Circular RNA for translation in eukaryotic cells
Methods and constructs for engineering circular RNA are disclosed. In some embodiments, the methods and constructs comprise a vector for making circular RNA, the vector comprising the following elements operably connected to each other and arranged in the following sequence: a.) a 5′ homology arm, b.) a 3′ group I intron fragment containing a 3′ splice site dinucleotide, c.) optionally, a 5′ spacer sequence, d.) a protein coding or noncoding region, e.) optionally, a 3′ spacer sequence, f) a 5′ Group I intron fragment containing a 5′ splice site dinucleotide, and g.) a 3′ homology arm, the vector allowing production of a circular RNA that is translatable or biologically active inside eukaryotic cells. Methods for purifying the circular RNA produced by the vector and the use of nucleoside modifications in circular RNA produced by the vector are also disclosed.
1. A vector for making circular RNA, comprising:
a) at least one spacer sequence that increases splicing efficiency compared to a vector without the at least one spacer sequence,
b) a 3′ Group I self-splicing intron fragment containing a 3′ splice site dinucleotide,
c) an internal ribosome entry site (IRES),
d) a protein coding region, and
e) a 5′ Group I self-splicing intron fragment containing a 5′ splice site dinucleotide, wherein the vector allows production of a circular RNA that is translatable or biologically active inside eukaryotic cells.
2. The vector of claim 1 , wherein the 3′ Group I intron fragment and the 5′ Group I intron fragment are from a Cyanobacterium Anabeana sp. pre-tRNA-Leu gene or a T4 phage Td gene.
3. The vector of claim 1 , further comprising an RNA polymerase promoter positioned at the 5′ end of the vector.
4. The vector of claim 3 , wherein the RNA polymerase promoter is an RNA polymerase promoter from a T7 virus, T6 virus, SP6 virus, T3 virus, or T4 virus.
5. The vector of claim 1 , comprising the following elements operably connected to each other and arranged in the following sequence:
a) the 3′ Group I self-splicing intron fragment containing the 3′ splice site dinucleotide,
b) the at least one spacer sequence, wherein the at least one spacer sequence is a 5′ spacer sequence,
c) the IRES,
d) the protein coding region, and
e) the 5′ Group I self-splicing intron fragment containing the 5′ splice site dinucleotide.
6. The vector of claim 5 , further comprising a 5′ internal homology region positioned between (a) and (b) and a 3′ internal homology region positioned between (d) and (e).
7. The vector of claim 1 , comprising the following elements operably connected to each other and arranged in the following sequence:
a) the 3′ Group I self-splicing intron fragment containing the 3′ splice site dinucleotide,
b) the IRES,
c) the protein coding region,
d) the at least one spacer sequence, wherein the at least one spacer sequence is a 3′ spacer sequence, and
e) the 5′ Group I self-splicing intron fragment containing the 5′ splice site dinucleotide.
8. The vector of claim 7 , further comprising a 5′ internal homology region positioned between (a) and (b) and a 3′ internal homology region positioned between (d) and (e).
9. The vector of claim 1 , comprising the following elements operably connected to each other and arranged in the following sequence:
a) the 3′ Group I self-splicing intron fragment containing the 3′ splice site dinucleotide,
b) the at least one spacer sequence, wherein the at least one spacer sequence is a 5′ spacer sequence
c) the IRES,
d) the protein coding region,
e) a 3′ spacer sequence that increases splicing efficiency compared to a vector without the 3′ spacer sequence, and
f) the 5′ Group I self-splicing intron fragment containing the 3′ splice site dinucleotide.
10. The vector of claim 9 , further comprising a 5′ internal homology region positioned between (a) and (b) and a 3′ internal homology region positioned between (e) and (f).
11. The vector of claim 1 , wherein the protein coding region encodes a human protein, a non-human protein, or a synthetic protein for therapeutic use.
12. The vector of claim 1 , wherein the protein coding region encodes a chimeric antigen receptor (CAR).
13. The vector of claim 1 , wherein the at least one spacer sequence is about 10-60 nucleotides in length.
14. The vector of claim 1 , wherein the at least one spacer sequence comprises a polyA sequence or a polyA-C sequence.
15. The vector of claim 1 , wherein the vector produces a circular RNA having a size of at least 500 nucleotides.
16. The vector of claim 1 , wherein the at least one spacer sequence is designed using an RNA folding computer software.
17. The vector of claim 16 , wherein RNA folding computer software is RNAFold software.
18. The vector of claim 1 , wherein the at least one spacer sequence is at least 7 nucleotides in length.
19. The vector of claim 1 , wherein the at least one spacer sequence is no more than 100 nucleotides in length.