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Rna-selective hybridization reagent and use of the same

Foreign code F110004425
File No. K02703WO
Posted date Jul 15, 2011
Country Canada
Application number 2722479
Gazette No. 2722479
Gazette No. 2722479
Date of filing Mar 11, 2009
Gazette Date Sep 17, 2009
Gazette Date Jan 3, 2017
International application number JP2009054675
International publication number WO2009113580
Date of international publication Sep 17, 2009
Priority data
  • P2008-061751 (Mar 11, 2008) JP
  • 2009WO-JP54675 (Mar 11, 2009) WO
Title Rna-selective hybridization reagent and use of the same
Abstract (CA2722479)
Provided is a nucleoside derivative which has a high affinity for RNA.
Use is made of a nucleoside derivative represented by either formula (1) or formula (2). (In formulae (1) and (2), Z represents a carbon atom or a nitrogen atom; R1 represents a hydrogen atom or a hydroxyl-protecting group; and R2 represents a hydrogen atom or a phosphodiester group).
Scope of claims [claim1]
1. An RNA
hybridization reagent comprising one species or two or more species of nucleotide derivative units represented by Formula (5) or (6), or any combination thereof:
wherein:
Z represents a carbon atom or a nitrogen atom;
X1 represents O, S or Se;
and
X2 represents SH (or S-), S or Se-, or an alkyl group having 1 to 4 carbons or a
morpholino group;
wherein the RNA hybridization reagent selectively hybridizes RNA having a base sequence containing U corresponding to the Formula (5) and/or A corresponding to the
Formula (6).
[claim2]
2. The RNA hybridization reagent according to Claim 1, wherein the Z is a nitrogen atom.
[claim3]
3. The RNA hybridization reagent according to Claim 1 or 2, wherein the nucleotide derivative unit is represented by the Formula (5) and the Z is a nitrogen atom.
[claim4]
4. The RNA hybridization reagent according to Claim 1, 2 or 3, comprising the nucleotide derivative unit at an extremity.
[claim5]
5. The RNA hybridization reagent according to any one of Claims 1 to 4, having a base sequence which forms a stem-loop structure, and comprising the nucleotide derivative unit in the loop.
[claim6]
6. The RNA hybridization reagent according to any one of Claims 1 to 5, wherein the RNA hybridization reagent has one or more deoxyribonucleotides with natural bases as one or more units other than the one species or two or more species of nucleotide derivative units represented by formula (5) or (6), or any combination thereof
[claim7]
7. A probe set for detecting a mutation on an RNA, comprising:
a first probe comprising one species or two or more species of nucleotide derivative units represented by Formula (5) or (6), or any combination thereof, at the 5'
end or the 3' end corresponding to a site of the mutation;
and one species or two or more species of second probes comprising a deoxynucleotide having a base complementary to a base that has the possibility to be present in a site of the mutation at the 3' end or the 5' end corresponding to the site of the mutation:
wherein:
Z represents a carbon atom or a nitrogen atom;
X1 represents O, S or Se;
and
X2 represents SH (or S-), S or Se-, or an alkyl group having 1 to 4 carbons or a
morpholino group;
wherein the first probe selectively hybridizes RNA having a base sequence containing U corresponding to the Formula (5) and/or A corresponding to the
Formula (6).
[claim8]
8. A detecting method for a single base polymorphism, comprising:
providing an RNA sample as a gene expression product having a possibility of containing the single base polymorphism, with a first probe and one species or two or more species of second probes to contact one another allowing hybridization, wherein the first probe contains a nucleotide derivative unit represented by either the following
Formulae (5) or (6) at the 5' end or the 3' end corresponding to a site of the single base polymorphism, and the one species or the two or more species of the second probes comprises a deoxynucleotide having a base complementary to a base that has the possibility to be present in a site of the single base polymorphism at the 3'
end or the 5'
end corresponding to the site of the single base polymorphism;
wherein Z represents a carbon atom or a nitrogen atom;
X1 represents O, S or Se;
and
X2 represents SH (or S), S or Se-, or an alkyl group having 1 to 4 carbons or a
morpholino group;
causing the first probe, the second probe and the RNA sample to contact one another allowing hybridization in combinations of the one species or the two or more species obtained by combining one species of the first probe and one species of the second probe;
and detecting a fluorescence signal based on the first probe which is a hybridization product among the RNA sample, the first probe and the second probe;
wherein the first probe selectively hybridizes to the RNA sample having a base sequence containing U corresponding to the Formula (5) and/or A corresponding to the
Formula (6).
[claim9]
9. A method for forming a hybridized product with RNA comprising:
contacting a RNA hybridization reagent as defined in any one of Claims 1 to 6
with an RNA which has a base sequence containing U corresponding to the
Formula (5)
and/or A corresponding to the Formula (6).
[claim10]
10. The method according to Claim 9, wherein the RNA hybridization reagent has one or more deoxyribonucleotides with natural bases as one or more units other than the one species or two or more species of nucleotide derivative units represented by Formula
(5) or (6), or any combination thereof.
  • Applicant
  • JAPAN SCIENCE AND TECHNOLOGY AGENCY
  • Inventor
  • UENO YOSHIHITO
  • KITADE YUKIO
IPC(International Patent Classification)
Reference ( R and D project ) PRESTO RNA and biofunctions AREA
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