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-phosphonate moiety with a nucleoside/nucleotide.
1. A method for a 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 comprising a chiral X-phosphonate moiety is a compound of Formula 1:
wherein:
R 1 is —OH or —OR a ;
R a is a blocking moiety;
each instance of R 2 is independently hydrogen, —OH, halogen, alkyl-Y 1 —, alkenyl-Y 1 —, alkynyl-Y 1 —, aryl-Y 1 —, heteroaryl-Y 1 —, or —OR b ;
Y 1 is —O—;
R b is a blocking moiety;
each instance of Ba is independently a blocked or unblocked adenine, cytosine, guanine, thymine, uracil or modified nucleobase;
each instance of X is independently —S − Z + ;
Z + is an 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;
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.
2. The method of claim 1 , wherein the molecule comprising an achiral H-phosphonate moiety is a compound of Formula 2:
wherein:
R 1 is —OH or —OR a ;
R a is a blocking moiety;
R 2 is hydrogen, —OH, halogen, or —OR b ;
R b is a blocking moiety;
Ba independently a blocked or unblocked adenine, cytosine, guanine, thymine, uracil or modified nucleobase; and
Z + is an 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.
3. The method of claim 2 , wherein the chiral reagent is a compound of Formula 3:
wherein:
W 1 is —NG 5 -;
W 2 is —O—;
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 G 6 which are taken together to form 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 G 6 .
4. The method of claim 3 , wherein the nucleoside comprising a 5′-OH moiety is a compound of Formula 4:
wherein:
each instance of R 2 is independently hydrogen, halogen, or —OR b ;
R b is a blocking moiety;
each instance of Ba is independently a blocked or unblocked adenine, cytosine, guanine, thymine, uracil or modified nucleobase;
m is an integer of 0 to n−1;
O A is connected to a linking moiety connected to a solid support or a linking moiety connected to a nucleic acid;
J is O and D is H; or J is S, and D is a moiety of Formula A:
wherein:
W 1 and W 2 are independently NG 5 , O, or S;
A is hydrogen, acyl, aryl, alkyl, aralkyl, or silyl moiety; and
wherein G 1 , G 2 , G 3 , G 4 , and G 5 are independently hydrogen, alkyl, aralkyl, cycloalkyl, cycloalkylalkyl, heterocyclyl, heteroaryl, or aryl, or two of G 1 , G 2 , G 3 , G 4 , and G 5 are G 6 which are taken together to form 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 G 6 .
5. The method of claim 4 , wherein the step of converting the condensed intermediate to a compound of Formula 1 comprises: capping the condensed intermediate and modifying the capped condensed intermediate to produce a compound of Formula 5:
wherein:
R 1 is —OH or —OR a ;
R a is a blocking moiety;
each instance of R 2 is independently hydrogen, —OH, halogen, or —OR b ;
R b is a blocking moiety;
each instance of Ba is independently a blocked or unblocked adenine, cytosine, guanine, thymine, uracil or modified nucleobase;
each instance of J is S;
v is an integer of 2 to n−1;
O A is connected to a linking moiety connected to a solid support or a linking moiety connected to a nucleic acid;
A is an acyl, aryl, alkyl, aralkyl, or silyl moiety; and
W 1 and W 2 are independently NG 5 , O, or S; and
G 1 , G 2 , G 3 , G 4 , and G 5 are independently hydrogen, alkyl, aralkyl, cycloalkyl, cycloalkylalkyl, heterocyclyl, heteroaryl, or aryl, or two of G 1 , G 2 , G 3 , G 4 , and G 5 are G 6 which are taken together to form 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 G 6 .
6. The method of claim 5 , wherein in each of formulae 3-5, G 1 , G 2 , and G 3 are independently hydrogen, alkyl, aralkyl, cycloalkyl, cycloalkylalkyl, heterocyclyl, hetaryl, or aryl, and G 4 and G 5 are taken together to form a saturated or partially unsaturated heteroatom-containing ring of up to about 20 ring atoms which is monocyclic or polycyclic, fused or unfused.
7. The method of claim 6 , wherein G 4 and G 5 are taken together to form a saturated 5-membered saturated ring containing one nitrogen atom.
8. The method of claim 7 , wherein one of G 1 and G 2 is alkyl, aralkyl, cycloalkyl, cycloalkylalkyl, heterocyclyl, hetaryl, or aryl.
9. The method of claim 8 , wherein the other of G 1 and G 2 is alkyl, aralkyl, cycloalkyl, cycloalkylalkyl, heterocyclyl, hetaryl, or aryl.
10. The method of claim 8 , wherein the other of G 1 and G 2 is hydrogen.
11. The method of claim 9 , wherein G 3 is hydrogen.
12. The method of claim 11 , wherein the chiral reagent of formula 3 is
13. The method of claim 10 , wherein G 3 is hydrogen.
14. The method of claim 13 , wherein the chiral reagent of formula 3 is
15. The method of claim 6 , further comprising providing an activating reagent.
16. The method of claim 15 , wherein the activating reagent is imidazole, 4,5-dicyanoimidazole (DCI), 4,5-dichloroimidazole, 1-phenylimidazolium triflate (PhIMT), benzimidazolium triflate (BIT), benztriazole, 3-nitro-1,2,4-triazole (NT), tetrazole, 5-ethylthiotetrazole, 5-(4-nitrophenyl)tetrazole, N-cyanomethylpyrrolidinium triflate (CMPT), N-cyanomethylpiperidinium triflate, or N-cyanomethyldimethylammonium triflate.
17. The method of claim 5 , wherein R a is substituted or unsubstituted trityl or substituted silyl.
18. The method of claim 17 , wherein R b is substituted or unsubstituted methyl ether.
19. The method of claim 18 , wherein R 3 is a linking moiety connected to a solid support or a linking moiety connected to a nucleic acid.
20. The method of claim 5 , wherein n is about 10 to about 200.
21. The method of claim 1 , wherein at least one R 2 is —OMe.