Template-directed nucleic acid targeting compounds

1. A genetic recognition reagent, comprising:

a nucleic acid analog backbone, wherein the nucleic acid analog backbone comprises:

a first end and a second end, and

three to eight units, wherein each unit is independently a nucleic acid analog backbone residue;

a plurality of nucleobases wherein each nucleobase of the plurality of nucleobases is independently linked to a unit of the three to eight units, wherein the plurality of nucleobases has a sequence that is complementary to a target sequence of a target nucleic acid;

a first aryl moiety linked by a linker to the first end of the nucleic acid analog backbone; and

a second aryl moiety, linked by a linker to the second end of the nucleic acid analog backbone, wherein the first aryl moiety or the second aryl moiety stacks with an aryl moiety of an adjacent recognition reagent when the genetic recognition reagent and the adjacent recognition reagent are hybridized to adjacent target sequences of the target nucleic acid.

2. The genetic recognition reagent of claim 1 , having the structure:

where,

n is an integer ranging from 1 to 6;

each instance of R is, independently, a nucleobase of the plurality of nucleobases;

B is a unit of the three to eight units;

one instance of Ar is the first aryl moiety, and another instance of Ar is the second aryl moiety, wherein the first aryl moiety and the second aryl moiety are each independently a two- to five-ring fused polycyclic aromatic moiety; and

one instance of L is the linker to the first end of the nucleic acid analog backbone, and another instance of L is the linker to the second end of the nucleic acid analog backbone.

3. The genetic recognition reagent of claim 1 , wherein the nucleic acid analog backbone residues are RNA backbone residues.

4. The genetic recognition reagent of claim 3 , wherein one or more of the γPNA backbone residues are substituted with a group comprising an ethylene glycol unit, wherein the group comprising the ethylene glycol unit is: —(OCH 2 —CH 2 ) q OP 1 ; —(OCH 2 —CH 2 ) q —NHP 1 ; —(OCH 2 —CH 2 ) r —OH; —(OCH 2 —CH 2 ) r —NH 2 ; —(OCH 2 —CH 2 ) r —NHC(NH)NH 2 ; or —(OCH 2 —CH 2 ) r —S—S[CH 2 CH 2 ] s NHC(NH)NH 2 , where P 1 is H, (C 1 -C 8 )alkyl, (C 2 -C 8 )alkenyl, (C 2 -C 8 )alkynyl, (C 3 -C 8 )aryl, (C 3 -C 8 )cycloalkyl, (C 3 -C 8 )aryl(C 1 -C 6 )alkylene or (C 3 -C 8 )cycloalkyl(C 1 -C 6 )alkylene; q is an integer from 0 to 50; r is an integer from 1 to 50, and s is an integer from 1 to 50, wherein the group comprising the ethylene glycol unit is attached to the one or more γPNA backbone residues by a (C 1 -C 6 ) divalent hydrocarbyl linker or a covalent bond.

5. The genetic recognition reagent of claim 1 , having the structure:

where,

each R is independently, a nucleobase of the plurality of nucleobases;

n is 1, 2, 3, 4, 5, or 6;

one instance of L is the linker to the first end of the nucleic acid analog backbone, and another instance of L is the linker to the second end of the nucleic acid analog backbone, wherein the linker to the first end of the nucleic acid analog backbone and the linker to the second end of the nucleic acid analog backbone each independently comprises one or more guanidine-containing groups, one or more amino acid side chains, or one or more contiguous amino acid residues;

each R 3 is, independently, two- to five-ring fused polycyclic aromatic moieties,

R 1 and R 2 are each attached to a gamma carbon, and are, independently:

H, a guanidine-containing group, methyl, ethyl, an amino acid side chain, linear or branched ([C 3 -C 8 )alkyl, (C 2 -C 8 )alkenyl, (C 2 -C 8 )alkynyl, (C 1 -C 8 )hydroxyalkyl, (C 3 -C 8 )aryl, (C 3 -C 8 )cycloalkyl, (C 3 -C 8 )aryl(C 1 -C 6 )alkylene, or (C 3 -C 8 )cycloalkyl(C 1 -C 6 )alkylene; or

a guanidine-containing group, methyl, ethyl, an amino acid side chain, linear or branched (C 3 -C 8 )alkyl, (C 2 -C 8 )alkenyl, (C 2 -C 8 )alkynyl, (C 1 -C 8 )hydroxyalkyl, (C 3 -C 8 )aryl, (C 3 -C 8 )cycloalkyl, (C 3 -C 8 )aryl(C 1 -C 6 )alkylene, or (C 3 -C 8 )cycloalkyl(C 1 -C 6 )alkylene, wherein the guanidine-containing group, methyl, ethyl, an amino acid side chain, linear or branched (C 3 -C 8 )alkyl, (C 2 -C 8 )alkenyl, (C 2 -C 8 )alkynyl, (C 1 -C 8 )hydroxyalkyl, (C 3 -C 8 )aryl, (C 3 -C 8 )cycloalkyl, (C 3 -C 8 )aryl(C 1 -C 6 )alkylene, or (C 3 -C 8 )cycloalkyl(C 1 -C 6 )alkylene is substituted with an ethylene glycol unit comprising from 1 to 50 ethylene glycol moieties, —(OCH 2 —CH 2 ) q OP 1 , —(OCH 2 —CH 2 ) q —NHP 1 , —(SCH 2 —CH 2 ) q —SP 1 , —(OCH 2 —CH 2 ) r —OH, —(OCH 2 —CH 2 ) r —NH 2 , —(OCH 2 —CH 2 ) r —NHC(NH)NH 2 , or —(OCH 2 —CH 2 ) r —S—S[CH 2 CH 2 ] s NHC(NH)NH 2 , where P 1 is H, (C 1 -C 8 )alkyl, (C 2 -C 8 )alkenyl, (C 2 -C 8 )alkynyl, (C 3 -C 8 )aryl, (C 3 -C 8 )cycloalkyl, (C 3 -C 8 )aryl(C 1 -C 6 )alkylene or (C 3 -C 8 )cycloalkyl(C 1 -C 6 )alkylene; q is an integer from 0 to 50; r is an integer from 1 to 50, and s is an integer from 1 to 50,

or a pharmaceutically-acceptable salt thereof.

6. The genetic recognition reagent of claim 1 , having the structure:

where,

each R is independently, a nucleobase of the plurality of nucleobases;

n is 1, 2, 3, 4, 5, or 6;

R 1 and R 2 are independently: H, a guanidine-containing group; an amino acid side chain; methyl, ethyl, linear or branched (C 3 -C 8 )alkyl, (C 2 -C 8 )alkenyl, (C 2 -C 8 )alkynyl, (C 1 -C 8 )hydroxyalkyl, (C 3 -C 8 )aryl, (C 3 -C 8 )cycloalkyl, (C 3 -C 8 )aryl(C 1 -C 6 )alkylene, or (C 3 -C 8 )cycloalkyl(C 1 -C 6 )alkylene; or a guanidine-containing group, an amino acid side chain, methyl, ethyl, linear or branched (C 3 -C 8 )alkyl, (C 2 -C 8 )alkenyl, (C 2 -C 8 )alkynyl, (C 1 -C 8 )hydroxyalkyl, (C 3 -C 8 )aryl, (C 3 -C 8 )cycloalkyl, (C 3 -C 8 )aryl(C 1 -C 6 )alkylene, (C 3 -C 8 )cycloalkyl(C 1 -C 6 )alkylene, wherein the guanidine-containing group, the amino acid side chain, methyl, ethyl, linear or branched (C 3 -C 8 )alkyl, (C 2 -C 8 )alkenyl, (C 2 -C 8 )alkynyl, (C 1 -C 8 )hydroxyalkyl, (C 3 -C 8 )aryl, (C 3 -C 8 )cycloalkyl, (C 3 -C 8 )aryl(C 1 -C 6 )alkylene, (C 3 -C 8 )cycloalkyl(C 1 -C 6 )alkylene is substituted with an ethylene glycol unit comprising from 1 to 50 ethylene glycol moieties; —(OCH 2 —CH 2 ) q OP 1 ; —(OCH 2 —CH 2 ) q —NHP 1 ; —(SCH 2 —CH 2 ) q —SP 1 ; —(OCH 2 —CH 2 ) r —OH; —(OCH 2 —CH 2 ) r —NH 2 ; —(OCH 2 —CH 2 ) r —NHC(NH)NH 2 ; or —(OCH 2 —CH 2 ) r —S—S[CH 2 CH 2 ] s NHC(NH)NH 2 , where P 1 is H, (C 1 -C 8 )alkyl, (C 2 -C 8 )alkenyl, (C 2 -C 8 )alkynyl, (C 3 -C 8 )aryl, (C 3 -C 8 )cycloalkyl, (C 3 -C 8 )aryl(C 1 -C 6 )alkylene or (C 3 -C 8 )cycloalkyl(C 1 -C 6 )alkylene; q is an integer from 0 to 50; r is an integer from 1 to 50, and s is an integer from 1 to 50; and

one of R 4 and R 5 , and one of R 6 , R 7 , and R 8 are -L-R 3 , where each R 3 are, independently, two- to five-ring fused polycyclic aromatic moieties, wherein one instance of L is the linker to the first end of the nucleic acid analog backbone, and another instance of L is the linker to the second end of the nucleic acid analog backbone, and each of R 4 , R 5 , R 6 , R 7 , and R 8 that is not -L-R 3 are, independently: H, one or more contiguous amino acid residues, a guanidine-containing group, an amino acid side chain, methyl, ethyl, linear or branched (C 3 -C 8 )alkyl, (C 2 -C 8 )alkenyl, (C 2 -C 8 )alkynyl, (C 1 -C 8 )hydroxyalkyl, (C 3 -C 8 )aryl, (C 3 -C 8 )cycloalkyl, (C 3 -C 8 )aryl(C 1 -C 6 )alkylene, or (C 3 -C 8 )cycloalkyl(C 1 -C 6 )alkylene; or one or more contiguous amino acid residues, a guanidine-containing group, an amino acid side chain, methyl, ethyl, linear or branched (C 3 -C 8 )alkyl, (C 2 -C 8 )alkenyl, (C 2 -C 8 )alkynyl, (C 1 -C 8 )hydroxyalkyl, (C 3 -C 8 )aryl, (C 3 -C 8 )cycloalkyl, (C 3 -C 8 )aryl(C 1 -C 6 )alkylene, or (C 3 -C 8 )cycloalkyl(C 1 -C 6 )alkylene, wherein the one or more contiguous amino acid residues, the guanidine-containing group, the amino acid side chain, methyl, ethyl, linear or branched (C 3 -C 8 )alkyl, (C 2 -C 8 )alkenyl, (C 2 -C 8 )alkynyl, (C 1 -C 8 )hydroxyalkyl, (C 3 -C 8 )aryl, (C 3 -C 8 )cycloalkyl, (C 3 -C 8 )aryl(C 1 -C 6 )alkylene, or (C 3 -C 8 )cycloalkyl(C 1 -C 6 )alkylene is substituted with an ethylene glycol unit comprising from 1 to 50 ethylene glycol moieties; —(OCH 2 —CH 2 ) q OP 1 ; —(OCH 2 —CH 2 ) q —NHP 1 ; —(SCH 2 —CH 2 ) q —SP 1 ; —(OCH 2 —CH 2 ) r —OH; —(OCH 2 —CH 2 ) r —NH 2 ; —(OCH 2 —CH 2 ) r —NHC(NH)NH 2 ; or —(OCH 2 —CH 2 ) r —S—S[CH 2 CH 2 ] s NHC(NH)NH 2 , where P 1 is H, (C 1 -C 8 )alkyl, (C 2 -C 8 )alkenyl, (C 2 -C 8 )alkynyl, (C 3 -C 8 )aryl, (C 3 -C 8 )cycloalkyl, (C 3 -C 8 )aryl(C 1 -C 6 )alkylene or (C 3 -C 8 )cycloalkyl(C 1 -C 6 )alkylene; q is an integer from 0 to 50; r is an integer from 1 to 50, and s is an integer from 1 to 50,

or a pharmaceutically-acceptable salt thereof.

7. The genetic recognition reagent of claim 6 , wherein one or more of any R 1 , R 2 , R 4 , R 5 , R 6 , R 7 , or R 8 that is not -L-R 3 is (C 1 -C 8 )alkyl substituted with —(OCH 2 —CH 2 ) q OP 1 ; —(OCH 2 —CH 2 ) q —NHP 1 ; —(SCH 2 —CH 2 ) q —SP 1 ; —(OCH 2 —CH 2 ) r —OH; —(OCH 2 —CH 2 ) r —NH 2 ; —(OCH 2 —CH 2 ) r —NHC(NH)NH 2 ; or —(OCH 2 —CH 2 ) r —S—S[CH 2 CH 2 ] s NHC(NH)NH 2 , where P 1 is H, (C 1 -C 8 )alkyl, (C 2 -C 8 )alkenyl, (C 2 -C 8 )alkynyl, (C 3 -C 8 )aryl, (C 3 -C 8 )cycloalkyl, (C 3 -C 8 )aryl(C 1 -C 6 )alkylene or (C 3 -C 8 )cycloalkyl(C 1 -C 6 )alkylene; q is an integer from 0 to 50; r is an integer from 1 to 50, and s is an integer from 1 to 50.

8. The genetic recognition reagent of claim 6 , wherein R 4 and R 7 are -L-R 3 .

9. The genetic recognition reagent of claim 6 , wherein each of R 5 and R 8 comprise an arginine residue.

10. The genetic recognition reagent of claim 1 , having the structure:

where,

each R is independently, a nucleobase of the plurality of nucleobases;

each n is independently an integer ranging from 1 and 8;

each m is independently an integer ranging from 1 and 5;

each R 2 is independently: a guanidine-containing group, an amino acid side chain, methyl, ethyl, linear or branched (C 3 -C 8 )alkyl, (C 2 -C 8 )alkenyl, (C 2 -C 8 )alkynyl, (C 1 -C 8 )hydroxyalkyl, (C 3 -C 8 )aryl, (C 3 -C 8 )cycloalkyl, (C 3 -C 8 )aryl(C 1 -C 6 )alkylene, or (C 3 -C 8 )cycloalkyl(C 1 -C 6 )alkylene; or an amino acid side chain, methyl, ethyl, linear or branched (C 3 -C 8 )alkyl, (C 2 -C 8 )alkenyl, (C 2 -C 8 )alkynyl, (C 1 -C 8 )hydroxyalkyl, (C 3 -C 8 )aryl, (C 3 -C 8 )cycloalkyl, (C 3 -C 8 )aryl(C 1 -C 6 )alkylene, or (C 3 -C 8 )cycloalkyl(C 1 -C 6 )alkylene, wherein the amino acid side chain, methyl, ethyl, linear or branched (C 3 -C 8 )alkyl, (C 2 -C 8 )alkenyl, (C 2 -C 8 )alkynyl, (C 1 -C 8 )hydroxyalkyl, (C 3 -C 8 )aryl, (C 3 -C 8 )cycloalkyl, (C 3 -C 8 )aryl(C 1 -C 6 )alkylene, or (C 3 -C 8 )cycloalkyl(C 1 -C 6 )alkylene is substituted with an ethylene glycol unit comprising from 1 to 50 ethylene glycol moieties; —(OCH 2 —CH 2 ) q OP 1 ; —(OCH 2 —CH 2 ) q —NHP 1 ; —(SCH 2 —CH 2 ) q —SP 1 ; —(OCH 2 —CH 2 ) r —OH; —(OCH 2 —CH 2 ) r —NH 2 ; —(OCH 2 —CH 2 ) r —NHC(NH)NH 2 ; or —(OCH 2 —CH 2 ) r —S—S[CH 2 CH 2 ] s NHC(NH)NH 2 , where P 1 is H, (C 1 -C 8 )alkyl, (C 2 -C 8 )alkenyl, (C 2 -C 8 )alkynyl, (C 3 -C 8 )aryl, (C 3 -C 8 )cycloalkyl, (C 3 -C 8 )aryl(C 1 -C 6 )alkylene or (C 3 -C 8 )cycloalkyl(C 1 -C 6 )alkylene; q is an integer from 0 to 50; r is an integer from 1 to 50, and s is an integer from 1 to 50;

R 3 is an unsubstituted fused-ring polycyclic aromatic moiety; and

each of R 5 , R 7 , and R 8 are, independently H, a guanidine-containing group, an amino acid side chain, or one or more contiguous amino acid residues,

or a pharmaceutically-acceptable salt thereof.

11. The genetic recognition reagent of claim 10 , wherein R 2 is —CH 2 —O—CH 2 —CH 2 —O—CH 2 —CH 2 —OH, R 8 is H, R 5 is Arg-Dab(pyrene)-, Arg-Orn(pyrene)-, or Arg-Lys(pyrene)-; and R 7 is -Dab(pyrene)-Arg, -Orn(pyrene)-Arg, or -Lys(pyrene)-Arg.

12. The genetic recognition reagent of claim 2 , wherein either instance of Ar is unsubstituted or substituted pentalene, indene, naphthalene, azulene, heptalene, biphenylene, as-indacene, s-indacene, acenaphthylene, fluorene, phenalene, phenanthrene, anthracene, fluoranthene, acephenanthrylene, aceanthrylene, triphenylene, pyrene, chrysene, naphthacene/tetracene, pleiadene, picene, or perylene.

13. The genetic recognition reagent of claim 2 , wherein either instance of Ar comprises riboflavin (vitamin B2), mangostin, or mangiferin.

14. The genetic recognition reagent of claim 1 , comprising a guanidine-containing group that is

where n=1, 2, 3, 4, or 5.

15. The genetic recognition reagent of claim 5 , wherein, R 2 is —CH 2 —(OCH 2 —CH 2 ) r —OH, wherein r is an integer of from 1 to 50, from 1 to 10, or 2.

16. The genetic recognition reagent of claim 1 , wherein the linker to the first end of the nucleic acid analog backbone or the linker to the second end of the nucleic acid analog backbone comprises from 5 to 25 atoms, or a total of from 1 to 10 C, O, P, N, and S atoms.

17. The genetic recognition reagent of claim 1 , wherein the sequence that is complementary to the target sequence of the target nucleic acid is complementary to a nucleic acid having an expanded repeat associated with a repeat expansion disease.

18. The genetic recognition reagent of claim 17 , wherein the expanded repeat has one of the following sequences: (GAA) n , (CGG) n , (CCG) n , (CAG) n , (CTG) n , (CCTG) n , (ATTCT) n , or (GGGGCC) n , where n is at least 3.

19. The genetic recognition reagent of claim 17 , wherein the expanded repeat is (GTG) n , where n is at least 3.

20. The genetic recognition reagent of claim 17 , wherein the expanded repeat is (GUG) n , where n is at least 3.