Abstract
The analysis and fractionation of large DNA molecules plays a key role in many genome projects. The standard method, pulsed-field gel electrophoresis (PFGE), is slow, with running times ranging from 10 hours to more than 200 hours. In this report, we describe a thumbnail-sized device that sorts large DNA fragments (61–209 kilobases (kb)) in 15 seconds, with a resolution of ∼13%. An array of micron-scale posts serves as the sieving matrix, and integrated microfluidic channels spatially shape the electric fields over the matrix. Asymmetric pulsed fields are applied for continuous-flow operation, which sorts DNA molecules in different directions according to their molecular masses, much as a prism deflects light of different wavelengths at different angles. We demonstrate the robustness of the device by using it to separate large DNA inserts prepared from bacterial artificial chromosomes, a widely used DNA source for most genomics projects.
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References
Carle, G.F., Frank, M. & Olson, M.V. Electrophoretic separations of large DNA molecules by periodic inversion of the electric field. Science 232, 65–68 (1986).
Schwartz, D.C. & Cantor, C.R. Separation of yeast chromosome-sized DNAs by pulsed field gradient gel electrophoresis. Cell 37, 67–75 (1984).
Chu, G., Vollrath, D. & Davis, R.W. Separation of large DNA molecules by contour-clamped homogeneous electric fields. Science 234, 1582–1585 (1986).
Cox, E.C., Vocke, C.D., Walter, S., Gregg, K.Y. & Bain, E.S. Electrophoretic karyotype for Dictyostelium discoideum. Proc. Natl. Acad. Sci. USA 87, 8247–8251 (1990).
Sambrook, J., Fritsch, E.F. & Maniatis, T. Molecular Cloning: A Laboratory Manual, 2nd Edn. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, 1989).
Huang, Z. et al. Large DNA fragment sizing by flow cytometry: application to the characterization of P1 artificial chromosome (PAC) clones. Nucleic Acids Res. 24, 4202–4209 (1996).
Chou, H.P., Spence, C., Scherer, A. & Quake, S. A microfabricated device for sizing and sorting DNA molecules. Proc. Natl. Acad. Sci. USA 96, 11–13 (1999).
Guo, X.H., Huff, E.J. & Schwartz, D.C. Sizing single DNA molecules. Nature 359, 783–784 (1992).
Kim, Y. & Morris, M.D. Rapid pulsed field capillary electrophoretic separation of megabase nucleic acids. Anal. Chem. 67, 784–786 (1995).
Volkmuth, W.D. & Austin, R.H. DNA electrophoresis in microlithographic arrays. Nature 358, 600–602 (1992).
Chou, C.F. et al. Sorting by diffusion: an asymmetric obstacle course for continuous molecular separation. Proc. Natl. Acad. Sci. USA 96, 13762–13765 (1999).
Cabodi, M., Chen, Y. & Craighead, H. Continuous separation of biomolecules by the laterally asymmetric diffusion array with out-of-plane sample injection. Electrophoresis (in press).
Han, J. & Craighead, H.G. Separation of long DNA molecules in a microfabricated entropic trap array. Science 288, 1026–1029 (2000).
Bakajin, O. et al. Separation of 100-kilobase DNA molecules in 10 seconds. Anal. Chem. 73, 6053–6056 (2001).
Osoegawa, K. et al. Bacterial artificial chromosome libraries for mouse sequencing and functional analysis. Genome Res. 10, 116–128 (2000).
Giddings, J.C. Unified Separation Science (Wiley, New York, 1991).
Huang, L.R. et al. Generation of large-area tunable uniform electric fields in microfluidic arrays for rapid DNA separation. Int. Elect. Dev. Meet. Tech. Digest 363–366 (2001).
Doi, M. & Edwards, S.F. The Theory of Polymer Dynamics (Oxford Univ. Press, Oxford, UK, 1989).
Smith, S.B., Finzi, L. & Bustamante, C. Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads. Science 258, 1122–1126 (1992).
Acknowledgements
This work was supported by grants from the Defense Advanced Research Projects Agency (MDA972-00-1-0031), the National Institutes of Health (HG01506), and the State of New Jersey (NJCST 99-100-082-2042-007). We thank K. Osoegawa and P. de Jong, who supplied the BAC and PAC libraries, and members of our laboratories for discussion.
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Huang, L., Tegenfeldt, J., Kraeft, J. et al. A DNA prism for high-speed continuous fractionation of large DNA molecules. Nat Biotechnol 20, 1048–1051 (2002). https://doi.org/10.1038/nbt733
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DOI: https://doi.org/10.1038/nbt733
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