A computer model for the analysis of DNA replication intermediates by two-dimensional agarose gel electrophoresis

Gene

Volumn 217, Issue 1-2, 1998, Pages 41-49

  Viguera, E ^a   Rodriguez A ^b   Hernandez P ^a   Krimer, D B ^a   Trellez, O ^b   Schvartzman, J B ^a  

^a CENTRO DE INVESTIGACIONES BIOLÓGICAS   (Spain)

^b UNIVERSITY OF MÁLAGA   (Spain)

Author keywords

2D agarose gel electrophoresis; DNA replication; Origins; Replication fork barriers (RFBs); Replication intermediates; Termini

Indexed keywords

DNA; DNA FRAGMENT;

AGAR GEL ELECTROPHORESIS; ARTICLE; COMPUTER MODEL; DNA REPLICATION; ELECTROPHORETIC MOBILITY; ESCHERICHIA COLI; PLASMID; PRIORITY JOURNAL; RESTRICTION FRAGMENT; TWO DIMENSIONAL GEL ELECTROPHORESIS;

COMPUTER SIMULATION; DEOXYRIBONUCLEASE ECORI; DEOXYRIBONUCLEASE HINDIII; DNA; DNA REPLICATION; ELECTROPHORESIS, AGAR GEL; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; ESCHERICHIA COLI; OLIGODEOXYRIBONUCLEOTIDES; PLASMIDS; RESTRICTION MAPPING;

ESCHERICHIA COLI;

EID: 0345698880     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0378-1119(98)00375-8     Document Type: Article

References (28)

1. Bell L., Byers B. Separation of branched from linear DNA by two-dimensional gel electrophoresis. Anal. Biochem. 130:1983;527-535.
2. Brewer B.J., Fangman W.L. The localization of replication origins on ARS plasmids in S. cerevisiae. Cell. 51:1987;463-471.
3. Brewer B.J., Fangman W.L. A replication fork barrier at the 3′ end of yeast ribosomal RNA genes. Cell. 55:1988;637-643.
4. Brewer B.J., Fangman W.L. Initiation at closely spaced replication origins in a yeast chromosome. Science. 262:1993;1728-1731.
5. Brewer B.J., Fangman W.L. Initiation preference at a yeast origin of replication. Proc. Natl. Acad. Sci. USA. 91:1994;3418-3422.
6. Brewer B.J., Lockshon D., Fangman W.L. The arrest of replication forks in the rDNA of yeast occurs independently of transcription. Cell. 71:1992;267-276.
7. Deshpande A.M., Newlon C.S. DNA replication fork pause sites dependent on transcription. Science. 272:1996;1030-1033.
8. Dhar V., Schildkraut C.L. Role of EBNA-1 in arresting replication forks at the Epstein-Barr virus oriP family of tandem repeats. Mol. Cell. Biol. 11:1991;6268-6278.
9. Fischer S.G., Lerman L.S. Length-independent separation of DNA restriction fragments in two-dimensional gel electrophoresis. Cell. 16:1979;191-200.
10. Friedman K.L., Brewer B.J. Analysis of replication intermediates by two-dimensional agarose gel electrophoresis. DNA Replication. 262:1995;613-627.
11. Gahn T.A., Schildkraut C.L. The Epstein-Barr virus origin of plasmid replication, oriP, contains both the initiation and termination sites of DNA replication. Cell. 58:1989;527-535.
12. Hernández P., Martín-Parras L., Martínez-Robles M.L., Schvartzman J.B. Conserved features in the mode of replication of eukaryotic ribosomal RNA genes. EMBO J. 12:1993;1475-1485.
13. Kalejta R.F., Hamlin J.L. Composite patterns in neutral/neutral two-dimensional gels demonstrate inefficient replication origin usage. Mol. Cell. Biol. 16:1996;4915-4922.
14. Linskens M.H.K., Huberman J.A. Organization of replication of ribosomal DNA in Saccharomyces cerevisiae. Mol. Cell. Biol. 8:1988;4927-4935.
15. Linskens M.H.K., Huberman J.A. Ambiguities in results obtained with 2D gel replicon mapping techniques. Nucl. Acids Res. 18:1990;647-652.
16. Little R.D., Platt T.H.K., Schildkraut C.L. Initiation and termination of DNA replication in human rRNA genes. Mol. Cell. Biol. 13:1993;6600-6613.
17. Liu Y., Botchan M. Replication of bovine papillomavirus type-1 DNA initiates within an E2-responsive enhancer element. J. Virol. 64:1990;5903-5911.
18. López-Estraño C., Schvartzman J.B., Hernández P. The replication of ribosomal RNA genes in eukaryotes. Chromosomes Today. 12:1997;149-169.
19. López-Estraño C., Schvartzman J.B., Krimer D.B., Hernández P. Co-localization of polar replication fork barriers and rRNA transcription terminators in mouse rDNA. J. Mol. Biol. 277:1998;249-256.
20. Marahrens Y., Stillman B. A yeast chromosomal origin of DNA replication defined by multiple functional elements. Science. 255:1992;817-823.
21. Martín-Parras L., Hernández P., Martínez-Robles M.L., Schvartzman J.B. Unidirectional replication as visualized by two-dimensional agarose gel electrophoresis. J. Mol. Biol. 220:1991;843-853.
22. Martín-Parras L., Hernández P., Martínez-Robles M.L., Schvartzman J.B. Initiation of DNA replication in ColE1 plasmids containing multiple potential origins of replication. J. Biol. Chem. 267:1992;22496-22505.
23. Sánchez J.A., Kim S.M., Huberman J.A. Ribosomal DNA replication in the fission yeast Schizosaccharomyces pombe. Exp. Cell. Res. 238:1998;220-230.
24. Schvartzman J.B., Adolph S., Martín-Parras L., Schildkraut C.L. Evidence that replication initiates at only some of the potential origins in each oligomeric form of Bovine Papillomavirus Type 1 DNA. Mol. Cell. Biol. 10:1990;3078-3086.
25. Southern E.M. Measurement of DNA length by gel electrophoresis. Anal. Biochem. 100:1979;319-323.
26. Stellwagen N.C. Anomalous electrophoresis of deoxyribonucleic acid restriction fragments on polyacrylamide gels. Biochemistry. 22:1983;6186-6193.
27. Viguera E., Hernandez P., Krimer D.B., Boistov A.S., Lurz R., Alonso J.C., Schvartzman J.B. The ColE1 unidirectional origin acts as a polar replication fork pausing site. J. Biol. Chem. 271:1996;22414-22421.
28. Wiesendanger B., Lucchini R., Koller T., Sogo J.M. Replication fork barriers in the Xenopus rDNA. Nucl. Acids Res. 22:1994;5038-5046.