Gate-controlled microfluidic chamber with magnetic bead for DNA sequencing-by-synthesis technology

Proceedings of the 5th International Conference on Nanochannels, Microchannels and Minichannels, ICNMM2007

Volumn , Issue , 2007, Pages 163-167

  Esfandyarpour, Hesaam ^a,b   Davis, Ronald W ^b,c  

^a Stanford University   (United States)

^b STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c STANFORD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA POLYMERIZATION; GATE-CONTROLLED MAGNETIC BEAD (GCMB) PLATFORMS; MAGNETIC BEADS; SORTING TEMPLATES;

BIOSYNTHESIS; CROSSTALK; DNA; MAGNETIC FIELDS; POLYDIMETHYLSILOXANE; POLYMERIZATION;

MICROFLUIDICS;

EID: 37249072283     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1115/ICNMM2007-30119     Document Type: Conference Paper

References (35)

1. F. Sanger, et al., "DNA Sequencing with ChainTerminating Inhibitors", PNAS, 74: 5463-5467(1977).
2. L.M. Smith, et al.," Fluorescence detection in automated DNA sequence analysis". Nature 321: 674-679 (1986).
3. F. Collins, Ari Patrinos, et al., "New Goals for the U.S. Human Genome Project: 1998-2003", Science 282: 682-689 (1998).
4. F. Collins, Ari Patrinos, et al., "The Human Genome Project: Lessons from Large-Scale Biology", Science 300: 286-290 (2003).
5. D.H. Jones, "An iterative and regenerative method for DNA sequencing", Biotechniques 22: 938-946(1997).
6. B. B. Rosenblum, et al., "New dye-labeled terminators for improved DNA sequencing patterns", Nuc. Acids. Res. 25: 4500-4504 (1997).
7. M. A. Innis, et al., "DNA Sequencing with Thermus aquaticus DNA Polymerase and Direct Sequencing of Polymerase Chain Reaction-Amplified DNA", PNAS, 85: 9436-9440 (1988).
8. M. Ronaghi, et al., "A Sequencing Method Based on Real-Time Pyrophosphate", Science 281: 262-265 (1998).
9. M. J. Levene, et al., "Zero-Mode Waveguides for Single-Molecule Analysis at High Concentrations", Science 299: 682-686 (2003).
10. M. Margulies, et al., "Genome sequencing in microfabricated high-density picolitre reactors", Nature, 03959: 1-5 (2005).
11. H. Fakhrai-Rad, et al., "Pyrosequencing: An Accurate Detection Platform for Single Nucleotide Polymorphisms", Human Mutation 19:479.485 (2002).
12. M. Ronaghi, "Improved Performance of Pyrosequencing Using Single-Stranded DNA-Binding Protein", Anal. Biochem., 286(2), 282-288 (2000).
13. Dynabeads® M-270 Streptavidin, Invitrogen Co., Online source: https://catalog.invitrogen.com/index.cfm?fuseaction=viewCatalog. viewProductDetails&productDescription=15072&catname= North%20America%20Main.
14. E. P. Kartalov, S.R. Quake, "Microfluidic device reads up to four consecutive base pairs in DNA sequencing-bysynthesis." Nucleic Acids Res., 32(9):2873-9(2004).
15. J. D. Gruber, "Estimation of single nucleotide polymorphism allele frequency in DNA pools by using Pyrosequencing", Human Genetics, 110:395-401 (2002).
16. T. Thorsen, et al., "Microfluidic Large Scale Integration", Science 298: 580-584 (2002).
17. S.R. Quake and A. Scherer, "From Micro to Nano Fabrication with Soft Materials", Science 290: 1536-40 (2000).
18. F.K. Balagadde, et al., "Long-term monitoring of bacteria undergoing programmed population control in a microchemostat", Science, 309(5731): 137-40 (2005).
19. C.L, Hansen, et al., "A microfluidic device for kinetic optimization of protein crystallization and in situ structure determination", J Am. Chem. Soc., 128(10):3142-3 (2006).
20. J.S. Marcus, et al., "Microfluidic Single-Cell mRNA Isolation and Analysis", Anal. Chem. 10.1021 (2006).
21. L.M. Metzker, et al., "Termination of DNA synthesis by novel 3'-modified-deoxyribonucleoside 5'-triphosphates" Nucleic Acids Res. 22:4259-4267(1994).
22. H. Koster., et al., "A strategy for rapid and efficient DNA sequencing by mass spectroscopy", Nat. Biotechnol. 14: 1123-1128 (1996).
23. D.-J. Fu, et al., "Sequencing exons 5 to 8 of the p53 gene by MALDI-TOF mass spectrometry", Nat. Biotechnol., 16: 381-384(1998).
24. M.T. Roskey, et al., "DNA sequencing by delayed extraction -matrix-assisted laser desorption/ionization time of light mass spectrometry", PNAS 93: 4724-4729(1996).
25. J.R. Edwards, et al., "DNA sequencing using biotinylated dideoxynucleotides and mass spectroscopy". Nucleic Acids Res. 29: e104 (2001).
26. R. Drmanac, et al., "Sequencing of megabase plus DNA by hybridization: theory of the method", Genomics 4: 114-128 (1989).
27. J. J. Nakane, et al., "Nanopore sensors for nucleic acid analysis" J. Phys. Condens. Matter 15:R1365-1393(2003).
28. M. Akeson, et al., "Microsecond time-scale discrimination among polycytidylic acid, polyadenylic acid and polyuridylic acid as homopolymers or as segments within single RNA molecules", Biophys. J. 11: 3227-3233 (1999).
29. S. Howorka, et al., "Sequence-specific detection of individual DNA strands using engineered nanopores", Nat. Biotechno.,19: 636-639(2001).
30. D.W. Deamer and M. Akeson, "Nanopores and nucleic acids: prospects for ultrarapid sequencing", Trends Biotechnol., 18: 147-154 (2000).
31. E.D. Hyman, "A new method of sequencing DNA", Anal. Biochem., 174, 423-436(1988).
32. M. Ronaghi, "Pyrosequencing sheds light on DNA sequencing", Genome Res., 11: 3-11(2001).
33. N. Pourmand, et al., "Multiplex pyrosequencing", Nucleic Acids Res., 30: e31(2002).
34. http://thebigone.stanford.edu/foundry
35. M. Ehn, et al., "Escherichia coli single-stranded DNA-binding protein, a molecular tool for improving sequence quality in pyrosequencing" , Electrophoresis, 23: 3289-3299 (2002).