Propargyl substituted nucleoside compounds and methods

Abstract

The present teachings relate to nucleobase, nucleoside and nucleotide compounds, methods of synthesis, and uses thereof. The present teachings provide compounds, such as nucleobase, nucleoside and/or nucleotide compounds including a propargyl linker, and methods for making or using such compounds.

1 - 23 . (canceled)  
     
     
         24 . A labeled nucleoside comprising a nucleobase disposed between a sugar or a sugar analog and a propargylic moiety, wherein the nucleobase is selected from a pyrimidine base or a pyrimidine base analog, the propargylic moiety is covalently attached to the nucleobase at the C-5 position of the nucleobase, the sugar or sugar analog is covalently attached to the nucleobase at the N−1 position of the nucleobase, and wherein the propargylic moiety comprises 
 (i) a propargyl group covalently attached by its methylene carbon to the nucleobase,    (ii) a detectable label, and    (iii) a linker covalently linking the acetylene carbon of the propargyl group to the detectable label.    
     
     
         25 . The nucleoside of  claim 24  wherein the nucleobase comprises a pyrimidine base.  
     
     
         26 . The nucleoside of  claim 24  wherein the pyrimidine base is uridine.  
     
     
         27 . The nucleoside of  claim 24  wherein the sugar comprises ribose, 2′-deoxyribose or 2′,3′-dideoxyribose.  
     
     
         28 . The nucleoside of  claim 27  wherein the sugar is 2′,3′-dideoxyribose.  
     
     
         29 . The nucleoside of  claim 24  wherein the sugar or sugar analog comprises a compound of the structure:  
       
         
           
           
               
               
           
         
         W 1  when taken alone is —H or —OH,  
         W 2  is —OH or a nonextendable moiety,  
         W 3  when taken alone is —H or when taken together with W 1  is —CH 2 —O—, and  
         W 4  is monophosphate, diphosphate, or triphosphate.  
       
     
     
         30 . The nucleoside of  claim 24  wherein the linker comprises from 1-50 atoms selected from C, H, N, O, S, P and Si.  
     
     
         31 . The nucleoside of  claim 24  wherein the linker comprises at least one anionic moiety.  
     
     
         32 . The nucleoside of  claim 24  wherein the linker comprises at least one cationic moiety.  
     
     
         33 . The nucleoside of  claim 24  wherein the linker comprises at least one amide linkage.  
     
     
         34 . The nucleoside of  claim 33  wherein the linker comprises at least one diradical selected from  
       
         
           
           
               
               
           
         
       
     
     
         35 . The nucleoside of  claim 33  wherein the linker comprises at least one diradical selected from  
       
         
           
           
               
               
           
         
       
       wherein Z is selected from oxygen, sulfur, substituted amine and unsubstituted amine, and the carbonyl carbon is covalently attached to X.  
     
     
         36 . The nucleoside of  claim 35  wherein Z is unsubstituted amine.  
     
     
         37 . The nucleoside of  claim 35  wherein Z is substituted amine.  
     
     
         38 . The nucleoside of  claim 24  wherein the detectable label comprises at least one of a fluorescent dye, an energy transfer dye, a quencher or biotin.  
     
     
         39 . The nucleoside of  claim 24  wherein the detectable label comprises a rhodamine dye, a fluorescein dye, a rhodol dye, an energy transfer dye, a cyanine dye, a phthalocyanine and a squaraine.  
     
     
         40 . The nucleoside of  claim 24  wherein the detectable label comprises a fluorescein dye, a rhodamine dye or an energy transfer dye.  
     
     
         41 . The nucleoside of  claim 24  wherein the detectable label comprises an energy transfer dye comprising a donor dye covalently attached to an acceptor dye, wherein either the donor dye or the acceptor dye is covalently attached to the linker, and the acceptor dye is capable of absorbing the light emitted by the donor dye.  
     
     
         42 . The nucleoside of  claim 41  wherein the donor dye is covalently attached to the linker.  
     
     
         43 . The nucleoside of  claim 41  wherein the donor dye comprises a fluorescein dye or a rhodamine dye.  
     
     
         44 . The nucleoside of  claim 43  wherein the acceptor dye comprises one of a rhodamine dye, a fluorescein dye, a cyanine dye or a non-fluorescent quencher.  
     
     
         45 . The nucleoside of  claim 44  wherein the donor dye is covalently linked to the acceptor dye through a linker-moiety.  
     
     
         46 . The nucleoside of  claim 41  wherein the donor dye comprises a fluorescein or a rhodamine dye and the acceptor dye is a non-fluorescent quencher.  
     
     
         47 - 69 . (canceled)  
     
     
         70 . A nucleoside comprising a nucleobase disposed between a sugar or a sugar analog and a propargylic moiety, wherein the nucleobase is selected from a pyrimidine base or a pyrimidine base analog, the propargylic moiety is covalently attached to the nucleobase at the C-5 position of the nucleobase, the sugar or sugar analog is covalently attached to the nucleobase at the N−1 position of the nucleobase, and wherein the propargylic moiety comprises a propargyl group covalently attached to the nucleobase at the methylene carbon of the propargyl group.  
     
     
         71 . The nucleoside of  claim 70  wherein the nucleobase comprises a pyrimidine base.  
     
     
         72 . The nucleoside of  claim 70  wherein the pyrimidine base is uridine.  
     
     
         73 . The nucleoside of  claim 70  wherein the sugar comprises ribose, 2′-deoxyribose or 2′,3′-dideoxyribose.  
     
     
         74 . The nucleoside of  claim 70  wherein the sugar is 2′,3′-dideoxyribose.  
     
     
         75 . The nucleoside of  claim 70  wherein the sugar or sugar analog comprises a compound of the structure:  
       
         
           
           
               
               
           
         
         W 1  when taken alone is —H or —OH,  
         W 2  is —OH or a nonextendable moiety,  
         W 3  when taken alone is —H or when taken together with W 1  is —CH 2 —O—, and  
         W 4  is monophosphate, diphosphate, or triphosphate.  
       
     
     
         76 . The nucleoside of  claim 70  wherein the linker comprises from 1-50 atoms selected from C, H, N, O, S, P and Si.  
     
     
         77 . The nucleoside of  claim 70  wherein the linker comprises at least one anionic moiety.  
     
     
         78 . The nucleoside of  claim 70  wherein the linker comprises at least one cationic moiety.  
     
     
         79 . The nucleoside of  claim 70  wherein the linker comprises at least one amide linkage.  
     
     
         80 . The nucleoside of  claim 79  wherein the linker comprises at least one diradical selected from  
       
         
           
           
               
               
           
         
       
     
     
         81 . The nucleoside of  claim 79  wherein the linker comprises at least one diradical selected from  
       
         
           
           
               
               
           
         
       
       wherein Z is selected from oxygen, sulfur, substituted amine and unsubstituted amine, and the carbonyl carbon is covalently attached to X.  
     
     
         82 . The nucleoside of  claim 81  wherein Z is unsubstituted amine.  
     
     
         83 . The nucleoside of  claim 81  wherein Z is substituted amine.  
     
     
         84 - 102 . (canceled)  
     
     
         103 . A method for making a thymidine analog comprising: 
 contacting a protected or unprotected 5-halomethyl uridine nucleotide with a copper acetylide to form an adduct comprising a 5-propargyl uridine.    
     
     
         104 . The method of  claim 103  wherein the copper acetylide comprises a mixture comprising a copper reagent, a base and an alkyne.  
     
     
         105 . (canceled)