Circular single-stranded synthetic DNA delivery vectors for microRNA

PLoS ONE

Volumn 6, Issue 2, 2011, Pages

  Seidl, Christine I ^a   Ryan, Kevin ^a,b  

^a CITY COLLEGE OF NEW YORK   (United States)

^b CITY UNIVERSITY OF NEW YORK   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EXONUCLEASE; MICRORNA; POLYDEOXYRIBONUCLEOTIDE SYNTHASE; RNA LIGASE; RNA POLYMERASE; SINGLE STRANDED CIRCULAR OLIGONUCLEOTIDE; SYNTHETIC DNA; UNCLASSIFIED DRUG; CIRCULAR DNA; SINGLE STRANDED DNA;

ARTICLE; BACTERIOPHAGE T7; CELL STRAIN HEK293; CONTROLLED STUDY; DENATURING GRADIENT GEL ELECTROPHORESIS; DNA FLANKING REGION; DNA TRANSCRIPTION; DNA VECTOR; ESCHERICHIA COLI; GENE TARGETING; HUMAN; HUMAN CELL; IN VITRO STUDY; NONVIRAL GENE DELIVERY SYSTEM; PROTEIN EXPRESSION; PROTEIN SECONDARY STRUCTURE; RNA PROCESSING; ROLLING CIRCLE TRANSCRIPTION; THERMOSTABILITY; BIOLOGICAL MODEL; CHEMISTRY; CONFORMATION; EVALUATION; GENE TRANSFER; GENE VECTOR; GENETIC TRANSCRIPTION; GENETICS; METHODOLOGY; MOLECULAR CLONING; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; SYNTHESIS;

BACTERIA (MICROORGANISMS);

BASE SEQUENCE; CLONING, MOLECULAR; DNA, CIRCULAR; DNA, SINGLE-STRANDED; ESCHERICHIA COLI; GENE TRANSFER TECHNIQUES; GENETIC VECTORS; HUMANS; MICRORNAS; MODELS, BIOLOGICAL; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; TRANSCRIPTION, GENETIC;

EID: 79951890818     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0016925     Document Type: Article

References (28)

1. Chu CY, Rana TM, (2007) Small RNAs: regulators and guardians of the genome. J Cell Physiol 213: 412-419.
2. Elbashir SM, Lendeckel W, Tuschl T, (2001) RNA interference is mediated by 21- and 22-nucleotide RNAs. Genes Dev 15: 188-200.
3. Siolas D, Lerner C, Burchard J, Ge W, Linsley PS, et al. (2005) Synthetic shRNAs as potent RNAi triggers. Nat Biotechnol 23: 227-231.
4. Manjunath N, Wu H, Subramanya S, Shankar P, (2009) Lentiviral delivery of short hairpin RNAs. Adv Drug Deliv Rev 61: 732-745.
5. Paddison PJ, Caudy AA, Bernstein E, Hannon GJ, Conklin DS, (2002) Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells. Genes Dev 16: 948-958.
6. Brummelkamp TR, Bernards R, Agami R, (2002) A system for stable expression of short interfering RNAs in mammalian cells. Science 296: 550-553.
7. Glover DJ, Lipps HJ, Jans DA, (2005) Towards safe, non-viral therapeutic gene expression in humans. Nat Rev Genet 6: 299-310.
8. Daubendiek SL, Ryan K, Kool ET, (1995) Rolling-Circle RNA Synthesis: Circular Oligonucleotides as Efficient Substrates for T7 RNA Polymerase. J Amer Chem Soc 117: 7818-7819.
9. Diegelman AM, Kool ET, (1998) Generation of circular RNAs and trans-cleaving catalytic RNAs by rolling transcription of circular DNA oligonucleotides encoding hairpin ribozymes. Nucleic Acids Res 26: 3235-3241.
10. Diegelman AM, Kool ET, (1999) Mimicry of the hepatitis delta virus replication cycle mediated by synthetic circular oligodeoxynucleotides. Chem Biol 6: 569-576.
11. Daubendiek SL, Kool ET, (1997) Generation of catalytic RNAs by rolling transcription of synthetic DNA nanocircles. Nat Biotechnol 15: 273-277.
12. Seyhan AA, Vlassov AV, Johnston BH, (2006) RNA interference from multimeric shRNAs generated by rolling circle transcription. Oligonucleotides 16: 353-363.
13. Lee Y, Jeon K, Lee JT, Kim S, Kim VN, (2002) MicroRNA maturation: stepwise processing and subcellular localization. Embo J 21: 4663-4670.
14. Zeng Y, Yi R, Cullen BR, (2005) Recognition and cleavage of primary microRNA precursors by the nuclear processing enzyme Drosha. Embo J 24: 138-148.
15. Han J, Lee Y, Yeom KH, Nam JW, Heo I, et al. (2006) Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex. Cell 125: 887-901.
16. Lee Y, Ahn C, Han J, Choi H, Kim J, et al. (2003) The nuclear RNase III Drosha initiates microRNA processing. Nature 425: 415-419.
17. Michlewski G, Guil S, Semple CA, Caceres JF, (2008) Posttranscriptional regulation of miRNAs harboring conserved terminal loops. Mol Cell 32: 383-393.
18. Zeng Y, Cullen BR, (2003) Sequence requirements for micro RNA processing and function in human cells. RNA 9: 112-123.
19. Ohmichi T, Maki A, Kool ET, (2002) Efficient bacterial transcription of DNA nanocircle vectors with optimized single-stranded promoters. Proc Natl Acad Sci U S A 99: 54-59.
20. Zuker M, (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31: 3406-3415.
21. Diegelman AM, Kool ET, (2000) Chemical and Enzymatic Methods for Preparing circular Single-Stranded DNAs. Protocols in Nucleic Acid Chemistry pp. 5.2.1-5.2.27.
22. Blondal T, Thorisdottir A, Unnsteinsdottir U, Hjorleifsdottir S, Aevarsson A, et al. (2005) Isolation and characterization of a thermostable RNA ligase 1 from a Thermus scotoductus bacteriophage TS2126 with good single-stranded DNA ligation properties. Nucleic Acids Res 33: 135-142.
23. Han J, Lee Y, Yeom KH, Kim YK, Jin H, et al. (2004) The Drosha-DGCR8 complex in primary microRNA processing. Genes Dev 18: 3016-3027.
24. Gregory RI, Yan KP, Amuthan G, Chendrimada T, Doratotaj B, et al. (2004) The Microprocessor complex mediates the genesis of microRNAs. Nature 432: 235-240.
25. Masters BS, Stohl LL, Clayton DA, (1987) Yeast mitochondrial RNA polymerase is homologous to those encoded by bacteriophages T3 and T7. Cell 51: 89-99.
26. Kravchenko JE, Rogozin IB, Koonin EV, Chumakov PM, (2005) Transcription of mammalian messenger RNAs by a nuclear RNA polymerase of mitochondrial origin. Nature 436: 735-739.
27. Ebright RH, (2000) RNA polymerase: structural similarities between bacterial RNA polymerase and eukaryotic RNA polymerase II. J Mol Biol 304: 687-698.
28. Sambrook J, Russell D, (2001) Molecular cloning: A laboratory manual. Cold Spring Harbor, NY Cold Spring Harbor Press.