A DNA prism for high-speed continuous fractionation of large DNA molecules

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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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Figure 1: Structure of the microfabricated device illustrating the sieving matrix integrated with the microfluidic channels.
Figure 2: (A) Schematic showing the behavior of small and large DNA molecules in microfabricated arrays through a full cycle of asymmetric electric fields of alternating angles.
Figure 3: Separation of BAC and PAC inserts at different frequencies.

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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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Correspondence to Edward C. Cox.

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The authors declare no competing financial interests.

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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) doi:10.1038/nbt733

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