Active transcription promotes single-stranded oligonucleotide mediated gene repair

Biochemical and Biophysical Research Communications

Volumn 353, Issue 1, 2007, Pages 33-39

  Huen, Michael S Y ^a   Lu, Lin Yu ^a   Liu, De Pei ^b   Huang, Jian Dong ^a  

^a UNIVERSITY OF HONG KONG   (Hong Kong)

^b INSTITUTE OF BASIC MEDICAL SCIENCES   (China)

Author keywords

Red; Gene therapy; Recombination; Strand bias

Indexed keywords

OLIGONUCLEOTIDE; SINGLE STRANDED DNA;

ARTICLE; CONTROLLED STUDY; ESCHERICHIA COLI; GENETIC MANIPULATION; GENETIC RECOMBINATION; MISMATCH REPAIR; MUTANT; NONHUMAN; NUCLEOTIDE SEQUENCE; PLASMID; PRIORITY JOURNAL; PROMOTER REGION; REPORTER GENE; TRANSCRIPTION INITIATION;

DNA DAMAGE; DNA REPAIR; DNA, BACTERIAL; ESCHERICHIA COLI; RECOMBINATION, GENETIC; TARGETED GENE REPAIR; TRANS-ACTIVATION (GENETICS);

ESCHERICHIA COLI;

EID: 33845608839     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2006.11.146     Document Type: Article

References (25)

1. Copeland N.G., Jenkins N.A., and Court D.L. Recombineering: a powerful new tool for mouse functional genomics. Nat. Rev. Genet. 2 (2001) 769-779
2. Lee E.C., Yu D., Martinez de Velasco J., Tessarollo L., Swing D.A., Court D.L., Jenkins N.A., and Copeland N.G. A highly efficient Escherichia coli-based chromosome engineering system adapted for recombinogenic targeting and subcloning of BAC DNA. Genomics 73 (2001) 56-65
3. Yu D., Ellis H.M., Lee E.C., Jenkins N.A., Copeland N.G., and Court D.L. An efficient recombination system for chromosome engineering in Escherichia coli. Proc. Natl. Acad. Sci. USA 97 (2000) 5978-5983
4. Huen M.S., Li X.T., Lu L.Y., Watt R.M., Liu D.P., and Huang J.D. The involvement of replication in single stranded oligonucleotide-mediated gene repair. Nucleic Acids Res. (2006) 10.1093/nar/gkl852 Epub ahead of print
5. Li X.T., Costantino N., Lu L.Y., Liu D.P., Watt R.M., Cheah K.S., Court D.L., and Huang J.D. Identification of factors influencing strand bias in oligonucleotide-mediated recombination in Escherichia coli. Nucleic Acids Res. 31 (2003) 6674-6687
6. Ellis H.M., Yu D., DiTizio T., and Court D.L. High efficiency mutagenesis, repair, and engineering of chromosomal DNA using single-stranded oligonucleotides. Proc. Natl. Acad. Sci. USA 98 (2001) 6742-6746
7. Costantino N., and Court D.L. Enhanced levels of lambda Red-mediated recombinants in mismatch repair mutants. Proc. Natl. Acad. Sci. USA 100 (2003) 15748-15753
8. Barras F., and Marinus M.G. The great GATC: DNA methylation in E. coli. Trends Genet. 5 (1989) 139-143
9. Stancheva I., Koller T., and Sogo J.M. Asymmetry of Dam remethylation on the leading and lagging arms of plasmid replicative intermediates. Embo J. 18 (1999) 6542-6551
10. Brachman E.E., and Kmiec E.B. DNA replication and transcription direct a DNA strand bias in the process of targeted gene repair in mammalian cells. J. Cell Sci. 117 (2004) 3867-3874
11. Hu Y., Parekh-Olmedo H., Drury M., Skogen M., and Kmiec E.B. Reaction parameters of targeted gene repair in Mammalian cells. Mol. Biotechnol. 29 (2005) 197-210
12. Suzuki T., Murai A., and Muramatsu T. Bleomycin stimulates targeted gene repair directed by single-stranded oligodeoxynucleotides in BHK-21 cells. Int. J. Mol. Med. 16 (2005) 615-620
13. Yu D., Sawitzke J.A., Ellis H., and Court D.L. Recombineering with overlapping single-stranded DNA oligonucleotides: testing a recombination intermediate. Proc. Natl. Acad. Sci. USA 100 (2003) 7207-7212
14. Li X.T., Costantino N., Lu L.Y., Liu D.P., Watt R.M., Cheah K.S., Court D.L., and Huang J.D. Identification of factors influencing strand bias in oligonucleotide-mediated recombination in Escherichia coli. Nucleic Acids Res. 31 (2003) 6674-6687
15. Wong Q.N., Ng V.C., Lin M.C., Kung H.F., Chan D., and Huang J.D. Efficient and seamless DNA recombineering using a thymidylate synthase A selection system in Escherichia coli. Nucleic Acids Res. 33 (2005) e59
16. Su S.S., Lahue R.S., Au K.G., and Modrich P. Mispair specificity of methyl-directed DNA mismatch correction in vitro. J. Biol. Chem. 263 (1988) 6829-6835
17. Kramer B., Kramer W., and Fritz H.J. Different base/base mismatches are corrected with different efficiencies by the methyl-directed DNA mismatch-repair system of E. coli. Cell 38 (1984) 879-887
18. Liu L., Rice M.C., Drury M., Cheng S., Gamper H., and Kmiec E.B. Strand bias in targeted gene repair is influenced by transcriptional activity. Mol. Cell Biol. 22 (2002) 3852-3863
19. Takeuchi Y., Horiuchi T., and Kobayashi T. Transcription-dependent recombination and the role of fork collision in yeast rDNA. Genes Dev. 17 (2003) 1497-1506
20. Elias-Arnanz M., and Salas M. Bacteriophage phi29 DNA replication arrest caused by codirectional collisions with the transcription machinery. Embo J. 16 (1997) 5775-5783
21. Gerber J.K., Gogel E., Berger C., Wallisch M., Muller F., Grummt I., and Grummt F. Termination of mammalian rDNA replication: polar arrest of replication fork movement by transcription termination factor TTF-I. Cell 90 (1997) 559-567
22. Mirkin E.V., and Mirkin S.M. Mechanisms of transcription-replication collisions in bacteria. Mol. Cell. Biol. 25 (2005) 888-895
23. Olavarrieta L., Hernandez P., Krimer D.B., and Schvartzman J.B. DNA knotting caused by head-on collision of transcription and replication. J. Mol. Biol. 322 (2002) 1-6
24. Elias-Arnanz M., and Salas M. Resolution of head-on collisions between the transcription machinery and bacteriophage phi29 DNA polymerase is dependent on RNA polymerase translocation. Embo J. 18 (1999) 5675-5682
25. Wu X.S., Xin L., Yin W.X., Shang X.Y., Lu L., Watt R.M., Cheah K.S., Huang J.D., Liu D.P., and Liang C.C. Increased efficiency of oligonucleotide-mediated gene repair through slowing replication fork progression. Proc. Natl. Acad. Sci. USA 102 (2005) 2508-2513