US 2013/0158884 A1 · METHOD FOR IDENTIFYING NUCLEOTIDE SEQUENCE, METHOD FOR ACQUIRING SECONDARY STRUCTURE OF NUCLEIC ACID MOLECULE, APPARATUS FOR IDENTIFYING NUCLEOTIDE SEQUENCE, APPARATUS FOR ACQUIRING SECONDARY STRUCTURE OF NUCLEIC ACID MOLECULE, PROGRAM FOR IDENTIFYING NUCLEOTIDE SEQUENCE, AND PROGRAM FOR ACQUIRING SECONDARY STRUCTURE OF NUCLEIC ACID MOLECULE

Abstract

The object of the present invention is to provide a method for identifying a nucleotide sequence necessary for expressing affinity for a target substance with respect to a nucleotide sequence of a nucleic acid molecule such as an aptamer having such affinity for the target substance, based on similarity between nucleotide sequences and an evaluated value of the affinity of the nucleotide sequence, and a method for predicting a secondary structure of the nucleic acid molecule including the identified nucleotide sequence. The method of present invention includes the steps of extracting a single-stranded region by excluding based capable of forming a stem structure from the nucleotide sequence of the nucleic acid molecule; and searching a motif sequence from the single-stranded region, based on an evaluated value of the affinity.

Claims20

Dependent claims

A method for preparing nucleic acids, comprising the step of screening the nucleic acids by identifying a region within a nucleic acid molecule that binds to a target substance;

wherein the method for identifying the region comprising the steps of:
(1) extracting data of a single-stranded region, by excluding bases capable of forming a stem structure from the sequence of the nucleic acid molecule;
and
(2) searching a motif sequence from the single-stranded region, by weighing the appearance frequency of a specific sequence in the extracted data with an evaluated value of the affinity of the nucleic acid molecule for the target substance,
wherein steps (1) and (2) are performed using an apparatus comprising a nucleic acids-screening unit comprising:
a single-stranded region-extracting unit that extracts the data of the single-stranded region;
and
a motif sequence-searching unit that searches the motif sequence from the single-stranded region.

5 more elements

An apparatus for preparing nucleic acids, comprising the nucleic acids-screening unit for acquiring a secondary structure of a nucleic acid molecule that contains a region that binds to a target substance, said apparatus comprising:

(1) a single-stranded region-extracting unit that extracts data of a single-stranded region, by excluding bases capable of forming a stem structure from the sequence of the nucleic acid molecule;
(2) a motif sequence-searching unit that searches a motif sequence from the single-stranded region, by weighing the appearance frequency of a specific sequence in the extracted data with an evaluated value of the affinity of the nucleic acid molecule for the target substance;
and
(3) a general structure-acquiring unit that acquires a general structure from a secondary structure of the nucleic acid molecule, based on the single-stranded region that accords with the motif sequence and based on bases forming the stem structure positioned at both ends of the single-stranded region.

1 more element

Dependencies are inferred from the claim text.

Life of this patent

Life of this patent

Abstract

Claims20