Method for the synthesis of phosphorus atom modified nucleic acids
Described herein are methods of syntheses of phosphorous atom-modified nucleic acids comprising chiral X-phosphonate moieties. The methods described herein provide backbone-modified nucleic acids in high diasteteomeric purity via an asymmetric reaction of an achiral molecule comprising a chemically stable H-phophonate moiety with a nucleoside/nucleotide.
1. A method for the synthesis of a nucleic acid comprising a chiral X-phosphonate moiety comprising:
reacting a molecule comprising an achiral H-phosphonate moiety, a chiral reagent, and a nucleoside comprising a 5′-OH moiety to form a condensed intermediate; and
converting the condensed intermediate to the nucleic acid comprising a chiral X-phosphonate moiety, wherein:
the nucleic acid comprises a modified sugar, wherein the modified sugar contains one or more substituents at the 2′-position selected from the group consisting of F, CF 3 , CN, N 3 , NO, NO 2 , O-, S-, or N-alkyl; O-, S-, or N-alkenyl; O-, S-, or N-alkynyl; or O-alkyl-O-alkyl, O-alkyl-N-alkyl or N-alkyl-O-alkyl wherein the alkyl, alkenyl and alkynyl may be substituted or unsubstituted C 1 -C 10 alkyl or C 2 -C 10 alkenyl and alkynyl;
each instance of X is independently alkyl, alkoxy, aryl, alkylthio, acyl, —NR f R f , alkenyloxy, alkynyloxy, alkenylthio, alkynylthio, —S − Z + , —Se − Z + , or —BH 3 − Z + ;
each instance of R f is independently hydrogen, alkyl, alkenyl, alkynyl, or aryl;
Z + is ammonium ion, alkylammonium ion, heteroaromatic iminium ion, or heterocyclic iminium ion, any of which is primary, secondary, tertiary or quaternary, or Z + is a monovalent metal ion.
2. The method of claim 1 , wherein a substituent at the 2′-position of the modified sugar is O-alkyl-O-alkyl, wherein alkyl is substituted or unsubstituted C 1 -C 10 alkyl.
3. The method of claim 2 , wherein a substituent at the 2′-position of the modified sugar is —O(CH 2 ) n OCH 3 , wherein n is from 1 to about 10.
4. The method of claim 3 , wherein n is 1.
5. The method of claim 2 , wherein a substituent at the 2′-position of the modified sugar is O-methoxyethyl.
6. The method of claim 1 , wherein a substituent at the 2′-position of the modified sugar is F.
7. The method of claim 1 , wherein a substituent at the 2′-position of the modified sugar is O-alkyl, wherein alkyl is substituted or unsubstituted C 1 -C 10 alkyl.
8. The method of claim 1 , wherein the nucleic acid comprises one or more natural sugars of DNA or RNA.
9. The method of claim 1 , wherein the step of reacting the molecule comprising an achiral H-phosphonate moiety and the nucleoside comprising a 5′-OH moiety to form a condensed intermediate is a one-pot reaction.
10. The method of claim 1 , wherein the nucleic acid comprising a chiral X— phosphonate moiety is a compound of Formula 1:
wherein R 1 is —OH, —SH, —NR d R d , —N 3 , halogen, hydrogen, alkyl, alkenyl, alkynyl, alkyl-Y 1 —, alkenyl-Y 1 —, alkynyl-Y 1 —, aryl-Y 1 —, heteroaryl-Y 1 —, —P(O)(R e ) 2 , —HP(O)(R e ), —OR a or —SR c ;
Y 1 is O, NR d , S, or Se;
R a is a blocking moiety;
R e is a blocking group;
each instance of R d is independently hydrogen, alkyl, alkenyl, alkynyl, aryl, acyl, substituted silyl, carbamate, —P(O)(R e ) 2 , or —HP(O)(R e );
each instance of R e is independently hydrogen, alkyl, aryl, alkenyl, alkynyl, alkyl-Y 2 —, alkenyl-Y 2 —, alkynyl-Y 2 —, aryl-Y 2 —, or heteroaryl-Y 2 —, or a cation which is Na +1 , Li +1 , or K +1 ;
Y 2 is O, NH, N-alkyl, N-alkenyl, N-alkynyl, N-aryl, N-acyl, N-silyl, N-carbamate, or S;
each instance of R 2 is independently hydrogen, —OH, —SH, —NR d R d , —N 3 , halogen, alkyl, alkenyl, alkynyl, alkyl-Y 1 —, alkenyl-Y 1 —, alkynyl-Y 1 —, aryl-Y 1 —, heteroaryl-Y 1 —, —OR b , or —SR c , wherein R b is a blocking moiety;
R 3 is hydrogen, a blocking group, a linking moiety connected to a solid support or a linking moiety connected to a nucleic acid; and
n is an integer of 1 to about 200.
11. The method of claim 10 , wherein:
each instance of R d is independently hydrogen, alkyl, alkenyl, alkynyl, aryl, acyl, or substituted silyl;
each instance of R e is independently hydrogen, alkyl, aryl, alkenyl, alkynyl, alkyl-Y 2 —, alkenyl-Y 2 —, alkynyl-Y 2 —, aryl-Y 2 —, or heteroaryl-Y 2 ; and
Y 2 is O, NH, N-alkyl, N-alkenyl, N-alkynyl, N-aryl, N-acyl, N-silyl, N-carbamate, or S.
12. The method of claim 10 , wherein n is about 10 to about 200.
13. The method of claim 10 , wherein each X-phosphonate moiety of the compound of Formula 1 is more than 98% diastereomerically pure as determined by 31 P NMR spectroscopy or reverse-phase HPLC.
14. The method of claim 1 , wherein the chiral reagent is a compound of Formula 3:
wherein:
W 1 and W 2 are independently —NG 5 -, —O—, or —S—;
G 1 , G 2 , G 3 , G 4 , and G 5 are independently hydrogen, alkyl, aralkyl, cycloalkyl, cycloalkylalkyl, heterocyclyl, hetaryl, or aryl, or two of G 1 , G 2 , G 3 , G 4 , and G 5 are taken together to form G 6 a saturated, partially unsaturated or unsaturated carbocyclic or heteroatom-containing ring of up to about 20 ring atoms which is monocyclic or polycyclic, fused or unfused, and wherein no more than four of G 1 , G 2 , G 3 , G 4 , and G 5 are taken together to form are G 6 .
15. The method of claim 14 , wherein G 5 and one of G 3 and G 4 are taken together to form G 6 .
16. The method of claim 14 , wherein the chiral reagent is the compound of Formula 3 wherein W 1 is NG 5 and W 2 is O.
17. The method of claim 1 , wherein the chiral reagent is Formula O, Formula P, Formula Q or Formula R: