RNA molecules, methods of producing circular RNA, and treatment methods
The present invention relates to a RNA molecule comprising a first ribozyme, a first ligation sequence, an effector molecule, a second ligation sequence, and a second ribozyme. Methods of producing circular RNA molecules and treatment methods are also disclosed.
1. An RNA molecule comprising:
a first ribozyme;
a first ligation sequence positioned 3′ to the first ribozyme;
an effector molecule positioned 3′ to the first ligation sequence;
a second ligation sequence positioned 3′ to the effector molecule; and
a second ribozyme positioned 3′ to the second ligation sequence,
wherein a portion of the first ligation sequence is complementary to a portion of the first ribozyme and a portion of the second ligation sequence is complementary to a portion of the second ribozyme; wherein a portion of the first ligation sequence is complementary to a portion of the second ligation sequence; and wherein the portion of the first ligation sequence complementary to the portion of the first ribozyme is complementary to the portion of the second ligation sequence complementary to the portion of the second ribozyme.
2. The RNA molecule of claim 1 , wherein the RNA molecule comprises a non-natural or modified nucleotide.
3. The RNA molecule of claim 1 , wherein each of the first ribozyme and the second ribozyme comprises a sequence that may be cleaved to produce a 5′-OH end and a 2′,3′-cyclic phosphate end.
4. The RNA molecule of claim 3 , wherein each of the first and the second ribozyme is independently selected from the group consisting of Hammerhead, Hairpin, Hepatitis Delta Virus (“HDV”), Varkud Satellite (“VS”), Vg1, glucosamine-6-phosphate synthase (“glmS”), Twister, Twister Sister, Hatchet, Pistol ribozymes, engineered synthetic ribozymes, or derivatives thereof.
5. The RNA molecule of claim 4 , wherein each of the first and the second ribozyme is, independently, a split ribozyme or ligand-activated ribozyme derivative.
6. The RNA molecule of claim 3 , wherein the first ribozyme is a P3 Twister ribozyme and the second ribozyme is a P1 Twister ribozyme.
7. The RNA molecule of claim 1 , wherein each of the first ligation sequence and the second ligation sequence are substrates for an RNA ligase.
8. The RNA molecule of claim 7 , wherein each of the first ligation sequence and the second ligation sequence comprise a portion of a tRNA exon sequence or derivative thereof.
9. The RNA molecule of claim 7 , wherein the RNA ligase is RtcB.
10. The RNA molecule of claim 1 , wherein the effector molecule is selected from the group consisting of a RNA sequence that binds a protein; an RNA sequence that is complementary to a microRNA or siRNA; an RNA sequence that has partial complementarity to a microRNA or siRNA or piRNA; an RNA sequence that hybridizes completely or partially to a cellularly expressed microRNA, siRNA, piRNA, mRNA, lncRNA, ncRNA, or other cellular RNA; a hairpin structure that is a substrate for DICER or endogenous nucleases; a sequence that binds to viral proteins; an antisense RNA, an antagomir, a microRNA, a siRNA, an anti-miRNA, a ribozyme, a decoy oligonucleotide, an RNA activator, an immunostimulatory oligonucleotide, an aptamer, an RNA device; and an RNA molecule encoding a peptide sequence.
11. The RNA molecule of claim 10 , wherein the effector molecule comprises an IRES coupled to an RNA molecule encoding a peptide sequence.
12. The RNA molecule of claim 10 , wherein the effector molecule is a sensor comprising a fluorogenic aptamer coupled to a metabolite binding partner.
13. The RNA molecule of claim 12 , wherein the fluorogenic aptamer is selected from Spinach, Spinach 2, Broccoli, Red-Broccoli, Orange Broccoli, Corn, Mango, Malachite Green, cobalamine-binding aptamer, and derivatives thereof.
14. The RNA molecule of claim 13 , wherein the fluorogenic aptamer binds to a fluorophore whose fluorescence, absorbance, spectral properties, or quenching properties are increased, decreased, or altered by interaction with the fluorogenic aptamer.
15. A circular RNA molecule produced from the RNA molecule of claim 1 , wherein the circular molecule comprises the effector molecule.
16. A vector encoding the RNA molecule of claim 1 .
17. The vector of claim 16 , wherein the vector comprises a prokaryotic promoter selected from the group consisting of T7, T3, SP6 RNA polymerases, and derivatives thereof.
18. The vector of claim 16 , wherein the vector comprises a eukaryotic RNA polymerase I promoter or RNA Polymerase III promoter selected from the group consisting of U6, H1, 5S, 7SK promoter, and derivatives thereof.
19. An isolated cell comprising the vector of claim 16 .
20. A method of producing a circular RNA molecule, said method comprising:
providing one or more vectors comprising:
a nucleic acid sequence encoding a 5′ polymerase promoter sequence;
a nucleic acid sequence encoding a first ribozyme;
a nucleic acid sequence encoding a first ligation sequence;
a nucleic acid sequence encoding an effector molecule;
a nucleic acid sequence encoding a second ligation sequence;
a nucleic acid sequence encoding a second ribozyme; and
a nucleic acid sequence encoding a 3′ polymerase terminator sequence, wherein (i) said nucleic acid sequence encoding the first ligation sequence is upstream of the nucleic acid sequence encoding the effector molecule, (ii) said nucleic acid sequence encoding the second ligation sequence is downstream of the effector molecule, (iii) a portion of the first ligation sequence is complementary to a portion of the first ribozyme and a portion of the second ligation sequence is complementary to a portion of the second ribozyme, (iv) a portion of the first ligation sequence is complementary to a portion of the second ligation sequence, and (v) wherein the portion of the first ligation sequence complementary to the portion of the first ribozyme is complementary to the portion of the second ligation sequence complementary to the portion of the second ribozyme;
transcribing the one or more vectors to produce one or more linear RNA molecules; and
contacting the linear RNA molecules with an RNA ligase to circularize the linear RNA molecule thereby producing a circular RNA molecule.
21. A method of treatment, said method comprising:
administering the RNA molecule of claim 1 to a subject in need thereof, wherein upon said administering to the subject, the effector molecule is expressed in a cell of the subject, thereby treating the subject.
22. The RNA molecule of claim 1 , wherein the first ribozyme or the second ribozyme are self-cleaving ribozymes.