Efficient production of superior dumbbell-shaped DNA minimal vectors for small hairpin RNA expression

Nucleic Acids Research

Volumn 43, Issue 18, 2015, Pages

  Yu, Han ^a   Jiang, Xiaoou ^a   Tan, Kar Tong ^a,b   Hang, Liting ^a,c   Patzel, Volker ^a  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^b NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^c NATIONAL NEUROSCIENCE INSTITUTE   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

SHORT HAIRPIN RNA; TETRAHYDROFURAN; VIRUS VECTOR; DNA; FURAN DERIVATIVE; PRIMER DNA; SMALL INTERFERING RNA;

ARTICLE; CONTROLLED STUDY; DNA HAIRPIN; DNA VECTOR; GENE CASSETTE; GENE CONVERSION; GENE EXPRESSION; GENETIC PURITY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; REACTION ANALYSIS; STRUCTURE ANALYSIS; BIOSYNTHESIS; CELL LINE; CHEMISTRY; ECONOMICS; GENE INACTIVATION; GENE VECTOR; GENETICS; HUMAN; PROCEDURES;

CELL LINE; DNA; DNA PRIMERS; FURANS; GENE EXPRESSION; GENE KNOCKOUT TECHNIQUES; GENETIC VECTORS; HUMANS; POLYMERASE CHAIN REACTION; RNA, SMALL INTERFERING;

EID: 84983735516     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv583     Document Type: Article

References (23)

1. Kay, M.A. (2011) State-of-the-art gene-based therapies: the road ahead. Nat. Rev. Genet., 12, 316-328.
2. Biasco, L., Baricordi, C. and Aiuti, A. (2012) Retroviral integrations in gene therapy trials. Mol. Ther., 20, 709-716.
3. Yin, H., Kanasty, R.L., Eltoukhy, A.A., Vegas, A.J., Dorkin, J.R. and Anderson, D.G. (2014) Non-viral vectors for gene-based therapy. Nat. Rev. Genet., 15, 541-555.
4. Mok, P.L., Cheong, S.K., Leong, C.F., Chua, K.H. and Ainoon, O. (2012) Extended and stable gene expression via nucleofection of MIDGE construct into adult human marrow mesenchymal stromal cells. Cytotechnology, 64, 203-216.
5. Kaur, T., Slavcev, R.A. and Wettig, S.D. (2009) Addressing the challenge: current and future directions in ovarian cancer therapy. Curr. Gene Ther., 9, 434-458.
6. López-Fuertes, L., Pérez-Jiménez, E., Vila-Coro, A.J., Sack, F., Moreno, S., Konig, S.A., Junghans, C., Wittig, B., Timón, M. and Esteban, M. (2002) DNA vaccination with linear minimalistic (MIDGE) vectors confers protection against Leishmania major infection in mice. Vaccine, 21, 247-257.
7. Schakowski, F., Gorschlüter, M., Junghans, C., Schroff, M., Buttgereit, P., Ziske, C., Schöttker, B., König-Merediz, S.A., Sauerbruch, T., Wittig, B. et al. (2001) A novel minimal-size vector (MIDGE) improves transgene expression in colon carcinoma cells and avoids transfection of undesired DNA. Mol. Ther., 3, 793-800.
8. Zanta, M.A., Belguise-Valladier, P. and Behr, J.-P. (1999) Gene delivery: a single nuclear localization signal peptide is sufficient to carry DNA to the cell nucleus. Proc. Natl. Acad. Sci. U.S.A., 96, 91-96.
9. Cost, G.J. (2007) Enzymatic ligation assisted by nucleases: simultaneous ligation and digestion promote the ordered assembly of DNA. Nat. Protoc., 2, 2198-2202.
10. Taki, M., Kato, Y., Miyagishi, M., Takagi, Y. and Taira, K. (2004) Small-interfering-RNA expression in cells based on an efficiently constructed dumbbell-shaped DNA. Angew. Chem., Int. Ed., 43, 3160-3163.
11. Taki, M., Kato, Y., Miyagishi, M., Takagi, Y., Sano, M. and Taira, K. (2003) A direct and efficient synthesis method for dumbell-shaped linear DNA using PCR in vitro. Nucleic Acids Symp. Ser., 3, 191-192.
12. Myslinski, E., Amé, J.-C., Krol, A. and Carbon, P. (2001) An unusually compact external promoter for RNA polymerase III transcription of the human H1RNA gene. Nucleic Acids Res., 29, 2502-2509.
13. Jung, U., Jiang, X., Kaufmann, S.H.E. and Patzel, V. (2013) A universal stem-loop primer-based TaqMan RT-PCR protocol for cost efficient detection of small non-coding RNA. RNA, 19, 1864-1873.
14. Rumney, S. and Kool, E.T. (1995) Structural optimization of non-nucleotide loop replacements for duplex and triplex DNAs. J. Am. Chem. Soc., 117, 5635-5646.
15. Takeshita, M., Chang, C.N., Johnson, F., Will, S. and Grollman, A.P. (1987) Oligodeoxynucleotides containing synthetic abasic sites. Model substrates for DNA polymerases and apurinic/apyrimidinic endonucleases. J. Biol. Chem., 262, 10171-10179.
16. Lin, C., Xie, M., Chen, J.J.L., Liu, Y. and Yan, H. (2006) Rolling-circle amplification of a DNA nanojunction. Angew. Chem., Int. Ed., 45, 7537-7539.
17. Chu, B.C.F. and Orgel, L.E. (1992) The stability of different forms of double-stranded decoy DNA in serum and nuclear extracts. Nucleic Acids Res., 20, 5857-5858.
18. Hori, K., Mark, D.F. and Richardson, C.C. (1979) Deoxyribonucleic acid polymerase of bacteriophage T7. Characterization of the exonuclease activities of the gene 5 protein and the reconstituted polymerase. J. Biol. Chem., 254, 11598-11604.
19. Patzel, V., Rutz, S., Dietrich, I., Köberle, C., Scheffold, A. and Kaufmann, S.H.E. (2005) Design of siRNAs producing unstructured guide-RNAs results in improved RNA interference efficiency. Nat. Biotechnol., 23, 1440-1444.
20. Köberle, C., Kaufmann, S.H.E. and Patzel, V. (2006) Selecting effective siRNAs based on guide RNA structure. Nat. Protoc., 1, 1832-1839.
21. Li, M. and Wilson, D.M. (2013) Human apurinic/apyrimidinic endonuclease 1. Antioxid. Redox Signal., 20, 678-707.
22. Mohr, D., Frey, S., Fischer, T., Güttler, T. and Görlich, D. (2009) Characterisation of the passive permeability barrier of nuclear pore complexes. EMBO J., 28, 2541-2553
23. Rybenkov, V.V., Cozzarelli, N.R. and Vologodskii, A.V. (1993) Probability of DNA knotting and the effective diameter of the DNA double helix. Proc. Natl. Acad. Sci. U.S.A., 90, 5307-5311.