US2003165888A1PendingUtilityA1

Oligonucleotide probes and primers comprising universal bases for diagnostic purposes

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Priority: Jul 18, 2001Filed: May 8, 2002Published: Sep 4, 2003
Est. expiryJul 18, 2021(expired)· nominal 20-yr term from priority
Inventors:Bob D. BrownTimothy A. Riley
C12N 2310/3181C12N 15/1034C12N 15/1135C12N 2310/31C12Q 2600/156C12N 2310/351C12N 2310/313C12N 15/113C12N 15/1137C12N 2310/315C12Q 1/6883C12N 2310/3125C12N 2310/318C12N 2310/12C07H 21/04C12N 2310/3533C12N 2310/33C12N 2310/321C12N 2310/346C07H 21/00
54
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Claims

Abstract

Aspects of the invention relate to novel oligonucleotides comprising universal and generic bases for use as primers and probes, as well as, methods of using said oligonucleotides for the diagnosis of disease.

Claims

exact text as granted — not AI-modified
What is claimed is:  
     
         1 . An oligonucleotide comprising between about 10 and 100 bases, wherein at least 2 of said bases are juxtaposed universal bases.  
     
     
         2 . The oligonucleotide of  claim 1 , wherein at least 3 of said bases are juxtaposed universal bases.  
     
     
         3 . The oligonucleotide of  claim 1 , wherein at least 4 of said bases are juxtaposed universal bases.  
     
     
         4 . The oligonucleotide of  claim 1 , wherein at least 5 of said bases are juxtaposed universal bases.  
     
     
         5 . The oligonucleotide of  claim 1 , wherein at least 6 of said bases are juxtaposed universal bases.  
     
     
         6 . The oligonucleotide of  claim 1 , wherein at least 7 of said bases are juxtaposed universal bases.  
     
     
         7 . The oligonucleotide of  claim 1  wherein said universal bases are selected from the group consisting of: 2-deoxyinosine, 5-nitroindole, 3-nitropyrrole, and 2-deoxynebularine.  
     
     
         8 . The oligonucleotide of  claim 1 , wherein said oligonucleotide comprises between about 10 and about 15 bases.  
     
     
         9 . The oligonucleotide of  claim 1 , wherein said oligonucleotide comprises between about 10 and about 25 bases..  
     
     
         10 . The oligonucleotide of  claim 1 , wherein said oligonucleotide comprises between about 10 and about 50 bases.  
     
     
         11 . The oligonucleotide of  claim 1 , further comprising a non-nucleic acid linker.  
     
     
         12 . The oligonucleotide of  claim 11 , wherein said non-nucleic acid linker is selected from the group consisting of: Spacer 9, Spacer 18, Spacer C3, and dSpacer.  
     
     
         13 . The oligonucleotide of  claim 1 , wherein said oligonucleotide comprises modifications that decrease the affinity of the oligonucleotide for a target.  
     
     
         14 . The oligonucleotide of  claim 1 , wherein said oligonucleotide comprises modifications that increase the affinity of the oligonucleotide for a target.  
     
     
         15 . The oligonucleotide of  claim 1 , wherein more than about 20% of said bases are universal or generic bases.  
     
     
         16 . The oligonucleotide of  claim 1 , wherein more than about 30% of said bases are universal or generic bases.  
     
     
         17 . An oligonucleotide comprising the formula: 
       XRY wherein X comprises between about 5 and 20 modified nucleic acid bases;    wherein R comprises between about 3 and 10 juxtaposed universal bases;    wherein Y comprises between about 5 and about 20 nucleic acid bases;    wherein X, R, and Y are covalently joined; and    wherein more than about 20% of the total number of bases in said oligonucleotide are said juxtaposed universal bases.    
     
     
         18 . The oligonucleotide of  claim 17 , further comprising a non-nucleic acid linker.  
     
     
         19 . The oligonucleotide of  claim 1  wherein said universal bases are selected from the group consisting of: 2-deoxyinosine, 5-nitroindole, 3-nitropyrrole, and 2-deoxynebularine.  
     
     
         20 . A method for detecting a polymorphism in a sample of genetic material, comprising: 
 providing an oligonucleotide comprising between about 10 and 100 bases, wherein at least 2 of said bases are juxtaposed universal bases;    contacting said genetic material with said oligonucleotide; and    identifying whether said oligonucleotide is bound to said genetic material, wherein said universal or generic bases are not located at the site or sites of said polymorphism.    
     
     
         21 . The method of  claim 20 , wherein said mutations are Single Nucleotide Polymorphisms (SNPs).  
     
     
         22 . The method of  claim 20  further comprising amplifying said mutation in said genetic material.  
     
     
         23 . The method of  claim 20 , wherein said genetic material is DNA.  
     
     
         24 . The method of  claim 20  wherein said universal bases are selected from the group consisting of: 2-deoxyinosine, 5-nitroindole, 3-nitropyrrole, and 2-deoxynebularine.  
     
     
         25 . The method of  claim 20 , wherein the presence of said polymorphism is diagnostic for a genetic disease.  
     
     
         26 . A method for diagnosing a genetic disease in a patient, comprising: 
 providing an oligonucleotide specific for a DNA sequence related to said disease, wherein said oligonucleotide comprises between about 10 and 100 bases, and wherein at least 2 of said bases are juxtaposed universal bases;    contacting genetic material from said patient with said oligonucleotide; and    identifying whether said oligonucleotide is bound to said genetic material, wherein binding of said oligonucleotide to said genetic material is indicative of said genetic disease.    
     
     
         27 . The method of  claim 26 , wherein said genetic disease comprises a DNA sequence comprising a Single Nucleotide Polymorphisms (SNPs).  
     
     
         28 . The method of  claim 26  further comprising amplifying said DNA sequence.  
     
     
         29 . The method of  claim 26 , wherein said genetic material is DNA.  
     
     
         30 . The method of  claim 26  wherein said universal bases are selected from the group consisting of: 2-deoxyinosine, 5-nitroindole, 3-nitropyrrole, and 2-deoxynebularine.  
     
     
         31 . The method of  claim 26 , wherein said oligonucleotide comprises 10 to 50 bases.  
     
     
         32 . The method of  claim 26 , wherein said oligonucleotide comprises 10 to 25 bases.  
     
     
         33 . The method of  claim 26 , wherein said oligonucleotide comprises 10 to 15 bases.

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