target substance,
• wherein each RNA probe in the multiplicity of RNA probes comprises:
• (i) a complementary strand sequence to each respective DNA barcode sequence in a multiplicity of DNA barcode sequences;
• (ii) a double stranded stem structure comprising a first stem portion complementary to and hybridized with a second stem portion;
• and
• (iii) a sequence of a loop portion linking said first and second stem portions,
• wherein each RNA probe is hybridized to each respective complementary DNA barcode sequence in the multiplicity of DNA barcode sequences;
• and wherein a combination of the sequence (i) and (iii) is different in the multiplicity of RNA probes so that each of the sequence (iii) in the multiplicity of RNA probes sequence can be identified by the corresponding sequence (i), and the sequence (ii) has a common sequence in the multiplicity of RNA probes,
• wherein the multiplicity of DNA barcode sequences is selected from a tag, a zip code, an orthonormal sequence or a barcode sequence so as to prevent cross-hybridization reaction;
• (2) a step of isolating the target substance bound to an RNA probe obtained in step (1) while maintaining binding to the RNA probe,
• (3) a step of extracting the RNA probe from the target substance obtained in step (2),
• (4) a step of bringing the RNA probe obtained in step (3) into contact with a slide having the multiplicity of DNA barcode sequences attached thereto,
• (5) a step of identifying the RNA probe hybridized with the slide, and
• (6) a step of detecting RNA containing the sequence (iii) contained in the RNA probe identified in step (5) as the RNA which binds to the target substance.