Transcription affects formation and processing of intermediates in oligonucleotide-mediated gene alteration

Nucleic Acids Research

Volumn 31, Issue 10, 2003, Pages 2659-2670

  Igoucheva, Olga ^a   Alexeev, Vitali ^a   Pryce, Melissa ^a   Yoon, Kyonggeun ^a  

^a THOMAS JEFFERSON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTISENSE OLIGONUCLEOTIDE; BETA LACTAMASE; MUTANT PROTEIN; OLIGONUCLEOTIDE; DNA; LUCIFERASE; RECA PROTEIN;

ANIMAL CELL; ARTICLE; CELL ASSAY; CELL LINE; CHROMOSOME; CONTROLLED STUDY; DNA MODIFICATION; DNA REPAIR; DNA STRAND; DNA SUPERCOILING; EPISOME; GENE LOCATION; GENE MUTATION; GENE TARGETING; GENETIC TRANSCRIPTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; REPORTER GENE; ANIMAL; CHEMISTRY; CHO CELL; CONFORMATION; GENETIC TRANSFECTION; GENETICS; HAMSTER; LACTOSE OPERON; METABOLISM; METHODOLOGY; MOLECULAR GENETICS; MUTATION; PLASMID;

ANIMALIA; MAMMALIA;

ANIMALS; BASE SEQUENCE; CHO CELLS; CRICETINAE; DNA; DNA REPAIR; LAC OPERON; LUCIFERASES; MOLECULAR SEQUENCE DATA; MUTATION; NUCLEIC ACID CONFORMATION; OLIGONUCLEOTIDES; OLIGONUCLEOTIDES, ANTISENSE; PLASMIDS; REC A RECOMBINASES; TRANSCRIPTION, GENETIC; TRANSFECTION;

EID: 0037705453     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg360     Document Type: Article

References (33)

1. Igoucheva,O. and Yoon,K. (2000) Targeted single-base correction by RNA-DNA oligonucleotides. Hum. Gene Ther., 11, 2307-2312.
2. Rice,M.C., Czymmek,K. and Kmiec,E.B. (2001) The potential of nucleic acid repair in functional genomics. Nat. Biotechnol., 19, 321-326.
3. Richardson,P.D., Augustin,L.B., Kren,B.T. and Steer,C.J. (2002) Gene repair and transposon-mediated gene therapy. Stem Cells, 20, 105-118.
4. Igoucheva,O., Peritz,A.E., Levy,D. and Yoon,K. (1999) A sequencespecific gene correction by an RNA-DNA oligonucleotide in mammalian cells characterized by transfection and nuclear extract using a lacZ shuttle system. Gene Ther., 6, 1960-1971.
5. Alexeev,V. and Yoon,K. (1998) Stable and inheritable changes in genotype and phenotype of albino melanocytes induced by an RNA-DNA oligonucleotide. Nat. Biotechnol., 16, 1343-1346.
6. Alexeev,V., Igoucheva,O., Domashenko,A., Cotsarelis,G. and Yoon,K. (2000) Localized in vivo genotypic and phenotypic correction of the albino mutation in skin by RNA-DNA oligonucleotide. Nat. Biotechnol., 18, 43-47.
7. Igoucheva,O., Alexeev,V. and Yoon,K. (2001) Targeted gene correction by small single-stranded oligonucleotides in mammalian cells. Gene Ther., 8, 391-399.
8. Igoucheva,O., Alexeev,V. and Yoon,K. (2002) Nuclear extracts promote gene correction and strand pairing of oligonucleotides to the homologous plasmid. Antisense Nucleic Acid Drug Dev., 12, 235-246.
9. Campbell,C.R., Keown,W., Lowe,L., Kirschling,D. and Kucherlapati,R. (1989) Homologous recombination involving small single-stranded oligonucleotides in human cells. New Biol., 1, 223-227.
10. Rauth,S., Song,K.Y., Ayares,D., Wallace,L., Moore,P.D. and Kucherlapati,R. (1986) Transfection and homologous recombination involving single-stranded DNA substrates in mammalian cells and nuclear extracts. Proc. Natl Acad. Sci. USA, 83, 5587-5591.
11. Simon,J.R. and Moore,P.D. (1987) Homologous recombination between single-stranded DNA and chromosomal genes in Saccharomyces cerevisiae. Mol. Cell. Biol., 7, 2329-2334.
12. Yamamoto,T., Moerschell,R.P., Wakem,L.P., Komar-Panicucci,S. and Sherman,F. (1992) Strand-specificity in the transformation of yeast with synthetic oligonucleotides. Genetics, 131, 811-819.
13. Pierce,E.A., Liu,Q., Igoucheva,O., Omarrudin,R., Ma,H.C., Diamond,S. and Yoon,K. (2003) Oligonucleotide-directed single-base DNA alterations in mouse embryonic stem cells. Gene Ther., 10, 24-33.
14. Alexeev,V., Igoucheva,O. and Yoon,K. (2002) Simultaneous targeted alteration of the tyrosinase and c-kit genes by single-stranded oligonucleotides. Gene Ther., 9, 1667-1675.
15. Liu,L., Rice,M.C. and Kmiec,E.B. (2001) In vivo gene repair of point and frameshift mutations directed by chimeric RNA/DNA oligonucleotides and modified single-stranded oligonucleotides. Nucleic Acids Res., 29, 4238-4250.
16. Liu,L., Rice,M.C., Drury,M., Cheng,S., Gamper,H. and Kmiec,E.B. (2002) Strand bias in targeted gene repair is influenced by transcriptional activity. Mol. Cell. Biol., 22, 3852-3863.
17. Chiu,S.K., Low,K.B., Yuan,A. and Radding,C.M. (1997) Resolution of an early RecA-recombination intermediate by a junction-specific endonuclease. Proc. Natl Acad. Sci. USA, 94, 6079-6083.
18. Holloman,W.K., Wiegand,R., Hoessli,C. and Radding,C.M. (1975) Uptake of homologous single-stranded fragments by superhelical DNA: a possible mechanism for initiation of genetic recombination. Proc. Natl Acad. Sci. USA, 72, 2394-2398.
19. Mooney,R.A., Artsimovitch,I. and Landick,R. (1998) Information processing by RNA polymerase: recognition of regulatory signals during RNA chain elongation. J. Bacteriol., 180, 3265-3275.
20. Citterio,E., Vermeulen,W. and Hoeijmakers,J.H. (2000) Transcriptional healing. Cell, 101, 447-450.
21. Leadon,S.A. (1999) Transcription-coupled repair of DNA damage: unanticipated players, unexpected complexities. Am. J. Hum. Genet., 64, 1259-1263.
22. Tornaletti,S. and Hanawalt,P.C. (1999) Effect of DNA lesions on transcription elongation. Biochimie, 81, 139-146.
23. van Gool,A.J., van der Horst,G.T., Citterio,E. and Hoeijmakers,J.H. (1997) Cockayne syndrome: defective repair of transcription? EMBO J., 16, 4155-4162.
24. Park,J.S., Marr,M.T. and Roberts,J.W. (2002) E. coli Transcription repair coupling factor (Mfd protein) rescues arrested complexes by promoting forward translocation. Cell, 109, 757-767.
25. Le Page,F., Kwoh,E.E., Avrutskaya,A., Gentil,A., Leadon,S.A., Sarasin,A. and Cooper,P.K. (2000) Transcription-coupled repair of 8-oxoguanine: requirement for XPG, TFIIH and CSB and implications for Cockayne syndrome. Cell, 101, 159-171.
26. Mellon,I., Rajpal,D.K., Koi,M., Boland,C.R. and Champe,G.N. (1996) Transcription-coupled repair deficiency and mutations in human mismatch repair genes. Science, 272, 557-560.
27. Gupta,R.C., Bazemore,L.R., Golub,E.I. and Radding,C.M. (1997) Activities of human recombination protein Rad51. Proc. Natl Acad. Sci. USA, 94, 463-468.
28. Mazin,A.V., Bornarth,C.J., Solinger,J.A., Heyer,W.D. and Kowalczykowski,S.C. (2000) Rad54 protein is targeted to pairing loci by the Rad51 nucleoprotein filament. Mol. Cell, 6, 583-592.
29. Van Komen,S., Petukhova,G., Sigurdsson,S., Stratton,S. and Sung,P. (2000) Superhelicity-driven homologous DNA pairing by yeast recombination factors Rad51 and Rad54. Mol. Cell, 6, 563-572.
30. O'Donovan,A., Davies,A.A., Moggs,J.G., West,S.C. and Wood,R.D. (1994) XPG endonuclease makes the 3′ incision in human DNA nucleotide excision repair. Nature, 371, 432-435.
31. Oda,S., Humbert,O., Fiumicino,S., Bignami,M. and Karran,P. (2000) Efficient repair of A/C mismatches in mouse cells deficient in long-patch mismatch repair. EMBO J., 19, 1711-1718.
32. Modrich,P. (1997) Strand-specific mismatch repair in mammalian cells. J. Biol. Chem., 272, 24727-24730.
33. Ellis,H.M., Yu,D., DiTizio,T. and Court,D.L. (2001) High efficiency mutagenesis, repair and engineering of chromosomal DNA using single-stranded oligonucleotides. Proc. Natl Acad. Sci. USA, 98, 6742-6746.