Method of preparing self-circularized RNA
A method of preparing a circular RNA includes transcribing a vector to form a precursor RNA, in which the vector includes the following elements operably connected to each other and arranged in the following sequence: a) a 5′ element, b) a 3′ Group I self-splicing intron fragment containing a 3′ splice site dinucleotide, c) none or an element containing an internal ribosome entry site (IRES) and a protein coding region or an element containing a noncoding region, d) a 5′ Group I self-splicing intron fragment containing a 5′ splice site dinucleotide, and e) a 3′ element, in which 5′ element and 3′ element form a stable structure with a Gibbs free energy (ΔG) from −190 kcal/mol to −9.0 kcal/mol, provided that the stable structure is not a duplex with at least 95% base pairing between the 5′ element and 3′ element, in which 3′ Group I self-splicing intron fragment and 5′ Group I self-splicing intron fragment form a self-cleaving and self-ligating RNA molecule, thereby generating circular RNA.
1. A method of preparing a circular ribonucleic acid (RNA), comprising:
transcribing a vector to form a precursor RNA comprising the following elements operably connected to each other and arranged in tandem in a 5′ to 3′ orientation:
a) a 5′ element,
b) a 3′ Group I self-splicing intron fragment,
c) none or an element comprising an internal ribosome entry site (IRES) and a protein coding region or an element comprising a noncoding region,
d) a 5′ Group I self-splicing intron fragment, and
e) a 3′ element;
wherein the 5′ element and the 3′ element form a thermodynamically stable multiple way junction RNA structure with a Gibbs free energy (ΔG) from −190 kcal/mol to −9.0 kcal/mol, provided that the stable structure is not a duplex with at least 95% base pairing between the 5′ element and the 3′ element,
wherein the 3′ Group I self-splicing intron fragment and the 5′ Group I self-splicing intron fragment form a self-cleaving and self-ligating RNA molecule, thereby generating the circular RNA,
wherein the thermodynamically stable multiple way junction RNA structure comprises a 4-way junction (4WJ) comprising
a first branch of the 4WJ domain is formed from a 5′ portion of a 4WJa sequence and a 3′ portion of a 4WJd sequence and comprises a first helical region,
a second branch of the 4WJ domain is formed from a 3′ portion of the 4WJa sequence and a 5′ portion of a 4WJb sequence and comprises a second helical region, and
a third branch of the 4WJ domain is formed from a 3′ portion of the 4WJb sequence and a 5′ portion of a 4WJc sequence and comprises a third helical region, and
a fourth branch of the 4WJ domain is formed from a 3′ portion of the 4WJc sequence and a 5′ portion of the 4WJd sequence and comprises a fourth helical region,
wherein each of said helical regions comprises a plurality of RNA nucleotide pairs that form canonical Watson-Crick bonds.
2. The method of claim 1 , wherein the 5′ element comprises none or a sequence that forms at least one stem-loop structure and the 3′ element comprises none or a sequence that forms at least one stem-loop structure, provided that, when the 5′ element does not comprise a stem-loop structure, then the 3′ element comprises at least one stem-loop structure; and, when the 3′ element does not comprise a stem-loop structure, then the 5′ element comprises at least one stem-loop structure.
3. The method of claim 1 , wherein
the 4WJa comprises or consists of SEQ ID NO: 7, 4WJb comprises or consists of SEQ ID NO: 8, 4WJc comprises or consists of SEQ ID NO: 9, and 4WJd comprises or consists of SEQ ID NO: 102; or
the 4WJa comprises or consists of SEQ ID NO: 103, 4WJb comprises or consists of SEQ ID NO: 104, 4WJc comprises or consists of SEQ ID NO: 105, and 4WJd comprises or consists of SEQ ID NO: 106; or
the 4WJa comprises or consists of SEQ ID NO: 115, 4WJb comprises or consists of SEQ ID NO: 116, 4WJc comprises or consists of SEQ ID NO: 117, and 4WJd comprises or consists of SEQ ID NO: 118; or
the 4WJa comprises or consists of UGCAGGUG, 4WJb comprises or consists of ACGGGC, 4WJc comprises or consists of CCAGCA, and 4WJd comprises or consists of SEQ ID NO: 67; or
the 4WJa comprises or consists of SEQ ID NO: 74, 4WJb comprises or consists of AACUG, 4WJc comprises or consists of SEQ ID NO: 75, and 4WJd comprises or consists of AUCAUG; or
the 4WJa comprises or consists of SEQ ID NO: 122, 4WJb comprises or consists of GAACU, 4WJc comprises or consists of SEQ ID NO: 123, and 4WJd comprises or consists of AAUCA; or
the 4WJa comprises or consists of SEQ ID NO: 125, 4WJb comprises or consists of SEQ ID NO: 126, 4WJc comprises or consists of SEQ ID NO: 127, and 4WJd comprises or consists of SEQ ID NO: 128.
4. The method of claim 1 , wherein the IRES is selected from an IRES sequence from a virus or a gene selected from the group consisting of: Taura syndrome virus, Triatoma virus, Theiler's encephalomyelitis virus, simian Virus 40, Solenopsis invicta virus 1, Rhopalosiphum padi virus, Reticuloendotheliosis virus, fuman poliovirus 1, Plautia stall intestine virus, Kashmir bee virus, Human rhinovirus 2, Homalodisca coagulata virus-1, Human Immunodeficiency Virus type 1, Homalodisca coagulata virus-1, Himetobi P virus, Hepatitis C virus, Hepatitis A virus, Hepatitis GB virus, foot and mouth disease virus, Human enterovirus 71, Equine rhinitis virus, Ectropis obliqua picoma-like virus, Encephalomyocarditis virus (EMCV), Drosophila C Virus, Crucifer tobamo virus, Cricket paralysis virus, Bovine viral diarrhea virus 1, Black Queen Cell Virus, Aphid lethal paralysis virus, Avian encephalomyelitis virus, Acute bee paralysis virus, Hibiscus chlorotic ringspot virus, Classical swine fever virus, Human fibroblast growth factor 2 (FGF2), Human surfactant protein A1 (SFTPA1), Human acute myeloid leukemia protein 1/runt-related transcription factor 1 (AML1/RUNX1), Drosophila antennapedia, Human aquaporin-4 (AQP4), Human type-1 angiotensin II receptor (AT1R), Human BCL2 associated athanogene 1 (BAG-1), Human B-cell lymphoma 2 (BCL2), Human binding immunoglobulin protein (BiP), Human inhibitor of apoptosis family protein 1 (c-IAP1), Human c-myc, Human eukaryotic translation initiation factor 4 G (eIF4G), Mouse N-deacetylase and N-sulfotransferase 4 (NDST4L), Human lymphoid enhancer-binding factor-1 (LEF1), Mouse hypoxia inducible factor 1 subunit alpha (HIF1 alpha), Human N-myc, Mouse glial and testis-specific homeobox protein (Gtx), Human cyclin-dependent kinase inhibitor 1B (p27kip1), Human platelet-derived growth factor B/human homolog of the simian sarcoma virus (PDGF2/c-sis), Human p53, Human Proviral integration site for Moloney murine leukemia virus-1 (Pim-1), Mouse RNA-binding protein 3 (Rbm3), Drosophila reaper, Canine Scamper, Drosophila Ultrabithorax (Ubx), Salivirus, Cosavirus, Parechovirus, Human upstream of N-ras (UNR), Mouse utrophin A (UtrA), Human vascular endothelial growth factor A (VEGF-A), Human X-linked inhibitor-of-apoptosis protein (XIAP), Drosophila hairless, S. cerevisiae transcription factor II D (TFIID), S. cerevisiae Yes1 Associated Transcriptional Regulator (YAP1), Human proto-oncogene tyrosine-protein kinase Src (c-src), Human fibroblast growth factor 1 (FGF-1), Simian picomavirus, Turnip crinkle virus, Coxsackievirus B3 (CVB3) and Coxsackievirus A (CVB1/2).
5. The method of claim 1 , wherein the 3′ Group I self-splicing intron fragment and the 5′ Group I self-splicing intron fragment are from a Cyanobacterium anabaena sp. Pre-tRNA-Leu gene and/or from a T4 phage Td gene.
6. The method of claim 1 , further comprising forming the circular RNA by splint-mediated ligation of the precursor RNA.
7. A precursor RNA comprising the following elements operably connected to each other and arranged in tandem in a 5′ to 3′ orientation:
a) a 5′ element,
b) a 3′ Group I self-splicing intron fragment,
c) none or an element comprising an IRES and a protein coding region or an element comprising a noncoding region,
d) a 5′ Group I self-splicing intron fragment, and
e) a 3′ element
wherein the 5′ element and the 3′ element form a thermodynamically stable multiple way junction RNA structure with a Gibbs free energy (ΔG) from −190 kcal/mol to −9.0 kcal/mol, provided that the stable structure is not a duplex with at least 95% base pairing between the 5′ element and the 3′ element,
wherein the 3′ Group I self-splicing intron fragment and the 5′ Group I self-splicing intron fragment form a self-cleaving and self-ligating RNA molecule, thereby generating the circular RNA
wherein the thermodynamically stable multiple way junction RNA structure comprises a 4-way junction (4WJ) comprising
a first branch of the 4WJ domain is formed from a 5′ portion of a 4WJa sequence and a 3′ portion of a 4WJd sequence and comprises a first helical region,
a second branch of the 4WJ domain is formed from a 3′ portion of the 4WJa sequence and a 5′ portion of a 4WJb sequence and comprises a second helical region, and
a third branch of the 4WJ domain is formed from a 3′ portion of the 4WJb sequence and a 5′ portion of a 4WJc sequence and comprises a third helical region, and
a fourth branch of the 4WJ domain is formed from a 3′ portion of the 4WJc sequence and a 5′ portion of the 4WJd sequence and comprises a fourth helical region,
wherein each of said helical regions comprises a plurality of RNA nucleotide pairs that form canonical Watson-Crick bonds.
8. The precursor RNA of claim 7 , wherein the 5′ element comprises none or a sequence that forms at least one stem-loop structure and the 3′ element comprises none or a sequence that forms at least one stem-loop structure, provided that, when the 5′ element does not comprise a stem-loop structure, then the 3′ element comprises at least one stem-loop structure; and, when the 3′ element does not comprise a stem-loop structure, then the 5′ element comprises at least one stem-loop structure.
9. The precursor RNA of claim 7 , wherein
the 4WJa comprises or consists of SEQ ID NO: 7, 4WJb comprises or consists of SEQ ID NO: 8, 4WJc comprises or consists of SEQ ID NO: 9, and 4WJd comprises or consists of SEQ ID NO: 102; or
the 4WJa comprises or consists of SEQ ID NO: 103, 4WJb comprises or consists of SEQ ID NO: 104, 4WJc comprises or consists of SEQ ID NO: 105, and 4WJd comprises or consists of SEQ ID NO: 106; or
the 4WJa comprises or consists of SEQ ID NO: 115, 4WJb comprises or consists of SEQ ID NO: 116, 4WJc comprises or consists of SEQ ID NO: 117, and 4WJd comprises or consists of SEQ ID NO: 118; or
the 4WJa comprises or consists of UGCAGGUG, 4WJb comprises or consists of ACGGGC, 4WJc comprises or consists of CCAGCA, and 4WJd comprises or consists of SEQ ID NO: 67; or
the 4WJa comprises or consists of SEQ ID NO: 74, 4WJb comprises or consists of AACUG, 4WJc comprises or consists of SEQ ID NO: 75, and 4WJd comprises or consists of AUCAUG; or
the 4WJa comprises or consists of SEQ ID NO: 122, 4WJb comprises or consists of GAACU, 4WJc comprises or consists of SEQ ID NO: 123, and 4WJd comprises or consists of AAUCA; or
the 4WJa comprises or consists of SEQ ID NO: 125, 4WJb comprises or consists of SEQ ID NO: 126, 4WJc comprises or consists of SEQ ID NO: 127, and 4WJd comprises or consists of SEQ ID NO: 128.
10. A method of producing a protein in a cell, comprising introducing to the cell the precursor RNA of claim 7 comprising the protein coding region, and producing the protein.
11. A method of editing a gene in a cell, comprising introducing to the cell the precursor RNA of claim 7 comprising the noncoding region capable of editing the gene, and editing the gene.
12. The precursor RNA of claim 9 , wherein the 4WJa comprises or consists of SEQ ID NO: 7, 4WJb comprises or consists of SEQ ID NO: 8, 4WJc comprises or consists of SEQ ID NO: 9, and 4WJd comprises or consists of SEQ ID NO: 102.
13. The precursor RNA of claim 9 , wherein the 4WJa comprises or consists of SEQ ID NO: 103, 4WJb comprises or consists of SEQ ID NO: 104, 4WJc comprises or consists of SEQ ID NO: 105, and 4WJd comprises or consists of SEQ ID NO: 106.
14. The precursor RNA of claim 9 , wherein the 4WJa comprises or consists of SEQ ID NO: 115, 4WJb comprises or consists of SEQ ID NO: 116, 4WJc comprises or consists of SEQ ID NO: 117, and 4WJd comprises or consists of SEQ ID NO: 118.
15. The precursor RNA of claim 9 , wherein the 4WJa comprises or consists of UGCAGGUG, 4WJb comprises or consists of ACGGGC, 4WJc comprises or consists of CCAGCA, and 4WJd comprises or consists of SEQ ID NO: 67.
16. The precursor RNA of claim 9 , wherein the 4WJa comprises or consists of SEQ ID NO: 74, 4WJb comprises or consists of AACUG, 4WJc comprises or consists of SEQ ID NO: 75, and 4WJd comprises or consists of AUCAUG.
17. The precursor RNA of claim 9 , wherein the 4WJa comprises or consists of SEQ ID NO: 122, 4WJb comprises or consists of GAACU, 4WJc comprises or consists of SEQ ID NO: 123, and 4WJd comprises or consists of AAUCA.
18. The precursor RNA of claim 9 , wherein the 4WJa comprises or consists of SEQ ID NO: 125, 4WJb comprises or consists of SEQ ID NO: 126, 4WJc comprises or consists of SEQ ID NO: 127, and 4WJd comprises or consists of SEQ ID NO: 128.
19. The method of claim 9 , wherein the 4WJa comprises or consists of SEQ ID NO: 7, 4WJb comprises or consists of SEQ ID NO: 8, 4WJc comprises or consists of SEQ ID NO: 9, and 4WJd comprises or consists of SEQ ID NO: 102.
20. The method of claim 9 , wherein the 4WJa comprises or consists of SEQ ID NO: 103, 4WJb comprises or consists of SEQ ID NO: 104, 4WJc comprises or consists of SEQ ID NO: 105, and 4WJd comprises or consists of SEQ ID NO: 106.
21. The method of claim 9 , wherein the 4WJa comprises or consists of SEQ ID NO: 115, 4WJb comprises or consists of SEQ ID NO: 116, 4WJc comprises or consists of SEQ ID NO: 117, and 4WJd comprises or consists of SEQ ID NO: 118.
22. The method of claim 9 , wherein the 4WJa comprises or consists of UGCAGGUG, 4WJb comprises or consists of ACGGGC, 4WJc comprises or consists of CCAGCA, and 4WJd comprises or consists of SEQ ID NO: 67.
23. The method of claim 9 , wherein the 4WJa comprises or consists of SEQ ID NO: 74, 4WJb comprises or consists of AACUG, 4WJc comprises or consists of SEQ ID NO: 75, and 4WJd comprises or consists of AUCAUG.
24. The method of claim 9 , wherein the 4WJa comprises or consists of SEQ ID NO: 122, 4WJb comprises or consists of GAACU, 4WJc comprises or consists of SEQ ID NO: 123, and 4WJd comprises or consists of AAUCA.
25. The method of claim 9 , wherein the 4WJa comprises or consists of SEQ ID NO: 125, 4WJb comprises or consists of SEQ ID NO: 126, 4WJc comprises or consists of SEQ ID NO: 127, and 4WJd comprises or consists of SEQ ID NO: 128.