RNA structure library

Patent metadata

Field	Value
Publication number	US-12091775-B2
Application number	US-201716313329-A
Country	US
Kind code	B2
Filing date	Jun 27, 2017
Priority date	Jun 27, 2016
Publication date	Sep 17, 2024
Grant date	Sep 17, 2024

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.

First claim

The invention claimed is:

1. A method for preparing an RNA probe, comprising the following steps:
(1) recognizing one or more stem structures contained in an RNA based on RNA sequence information, and selecting an RNA containing a plurality of stem-loop structures;
(2) extracting a plurality of RNA structures having a multi-branched loop from the RNA selected in the step (1), comprising the following steps (2a) to (2d):
(2a) selecting one stem-loop structure from the RNA selected in the step (1) and recording the stem-loop structure;
(2b) replacing the one stem-loop structure selected in the step (2a) with a single-stranded structure;
(2c) changing the selected stem-loop structure and repeating the steps (2a) and (2b) until the RNA is in a single single-stranded structure;
(2d) restoring the single single-stranded structure by all of the stem-loop structures recorded in the step (2a) or restoring a portion of the single single-stranded structure by one or more of the stem structures recorded in the step (2a);
(3) adding a first assistive stem portion sequence and a second assistive stem portion sequence to each of the extracted plurality of RNA structures having a multi-branched loop, wherein the second assistive stem portion sequence is complementary to the first assistive stem portion sequence and hybridizes to the first assistive stem portion sequence to form a double-stranded assistive stem;
(4) adding a barcode region, which represents a complementary sequence to a DNA barcode sequence, to the assistive stem region; and
(5) synthesizing the RNA probe determined by the steps (1) to (4), wherein the RNA probe reflects a functional structural unit.

Assignees

• Univ Kyoto

Inventors

• Saito Hirohide
• Komatsu Kaoru Richard

Classifications

• C12Q1/6811

  Selection methods for production or design of target specific oligonucleotides or binding molecules · CPC title

• C40B20/04 Primary

  Identifying library members by means of a tag, label, or other readable or detectable entity associated with the library members, e.g. decoding processes · CPC title

• C12Q1/6876

  Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes · CPC title

• C12N15/09

  Recombinant DNA-technology · CPC title

• C12N15/1065

  Preparation or screening of tagged libraries, e.g. tagged microorganisms by STM-mutagenesis, tagged polynucleotides, gene tags · CPC title