Closed-ended linear duplex DNA for non-viral gene transfer
Aspects of the disclosure relate to a nucleic acid comprising a heterologous nucleic acid insert flanked by interrupted self-complementary sequences, wherein one self-complementary sequence is interrupted by a cross-arm sequence forming two opposing, lengthwise-symmetric stem-loops, and wherein the other of the self-complementary sequences is interrupted by a truncated cross-arm sequence. Methods of delivering the nucleic acid to a cell are also provided.
1. An isolated nucleic acid comprising a nucleic acid insert comprising a transgene;
wherein the insert is flanked by at least two adeno-associated virus (AAV) inverted terminal repeat (ITR) sequences;
wherein the at least two ITR sequences are asymmetric and covalently linked with respect to one another;
wherein each of the at least two ITR sequences has an operative terminal resolution site and a rolling circle replication protein rep binding element (RBE);
wherein a first ITR sequence is interrupted by a cross-arm sequence forming two opposing, lengthwise-symmetric stem-loops, each of the opposing lengthwise-symmetric stem-loops having a stem portion in the range of 5 to 15 base pairs in length and a loop portion having 2 to 5 unpaired deoxyribonucleotides;
wherein a second ITR sequence is interrupted by a truncated cross-arm sequence having one or more deletions of between 11 and 20 nucleotides in a palindromic sequence region B-B′ and/or a palindromic sequence region C-C′; and
wherein the isolated nucleic acid is a closed-ended linear duplex DNA (ceDNA).
2. The isolated nucleic acid of claim 1 , wherein the at least two ITRs are in the range of 40 to 1000 nucleotides in length.
3. The isolated nucleic acid of claim 1 , wherein the truncated cross-arm sequence has a Gibbs free energy (ΔG) of unfolding under physiological conditions in the range of −12 kcal/mol to −30 kcal/mol.
4. The isolated nucleic acid of claim 1 , wherein the RBE comprises the sequence 5′-GCTCGCTCGCTC-3′ (SEQ ID NO: 1).
5. The isolated nucleic acid of claim 1 , wherein the operative terminal resolution site comprises a sequence 5′-TT-3′ or wherein the 3′ end of the operative terminal resolution site is 15 to 25 nucleotides from the 5′ end of the rolling circle replication protein binding element.
6. The isolated nucleic acid of claim 1 , wherein the truncated cross-arm sequence forms two opposing, lengthwise-asymmetric stem-loops, optionally wherein one of the opposing, lengthwise-asymmetric stem-loops has a stem portion in the range of 8 to 10 base pairs in length and a loop portion having 2 to 5 unpaired deoxyribonucleotides or one lengthwise-asymmetric stem-loop has a stem portion less than 8 base pairs in length and a loop portion having 2 to 5 deoxyribonucleotides.
7. The isolated nucleic acid of claim 1 , wherein the nucleic acid insert comprising a transgene is engineered to express a protein or functional RNA.
8. The isolated nucleic acid of claim 1 , wherein the nucleic acid insert is in the range of 500 to 50,000 nucleotides in length and is a promoterless construct as a substrate for gene editing selected from the group consisting of a substrate for TALENS, a substrate for zinc finger nucleases (ZFNs), a substrate for meganucleases, a substrate for Cas9, and a substrate for another gene editing protein.
9. The isolated nucleic acid of claim 1 , wherein the nucleic acid is contained within a vector.
10. A composition comprising a plurality of isolated nucleic acids as described in claim 1 , optionally wherein the plurality of isolated nucleic acids are linked end-to-end.
11. An isolated host cell comprising the isolated nucleic acid of claim 1 , optionally wherein the host cell further comprises a rolling circle replication protein that selectively binds to the RBE of the nucleic acid.
12. A method of delivering a heterologous nucleic acid to a cell, the method comprising delivering to the cell the isolated nucleic acid of claim 1 .
13. A method of delivering a heterologous nucleic acid to a subject, the method comprising delivering to the subject the isolated nucleic acid claim 1 , wherein the delivery of the nucleic acid does not result in an immune response against the isolated nucleic acid in the subject, wherein the immune response is a humoral response or a cellular response, and wherein the delivery is once or multiple times.
14. A method of delivering a heterologous nucleic acid to a subject, the method comprising delivering a host cell of claim 11 to the subject, wherein the host cell is delivered once or multiple times to the subject.
15. The isolated nucleic acid of claim 1 , wherein the two opposing, lengthwise-symmetric stem-loops formed by interrupted palindromic sequences B-B′ and C-C′.
16. The isolated nucleic acid of claim 1 , wherein the one or more deletions in the truncated cross-arm sequence are between 11 and 20 nucleotides.