Microfluidic-assisted analysis of replicating DNA molecules

Nature Protocols

Volumn 4, Issue 6, 2009, Pages 849-861

  Sidorova, Julia M ^a   Li, Nianzhen ^b,d   Schwartz, David C ^c   Folch, Albert ^b   Monnat Jr , Raymond J ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

^b University of Washington   (United States)

^c UNIVERSITY OF WISCONSIN MADISON   (United States)

^d Fluxion Biosciences   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DIMETICONE; DNA; GENOMIC DNA;

ARTICLE; BIOTECHNOLOGICAL PROCEDURES; CAPILLARY; CLINICAL PROTOCOL; CONVENTIONAL SOFT LITHOGRAPHY; DNA DETERMINATION; DNA REPLICATION; FLUORESCENCE MICROSCOPY; IMMUNOHISTOCHEMISTRY; INFORMATION PROCESSING; MICROFLUIDIC ANALYSIS; NANOFABRICATION; PRIMED IN SITU LABELING; PRIORITY JOURNAL; PROCESS DESIGN; PROCESS DEVELOPMENT; QUALITY CONTROL; REPLICON;

CHROMOSOME MAPPING; DNA; DNA REPLICATION; GENES; GENOMICS; GLASS; INDICATORS AND REAGENTS; MICROFLUIDIC ANALYTICAL TECHNIQUES; MINIATURIZATION; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; SILICON;

EID: 66749165907     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2009.54     Document Type: Article

References (32)

1. Alberts, B. DNA replication and recombination. Nature 421, 431-435 (2003).
2. Kelly, T. & Stillman, B. Duplication of DNA in eukaryotic cells. In DNA Replication and Human Disease (ed. DePamphilis, M.L.) 1-29 (Cold Spring Harbor Press, Cold Spring Harbor, New York, 2006).
3. Loeb, L.A. & Monnat, R.J. DNA polymerases and human disease. Nat. Rev. Genet. 9, 594-604 (2008).
4. McCulloch, S.D. & Kunkel, T.A. The fidelity of DNA synthesis by eukaryotic replicative and translesion synthesis polymerases. Cell Res. 18, 148-161 (2008).
5. Yang, W. & Woodgate, R. What a difference a decade makes: Insights into translesion DNA synthesis. Proc. Natl. Acad. Sci. USA 104, 15591-15598 (2007).
6. Gilson, E. & Geli, V. How telomeres are replicated. Nat. Rev. Mol. Cell Biol. 8, 825-838 (2007).
7. Bianchi, A. & Shore, D. How telomerase reaches its end: Mechanism of telomerase regulation by the telomeric complex. Mol. Cell 31 153-165 (2008).
8. Kornberg, A. & Baker, T.A. DNA Replication (W.H. Freeman, New York, 1991).
9. Pommier, Y. & Diasio, R.B. Pharmacologic agents that target DNA replication. In DNA Replication and Human Disease (ed. DePamphilis, M.L.) 519-546 (Cold Spring Harbor Press, Cold Spring Harbor, New York, 2006).
10. Berdis, A.J. DNA polymerases as therapeutic targets. Biochemistry 47, 8253-8260 (2008).
11. Vengrova, S. & Dalgaard, J.Z. Eds. DNA Replication Methods and Protocols (Humana Press, New York, 2009).
12. Manders, E.M., Stap, J., Brakenhoff, G.J., van Driel, R. & Aten, J.A. Dynamics of three-dimensional replication patterns during the S-phase, analysed by double labelling of DNA and confocal microscopy. J. Cell Sci. 103, 857-862 (1992).
13. Jackson, D.A. & Pombo, A. Replicon clusters are stable units of chromosome structure: Evidence that nuclear organization contributes to the efficient activation and propagation of S phase in human cells. J. Cell Biol. 140, 1285-95 (1998).
14. Huberman, J.A. & Riggs, A.D. Autoradiography of chromosomal DNA fibers from Chinese hamster cells. Proc. Natl. Acad. Sci. USA 55, 599-606 (1966).
15. Cairns, J. The chromosome of Escherichia coli. In Cold Spring Harbor Symposia on Quantitative Biology Vol. 28 43-46 (Cold Spring Harbor Press, Cold Spring Harbor, New York, 1963).
16. Bensimon, A. et al. Alignment and sensitive detection of DNA by a moving interface. Science 265, 2096-2098 (1994).
17. Yokota, H. et al. A new method for straightening DNA molecules for optical restriction mapping. Nucleic Acids Res. 25, 1064-1070 (1997).
18. Herrick, J. & Bensimon, A. Single molecule analysis of DNA replication. Biochimie 81, 859-871 (1999).
19. Norio, P. & Schildkraut, C.L. Visualization of DNA replication on individual Epstein-Barr virus episomes. Science 294, 2361-2364 (2001).
20. Sidorova, J.M., Li, N., Folch, A. & Monnat, R.J. Jr. The RecQ helicase WRN is required for normal replication fork progression after DNA damage or replication fork arrest. Cell Cycle 7, 796-807 (2008).
21. Dimalanta, E.T. et al. A microfluidic system for large DNA molecule arrays. Anal. Chem. 76, 5293-5301 (2004).
22. Zhou, S., Herschleb, J. & Schwartz, D.C. A single molecule system for whole genome analysis. In New High Throughput Technologies for DNA Sequencing and Genomics (ed. Mitchelson, K.R.) 265-302 (Elsevier, Amsterdam, 2007).
23. Zhou, S. et al. Validation of rice genome sequence by optical mapping. BMC Genomics 8, 278 (2007).
24. Valouev, A., Schwartz, D., Zhou, S. & Waterman, M.S. An algorithm for assembly of ordered restriction maps from single DNA molecules. Proc. Natl. Acad. Sci. USA 103, 15770-15775 (2006).
25. Kidd, J.M. et al. Mapping and sequencing of structural variation fromeight human genomes. Nature 453, 56-64 (2008).
26. McDonald, J.C. et al. Fabrication of microfluidic systems in poly(dimethylsiloxane). Electrophoresis 21, 27-40 (2000).
27. Beebe, D.J., Mensing, G.A. & Walker, G.M. Physics and applications of microfluidics in biology. Annu. Rev. Biomed. Eng. 4, 261-286 (2002).
28. Tegenfeldt, J. et al. Micro- and nanofluidics for DNA analysis. Anal. Bioanal. Chem. 378, 1678-1692 (2004).
29. Atencia, J. & Beebe, D.J. Controlled microfluidic interfaces. Nature 437, 648-655 (2005).
30. Whitesides, G.M. The origins and the future of microfluidics. Nature 442, 368-373 (2006).
31. Herschleb, J., Ananiev, G. & Schwartz, D.C. Pulsed-field gel electrophoresis. Nat. Protoc. 2, 677-684 (2007).
32. Lundin, C. et al. Methyl methanesulfonate (MMS) produces heat-labile DNA damage but no detectable in vivo DNA double-strand breaks. Nucleic Acids Res. 33, 3799-3811 (2005).