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RNA-selective hybridization reagent and use of the same

Foreign code F110005402
File No. K02703WO
Posted date Sep 5, 2011
Country United States of America
Application number 92190909
Gazette No. 20110033863
Gazette No. 8609826
Date of filing Mar 11, 2009
Gazette Date Feb 10, 2011
Gazette Date Dec 17, 2013
International application number JP2009054675
International publication number WO2009113580
Date of international filing Mar 11, 2009
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 (US8609826)
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 provided with one species or two or more species of nucleotide derivative units represented by any of the following Formulae (5) and (6):
where Z represents a carbon atom or a nitrogen atom; X1 represents 0, S or Se; 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 nucleotide derivative unit is represented by the Formula (5) and the Z is a nitrogen atom.
[claim3]
3. The RNA hybridization reagent according to claim 2, provided with the nucleotide derivative unit at an extremity.
[claim4]
4. The RNA hybridization reagent according to claim 1, having a base sequence which forms a stem-loop structure, and provided with the nucleotide derivative unit in the loop.
[claim5]
5. A probe set for detecting a mutation on an RNA, comprising: a first probe provided with one species or two or more species of nucleotide derivative units represented by any of the following Formulae (5) and (6) 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 provided with 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:
where Z represents a carbon atom or a nitrogen atom; X1 represents 0, S or Se; 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).
[claim6]
6. A detecting method for a single base polymorphism, comprising: preparing an RNA sample as a gene expression product having the possibility of containing the single base polymorphism;
with a probe set being provided containing a first probe provided with a nucleotide derivative unit represented by any of the following Formulae (5) and (6) at the 5' end or the 3' end corresponding to a site of the single base polymorphism, and one species or two or more species of second probes provided with 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,
causing the first probe, the second probe and the RNA sample to contact one another allowing hybridization in combinations of one species or two or more species obtained by combining one species of the first probe and one species of the second probe selected from the probe set,
where Z represents a carbon atom or a nitrogen atom; X' represents 0, S or Se; X2 represents SH (or S-), S or Se-, or an alkyl group having 1 to 4 carbons or a morpholino group; 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 the RNA sample having a base sequence containing U corresponding to the Formula 5 and/or A corresponding to the Formula (6).
[claim7]
7. The RNA hybridization reagent according to claim 2, provided with the nucleotide derivative unit at an extremity.
[claim8]
8. The RNA hybridization reagent according to claim 2, having a base sequence which forms a stem-loop structure, and provided with the nucleotide derivative unit in the loop.
[claim9]
9. The RNA hybridization reagent according to claim 3, having a base sequence which forms a stem-loop structure, and provided with the nucleotide derivative unit in the loop.
[claim10]
10. The RNA hybridization reagent according to claim 7, having a base sequence which forms a stern-loop structure, and provided with the nucleotide derivative unit in the loop.
[claim11]
11. The RNA hybridization reagent according to claim 1, wherein the Z is a nitrogen atom.
[claim12]
12. The RNA hybridization reagent according to claim 1, 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 any of the formulae (5) and (6).
[claim13]
13. A method for forming a hybridized product with RNA comprising: contacting the RNA hybridization reagent according to claim 1 with an RNA which has a base sequence containing U corresponding to the Formula (5) and/or A corresponding to the Formula (6).
[claim14]
14. The method according to claim 13, 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 any of the Formulae (5) and (6).
  • Inventor, and Inventor/Applicant
  • UENO YOSHIHITO
  • KITADE YUKIO
  • JAPAN SCIENCE AND TECHNOLOGY AGENCY
IPC(International Patent Classification)
Reference ( R and D project ) PRESTO RNA and biofunctions AREA
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