Stem-loop compositions and methods for inhibiting factor D
The application discloses methods and compositions for the inhibition of the alternative complement pathway. The methods and compositions involve the use of aptamers for inhibiting complement Factor D. The application further provides anti-Factor D aptamers for the treatment of dry age-related macular degeneration, geographic atrophy, wet age-related macular degeneration or Stargardt disease. In some cases, stem-loop aptamers are provided for the inhibition of 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, in a 5′ to 3′ direction, a first base-paired stem, a first loop, a second base-paired stem, a second loop, and a third loop, wherein said third loop comprises 6 or more nucleotides, non-nucleotidyl spacers, or a combination thereof, and wherein said third loop is adjacent to said first base-paired stem.
2. The aptamer of claim 1 , wherein said first loop has fewer nucleotides than said second loop.
3. The aptamer of claim 1 , wherein said first loop has from 1to 10 nucleotides, non-nucleotidyl spacers, or a combination thereof.
4. The aptamer of claim 1 , wherein said second loop comprises at least 6 nucleotides, non-nucleotidyl spacers, or a combination thereof.
5. The aptamer of claim 1 , wherein said third loop has from 6to 8 nucleotides, non-nucleotidyl spacers, or a combination thereof.
6. The aptamer of claim 1 , wherein said first base-paired stem has from 2 to 10 base pairs.
7. The aptamer of claim 1 , wherein said second base-paired stem has from 2 to 10 base pairs.
8. The aptamer of claim 1 , wherein said third loop comprises at least 4 nucleotides and up to 2 non-nucleotidyl spacers.
9. The aptamer of claim 1 , wherein said third loop comprises at least 6 nucleotides.
10. The aptamer of claim 1 , wherein:
a) said first base-paired stem is adjacent to said first loop;
b) said second base-paired stem is adjacent to said first loop, said second loop, and said third loop; or
c) said first base-paired stem is adjacent to said first loop and said second base-paired stem is adjacent to said first loop, said second loop, and said third loop.
11. The aptamer of claim 1 , wherein said aptamer is an RNA aptamer or a modified RNA aptamer.
12. The aptamer of claim 1 , wherein said aptamer is a DNA aptamer or a modified DNA aptamer.
13. The aptamer of claim 1 , wherein said aptamer comprises one or more modified nucleotides.
14. The aptamer of claim 13 , wherein said one or more modified nucleotides comprises a 2′F-modified nucleotide, a 2′OMe-modified nucleotide, or a combination thereof.
15. The aptamer of claim 1 , wherein said stem-loop structure has exactly two base-paired stems.
16. The aptamer of claim 1 , wherein said aptamer is an RNA aptamer comprising nucleotides having ribose in a β-D-ribofuranose configuration.
17. The aptamer of claim 1 , wherein said aptamer blocks an active site of fD.
18. The aptamer of claim 1 , wherein said aptamer inhibits a function associated with fD.
19. The aptamer of claim 1 , wherein said nucleic acid sequence comprises from 30 to 90 nucleotides, non-nucleotidyl spacers, or a combination thereof.
20. The aptamer of claim 1 , wherein: said aptamer is conjugated to a polyethylene glycol (PEG) molecule.
21. The aptamer of claim 1 , wherein said second loop comprises more than 5 nucleotides, non-nucleotidyl spacers, or a combination thereof.
22. The aptamer of claim 1 , wherein said first base-paired stem has no more than 5 base pairs.
23. The aptamer of claim 1 , wherein said first loop comprises a nucleic acid sequence of 5′-DUG-3′, where D is A, G, or U.
24. The aptamer of claim 1 , wherein said second loop comprises a nucleic acid sequence of 5′-DWWVGCBHWG-3′, where D is A, G, or U; W is A or U; V is A, C, or G; B is C, G, or U; and H is A, C, or U.
25. The aptamer of claim 1 , wherein said second loop comprises a nucleic acid sequence having a U at nucleotide position 2, a U at nucleotide position 3, or both.
26. The aptamer of claim 1 , wherein said third loop comprises a nucleic acid sequence comprising 5′-AAGUKN-3′, where K is G or U; and N is A, G, C, or U.
27. The aptamer of claim 1 , wherein said second base-paired stem comprises a terminal U-G base pair adjacent to said second loop.
28. The aptamer of claim 1 , wherein said second base-paired stem comprises a terminal C-G base pair adjacent to said second loop.