Stem-loop compositions and methods for inhibiting factor D

1. An aptamer comprising a nucleic acid sequence that selectively binds to complement factor D (fD) and having a stem-loop secondary structure comprising a base-paired terminal stem; an asymmetric internal loop; an internal base-paired stem; and exactly one terminal loop, wherein said exactly one terminal loop comprises more than 4 nucleotides, non-nucleotidyl spacers, or a combination thereof, and wherein said asymmetric internal loop is adjacent to exactly 2 base-paired stems, and wherein said aptamer comprises a nucleic acid sequence selected from the group consisting of: SEQ ID NO: 13, SEQ ID NO: 165, SEQ ID NO: 166, SEQ ID NO: 244, SEQ ID NO: 253, SEQ ID NO: 256, and SEQ ID NO: 262; or a nucleic acid sequence comprising at least 80% sequence identity to a nucleic acid sequence selected from the group consisting of: SEQ ID NO: 13, SEQ ID NO: 165, SEQ ID NO: 166, SEQ ID NO: 244, SEQ ID NO: 253, SEQ ID NO: 256, and SEQ ID NO: 262.

2. The aptamer of claim 1 , wherein said base-paired terminal stem comprises a tail at a 5′ end, at a 3′ end, or at both a 5′ end and a 3′ end, and wherein said tail comprises at least one unpaired nucleotide.

3. The aptamer of claim 1 , wherein said aptamer is an RNA aptamer or a modified RNA aptamer.

4. The aptamer of claim 1 , wherein said aptamer comprises one or more modified nucleotides.

5. The aptamer of claim 4 , wherein said one or more modified nucleotides comprises a 2′F-modified nucleotide, a 2′OMe-modified nucleotide, or a combination thereof.

6. The aptamer of claim 5 , wherein said one or more modified nucleotides are selected from the group consisting of: 2′F-G, 2′OMe-G, 2′OMe-U, 2′OMe-A, 2′OMe-C, a 3′ terminal inverted deoxythymidine, and any combination thereof.

7. The aptamer of claim 1 , wherein said aptamer comprises a nuclease-stabilized nucleic acid backbone.

8. The aptamer of claim 1 , wherein said aptamer is an RNA aptamer comprising nucleotides having ribose in a β-D-ribofuranose configuration.

9. The aptamer of claim 1 , wherein said aptamer blocks an active site of fD.

10. The aptamer of claim 1 , wherein said aptamer is conjugated to a polyethylene glycol (PEG) molecule.

11. The aptamer of claim 1 , wherein said asymmetric internal loop comprises, from a 5′ to 3′ direction, a first loop and a second loop, and wherein said first loop has from 1 to 10 nucleotides.

12. The aptamer of claim 1 , wherein said asymmetric internal loop comprises, from a 5′ to 3′ direction, a first loop and a second loop, and wherein said second loop has from 2 to 10 nucleotides.

13. The aptamer of claim 1 , wherein said exactly one terminal loop has from 2 to 15 nucleotides.

14. The aptamer of claim 1 , wherein said base-paired terminal stem has from 2 to 10 base pairs.

15. The aptamer of claim 1 , wherein said internal base-paired stem has from 2 to 10 base pairs.

16. A method for modulating complement factor D (fD) in a biological system, said method comprising: administering to said biological system an aptamer of claim 1 , thereby modulating fD in said biological system.

17. The method of claim 16 , wherein said modulating comprises inhibiting a function associated with fD.

18. An aptamer comprising a sequence selected from the group consisting of:

(i) Aptamer 76: 5′—C6NH 2 —CCG*ACUUGCCAGUAUUGGCGAUGGCUGGAAGUUUG*UCG*G*-idT-3′ (SEQ ID NO: 285),

wherein G is 2′F; G*, A, C, and U are 2′OMe modified RNA; C6NH 2 represents a six-carbon amino containing linker; and idT represents a 3′ inverted deoxythymidine residue;

(ii) Aptamer 116: 5′—C6NH 2 —CCG*CCUUGCCAGUAUUGGCGAUGGCUGGAAGUUUG*G*CG*G*-idT-3′ (SEQ ID NO: 316),

wherein G is 2′F; G*, A, C, and U are 2′OMe modified RNA; C6NH 2 represents a six-carbon amino containing linker; and idT represents a 3′ inverted deoxythymidine residue;

(iii) Aptamer 102: 5′—C6NH 2 —CG*ACUUGCCAGUAUUGGCGAUGGCUGGAAGUUUG*UCG*-idT-3′ (SEQ ID NO: 313),

wherein G is 2′F; G*, A, C, and U are 2′OMe modified RNA; C6NH 2 represents a six-carbon amino containing linker; and idT represents a 3′ inverted deoxythymidine residue;

(iv) Aptamer 104: 5′—C6NH 2 —CG*CCUUGCCAGUAUUGGCUUAGGCUGGAAGUUUG*GCG*-idT-3′ (SEQ ID NO: 314),

wherein G is 2′F; G*, A, C, and U are 2′OMe modified RNA; C6NH 2 represents a six-carbon amino containing linker; and idT represents a 3′ inverted deoxythymidine residue;

(v) Aptamer 106: 5′—C6NH 2 —CCG*ACUUGCCAGUAUUGGCUUAGGCUGGAAGUUUG*UCG*G*-idT-3′ (SEQ ID NO: 303),

wherein G is 2′F; G*, A, C, and U are 2′OMe modified RNA; C6NH 2 represents a six-carbon amino containing linker; and idT represents a 3′ inverted deoxythymidine residue;

(vi) Aptamer 108: 5′—C6NH 2 —G*CCUUGCGGGUAUUGGCGAUGGCCCGAAGUUUG*G*C-idT-3′ (SEQ ID NO: 306),

wherein G is 2′F; G*, A, C, and U are 2′OMe modified RNA; C6NH 2 represents a six-carbon amino containing linker; and idT represents a 3′ inverted deoxythymidine residue;

(vii) Aptamer 107: 5′—C6NH 2 —CG*ACUUGCCAGUAUUGGCUUAGGCUGGAAGUUUG*UCG*-idT-3′ (SEQ ID NO: 315),

wherein G is 2′F; G*, A, C, and U are 2′OMe modified RNA; C6NH 2 represents a six-carbon amino containing linker; and idT represents a 3′ inverted deoxythymidine residue;

(viii) Aptamer 109: 5′—C6NH 2 —G*G*CCUUGCCCGUAUUGGCGAUGGCGGGAAGUUUG*G*CC-idT-3′ (SEQ ID NO: 312),

wherein G is 2′F; G*, A, C, and U are 2′OMe modified RNA; C6NH 2 represents a six-carbon amino containing linker; and idT represents a 3′ inverted deoxythymidine residue; and

(ix) Aptamer 99: 5′—C6NH 2 —CG*CCUUGCCAGUAUUGGCGAUGGCUGGAAGUUUG*G*CG*-idT-3′ (SEQ ID NO: 294),

wherein G is 2′F; G*, A, C, and U are 2′OMe modified RNA; C6NH 2 represents a six-carbon amino containing linker; and idT represents a 3′ inverted deoxythymidine residue.

19. A method for modulating complement factor D (fD) in a biological system, said method comprising: administering to said biological system an aptamer of claim 18 , thereby modulating fD in said biological system.