Compounds and methods for the synthesis of 5-(N-protected-tryptaminocarboxyamide)-2′-deoxyuridine phosphoramidite for incorporation into a nucleic acid

1. A compound having the structure:

or a salt thereof;

wherein,

R 1 is selected from tent-butyl, 1,1-dimethyl-propyl; 1,1-dimethyl-butyl; 2-chlorophenyl; 2-cyanophenyl; 1-methyl-cyclopentyl; and 1-methyl-cyclohexyl;

X 1 and X 2 are each independently selected from methoxy and hydrogen; and

X 3 is selected from methoxy, fluoro, hydrogen, and tert-butyldimethylsilyloxy.

2. The compound of claim 1 , selected from:

and salts thereof.

3. A compound having the structure:

or a salt thereof;

wherein,

R 1 is selected from tent-butyl, 1,1-dimethyl-propyl; 1,1-dimethyl-butyl; 2-chlorophenyl; 2-cyanophenyl; 1-methyl-cyclopentyl; and 1-methyl-cyclohexyl;

X 1 and X 2 are each independently selected from methoxy and hydrogen; and

X 3 is selected from a methoxy, fluoro, hydrogen, and tert-butyldimethylsilyloxy.

4. The compound of claim 3 , selected from:

and salts thereof.

5. A compound having the structure:

or a salt thereof;

wherein,

R 1 is selected from tent-butyl, 1,1-dimethyl-propyl; 1,1-dimethyl-butyl; 2-chlorophenyl; 2-cyanophenyl; 1-methyl-cyclopentyl; and 1-methyl-cyclohexyl.

6. The compound of claim 5 , wherein the compound is:

or a salt thereof.

7. A compound having the structure:

wherein,

R 1 is selected from tent-butyl, 1,1-dimethyl-propyl; 1,1-dimethyl-butyl; 2-chlorophenyl; 2-cyanophenyl; 1-methyl-cyclopentyl; and 1-methyl-cyclohexyl.

8. The compound of claim 7 , wherein the compound is:

9. A method of producing a compound having the structure:

or a salt thereof;

wherein,

R 1 is selected from tent-butyl, 1,1-dimethyl-propyl; 1,1-dimethyl-butyl; 2-chlorophenyl; 2-cyanophenyl; 1-methyl-cyclopentyl; and 1-methyl-cyclohexyl;

the method comprising reacting N-α-BOC-tryptamine with an acid chloride selected from pivaloyl chloride, 2,2-dimethylbutyroyl chloride, 2,2-dimethylvaleroyl chloride, 1-methylcyclopentane-1-carbonyl chloride, 1-methylcyclohexane-1-carbonyl chloride, 2-chlorobenzoyl chloride, and 2-cyanobenzoyl chloride.

10. The method of claim 9 , wherein R 1 is tent-butyl, and wherein the acid chloride is pivaloyl chloride.

11. The method of claim 9 , wherein the compound is:

12. A method of producing a compound having the structure:

wherein,

R 1 is selected from tent-butyl, 1,1-dimethyl-propyl; 1,1-dimethyl-butyl; 2-chlorophenyl; 2-cyanophenyl; 1-methyl-cyclopentyl; and 1-methyl-cyclohexyl;

the method comprising reacting the compound

with trifluoroacetic acid.

13. The method of claim 12 , wherein the method produces a compound of the structure:

14. A method of producing a compound having the structure:

or a salt thereof;

wherein,

R 1 is selected from tent-butyl, 1,1-dimethyl-propyl; 1,1-dimethyl-butyl; 2-chlorophenyl; 2-cyanophenyl; 1-methyl-cyclopentyl; and 1-methyl-cyclohexyl;

X 1 and X 2 are each independently selected from methoxy and hydrogen;

X 3 is selected from a methoxy, fluoro, hydrogen, and tert-butyldimethylsilyloxy;

the method comprising reacting the compound

with 5′-O-DMT-5-(2,2,2-trifluoroethyoxy-carbonyl)- 2′-deoxyuridine (TFEdU).

15. The method of claim 14 , wherein the method produces a compound selected from:

and salts thereof.

16. The method of claim 14 , wherein the method further comprises reacting the compound

with trifluoroacetic acid to form the compound

17. The method of claim 16 , wherein the method further comprises reacting N-α-BOC-tryptamine with an acid chloride selected from pivaloyl chloride, 2,2-dimethylbutyroyl chloride, 2,2-dimethylvaleroyl chloride, 1-methylcyclopentane-1-carbonyl chloride, 1-methylcyclohexane-1-carbonyl chloride, 2-chlorobenzoyl chloride, and 2-cyanobenzoyl chloride, to form the compound

18. A method of producing a compound having the structure:

or a salt thereof;

wherein,

R 1 is selected from tent-butyl, 1,1-dimethyl-propyl; 1,1-dimethyl-butyl; 2-chlorophenyl; 2-cyanophenyl; 1-methyl-cyclopentyl; and 1-methyl-cyclohexyl;

X 1 and X 2 are each independently selected from methoxy and hydrogen;

X 3 is selected from a methoxy, fluoro, hydrogen, and tert-butyldimethylsilyloxy;

the method comprising reacting the compound

with 2-cyanoethyl-N,N,N′,N′-tetraisopropylphosphor-amidite.

19. The method of claim 18 , wherein the method comprises reacting the compound

with 5′-O-DMT-5-(2,2,2-trifluoroethyoxy-carbonyl)- 2′-deoxyuridine (TFEdU) to form the compound

20. The method of claim 19 , wherein the method comprises reacting the compound

with trifluoroacetic acid to form the compound

21. The method of claim 20 , wherein the method comprises reacting N-α-BOC-tryptamine with an acid chloride selected from pivaloyl chloride, 2,2-dimethylbutyroyl chloride, 2,2-dimethylvaleroyl chloride, 1-methylcyclopentane-1-carbonyl chloride, 1-methylcyclohexane-1-carbonyl chloride, 2-chlorobenzoyl chloride, and 2-cyanobenzoyl chloride, to form the compound

22. The method of claim 18 , which produces a compound selected from:

and salts thereof.

23. A method of producing a compound having the structure:

or a salt thereof

wherein,

R 1 is selected from tent-butyl, 1,1-dimethyl-propyl; 1,1-dimethyl-butyl; 2-chlorophenyl; 2-cyanophenyl; 1-methyl-cyclopentyl; and 1-methyl-cyclohexyl;

X 1 and X 2 are each independently selected from methoxy and hydrogen;

X 3 is selected from a methoxy, fluoro, hydrogen, and tert-butyldimethylsilyloxy;

comprising the steps of:

a) reacting N-α-BOC-tryptamine with an acid chloride selected from pivaloyl chloride, 2,2-dimethylbutyroyl chloride, 2,2-dimethylvaleroyl chloride, 1-methylcyclopentane-1-carbonyl chloride, 1-methylcyclohexane-l-carbonyl chloride, 2-chlorobenzoyl chloride, and 2-cyanobenzoyl chloride, to form the compound

b) reacting the compound

with trifluoroacetic acid to form the compound

c) reacting the compound

with 5′-O-DMT-5-(2,2,2-trifluoroethyoxy-carbonyl)- 2′-deoxyuridine (TFEdU) to form the compound

and

d) reacting the compound

with 2 cyanoethyl-N,N,N′,N′-tetraisopropylphosphoramidite.

24. The method of claim 23 , wherein the method produces a compound selected from:

and salts thereof.

25. An oligonucleotide comprising at least one protected TrpU nucleotide, wherein at least one protected TrpU nucleotide in the oligonucleotide has the structure:

wherein,

R 1 is selected from tent-butyl, 1,1-dimethyl-propyl; 1,1-dimethyl-butyl; 2-chlorophenyl; 2-cyanophenyl; 1-methyl-cyclopentyl; and 1-methyl-cyclohexyl;

X 3 is selected from a methoxy, fluoro, hydrogen, and tert-butyldimethylsilyloxy;

X 4 is selected from OH, —OR, —SR, and —Z—P(Z′)(Z″)O—R, wherein Z, Z′, and Z″ are each independently selected from O and S, and R is an adjacent nucleotide in the oligonucleotide; and

X 5 is selected from —O-ss, —OR, —SR, and —Z—P(Z′)(Z″)O—R, wherein ss is a solid support, Z, Z′, and Z″ are each independently selected from O and S, and R is an adjacent nucleotide in the oligonucleotide.

26. A method of producing an oligonucleotide comprising at least one TrpU nucleotide, comprising incorporating at least one nucleotide having the structure:

wherein,

R 1 is selected from tent-butyl, 1,1-dimethyl-propyl; 1,1-dimethyl-butyl; 2-chlorophenyl; 2-cyanophenyl; 1-methyl-cyclopentyl; and 1-methyl-cyclohexyl;

X 3 is selected from a methoxy, fluoro, hydrogen, and tert-butyldimethylsilyloxy;

X 4 is selected from OH, —OR, —SR, and —Z—P(Z′)(Z″)O—R, wherein Z, Z′, and Z″ are each independently selected from O and S, and R is an adjacent nucleotide in the oligonucleotide; and

X 5 is selected from —O-ss, —OR, —SR, and —Z—P(Z′)(Z″)O—R, wherein ss is a solid support, Z, Z′, and Z″ are each independently selected from O and S, and R is an adjacent nucleotide in the oligonucleotide;

into a nucleotide sequence on a solid support; and removing the

 protecting group from the at least one TrpU nucleotide incorporated into the oligonucleotide.