Replicative minicircle vectors with improved expression
The present invention relates to the production and use of covalently closed circular (ccc) recombinant DNA molecules such as plasmids, cosmids, bacterial artificial chromosomes (BACs), bacteriophages, viral vectors and hybrids thereof, and more particularly to vector modifications that improve expression of said DNA molecules.
1. A method of constructing a eukaryotic replicative minicircle expression vector and expressing a gene of interest therefrom comprising:
a) combining i) a eukaryotic region with 5′ and 3′ ends encoding a gene of interest and comprising an intron, the intron comprising a 5′ splice donor and a 3′ acceptor branch site, a bacterial replication origin selected from the group consisting of R6K replication origin, and ColE2-P9 replication origin, and an RNA selectable marker; with ii) a spacer region linking the 5′ and 3′ ends of the eukaryotic region, said spacer region being less than 500 basepairs in length, to create a eukaryotic replicative minicircle expression vector; and
b) introducing said replicative minicircle expression vector into a target eukaryotic cell or a eukaryotic organism comprising the target eukaryotic cell, under conditions wherein the target eukaryotic cell is transfected and said gene of interest is expressed.
2. The method of claim 1 , wherein said RNA selectable marker is an RNA-IN regulating RNA-OUT functional variant with at least 95% sequence identity to a sequence selected from the group consisting of SEQ ID NO:20, and SEQ ID NO:22.
3. The method of claim 1 , wherein said RNA selectable marker is selected from the group consisting of:
an RNA-OUT selectable marker that encodes an RNA-IN regulating RNA-OUT RNA with at least 95% sequence identity to SEQ ID NO: 21;
an RNAI selectable marker that encodes an RNAII regulating RNAI RNA with at least 95% sequence identity to SEQ ID NO: 33;
an IncB RNAI selectable marker encoding an RNAII regulating RNAI RNA with at least 95% sequence identity to SEQ ID NO: 35; and
an synthetic RNA selectable marker encoding an RNA selectable marker complement regulating RNA with at least 95% sequence identity to SEQ ID NO: 38.
4. The method of claim 1 , wherein said intron with a 5′ splice donor and a 3′ acceptor branch site is a functional variant with at least 95% sequence identity to a sequence selected from the group consisting of: SEQ ID NO: 1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10.
5. The method of claim 1 , wherein said pUC replication origin and said RNA selectable marker positioned within said intron is a functional variant with at least 95% sequence identity to SEQ ID NO: 29.
6. A method of constructing a eukaryotic replicative minicircle expression vector comprising:
a) combining i) a eukaryotic region with 5′ and 3′ ends encoding a gene of interest and comprising an intron the intron comprising a 5′ splice donor and a 3′ acceptor branch site, a bacterial region comprising an R6K origin or a ColE2-P9 bacterial replication origin, and a RNA selectable marker with ii) a spacer region linking the 5′ and 3′ ends of the eukaryotic region sequences, said spacer region being less than 500 basepairs in length, to create a eukaryotic replicative minicircle expression vector;
b) transforming said replicative minicircle expression vector into cells of an RNA selectable marker regulated bacterial cell line;
c) isolating the resultant transformed bacterial cells by selection; and
d) propagating the resultant transformed bacterial cells in culture.
7. The method of claim 6 , wherein said RNA selectable marker is an RNA-IN regulating RNA-OUT functional variant with at least 95% sequence identity to a sequence selected from the group consisting of SEQ ID NO:20, and SEQ ID NO:22.
8. The method of claim 6 , wherein said RNA selectable marker is selected from the group consisting of:
an RNA-OUT selectable marker that encodes an RNA-IN regulating RNA-OUT RNA with at least 95% sequence identity to SEQ ID NO: 21;
an RNAI selectable marker that encodes an RNAII regulating RNAI RNA with at least 95% sequence identity to SEQ ID NO: 33;
an IncB RNAI selectable marker encoding an RNAII regulating RNAI RNA with at least 95% sequence identity to SEQ ID NO: 35; and
an synthetic RNA selectable marker encoding an RNA selectable marker complement regulating RNA with at least 95% sequence identity to SEQ ID NO: 38.
9. The method of claim 6 , wherein said intron with a 5′ splice donor and a 3′ acceptor branch site is a functional variant with at least 95% sequence identity to a sequence selected from the group consisting of: SEQ ID NO: 1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10.
10. The method of claim 6 , wherein said pUC replication origin and said RNA selectable marker positioned within said intron is a functional variant with at least 95% sequence identity to SEQ ID NO: 29.
11. A eukaryotic replicative minicircle expression vector comprising i) a eukaryotic region sequence with 5′ and 3′ ends encoding a gene of interest and comprising an intron, the intron comprising a 5′ splice donor and a 3′ acceptor branch site, a bacterial replication origin selected from the group consisting of R6K replication origin, and ColE2-P9 replication origin, and an RNA selectable marker; and ii) a spacer region of less than 500 basepairs in length linking the 5′ and 3′ ends of the eukaryotic region sequences.
12. The vector of claim 11 , wherein said RNA selectable marker is an RNA-IN regulating RNA-OUT functional variant with at least 95% sequence identity to a sequence selected from the group consisting of SEQ ID NO:20, and SEQ ID NO:22.
13. The vector of claim 11 , wherein said RNA selectable marker is selected from the group consisting of: an RNA-OUT selectable marker that encodes an RNA-IN regulating RNA-OUT RNA with at least 95% sequence identity to SEQ ID NO: 21; an RNAI selectable marker that encodes an RNAII regulating RNAI RNA with at least 95% sequence identity to SEQ ID NO: 33; an IncB RNAI selectable marker encoding an RNAII regulating RNAI RNA with at least 95% sequence identity to SEQ ID NO: 35; an synthetic RNA selectable marker encoding an RNA selectable marker complement regulating RNA with at least 95% sequence identity to SEQ ID NO: 38.
14. The vector of claim 11 , wherein said intron with a 5′ splice donor and a 3′ acceptor branch site is a functional variant with at least 95% sequence identity to a sequence selected from the group consisting of: SEQ ID NO: 1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, SEQ ID NO:9, SEQ ID NO:10.
15. The vector of claim 11 , wherein said pUC replication origin and said RNA selectable marker positioned within said intron is a functional variant with at least 95% sequence identity to SEQ ID NO: 29.