Abstract
Microfluidics exhibit great promise as an alternative to conventional polyacrylamide slab gels to improve separation performance and decrease cross-contamination in the fractionation of selected DNA fragments from a complex mixture. This article provides a method to enable the spatial and temporal fractionation of multiple DNA fragments. We incorporate ten parallel extraction channels to increase the sampling range to cover multiple DNA fragments. Two neighboring fragments of 36, and 39 bases were first separated and simultaneously collected within 8 min. The ten recovered fractions were then analyzed by polymerase chain reaction amplification and capillary electrophoresis analysis. Six recovered DNA samples from the ten channels exhibited purities greater than 90 %, and two exhibited purities higher than 99 %. In contrast to a single extraction channel, this method also provides a better technical solution to high-throughput problems perceived to be more fundamental.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Baker CA, Roper MG (2010) A continuous-flow, microfluidic fraction collection device. J Chromatogr A 1217:4743–4748
Eftenhauser CS, Manz A, Wldmer HM (1995) Manipulation of sample fractions on a capillary electrophoresis chip. Anal Chem 67:2284–2287
Footz T, Wunsam S, Kulak S, Crabtree HJ et al (2001) Sample purification on a microfluidic device. Electrophoresis 22:3868–3875
Fukumura R, Takahashi H, Saito T, Tsutsumi Y et al (2003) A sensitive transcriptome analysis method that can detect unknown transcripts. Nucleic Acids Res 31(16):e94. doi:10.1093/nar/gng094
Huang LR, Tegenfeldt JR, Kraeft JJ, Sturm JC, Austin RH, Cox EC (2002) A DNA prism for high-speed continuous fractionation of large DNA molecules. Nat Biotech 20:1048–1051
Irie T, Oshida T, Hasegawa H, Matsuoka Y et al (2000) Automated DNA fragment collection by capillary array gel electrophoresis in search of differentially expressed genes. Electrophoresis 21(2):367–374
Khandurina J, Chovan T, Guttman A (2002) Micropreparative fraction collection in microfluidic devices. Anal Chem 74:1737–1740
Kim SL, Tai TH (2013) Identification of SNPs in closely related temperate Japonica Rice cultivars using restriction enzyme-phased sequencing. PLoS One 8(3):e60176. doi:10.1371/journal.pone.0060176
Li ZY, Sun K, Sunayama M, Matsuo Y et al (2011) On-chip fraction collection for multiple selected ssDNA fragments using isolated extraction channels. J Chromatogr A 1218:997–1003
Lin RS, Burke DT, Burns MA (2003) Selective extraction of size-fractioned DNA samples in microfabricated electrophoresis devices. J Chromatogr A 1010:255–268
Lin RS, Burke DT, Burns MA (2005) Addressable electric fields for size-fractioned sample extraction in microfluidic devices. Anal Chem 77:4338–4347
Shendure J, Ji H (2008) Next-generation DNA sequencing. Nat Biotech 26:1135–1145
Sinville R, Soper SA (2007) High resolution DNA separations using microchip electrophoresis. Sep Sci 30:1714–1728
Sun K, Li ZY, Ueno K, Juodkazis S et al (2007) Electrophoretic chip for high-fidelity fractionation of double-stranded DNA. Electrophoresis 28:1572–1578
Sun K, Suzuki N, Li ZY, Araki R, Ueno K, Juodkazis S et al (2009) High-fidelity fractionation of single-strand DNA fragments differing in size by one-base on spiral-channel electrophoretic chip. Electrophoresis 30:4277–4284
Tulock JJ, Shannon MA, Bohn PW, Sweedler JV (2004) Microfluidic separation and gateable fraction collection for mass-limited samples. Anal Chem 76:6419–6425
Wang Z, Taylor J, Jemere AB, Harrison DJ (2010) Microfluidic devices for electrokinetic sample fractionation. Electrophoresis 31:2575–2583
Zalewski DR, Gardeniers HJGE (2009) Continuous fractionation of a two-component mixture by zone electrophoresis. Electrophoresis 30:4187–4194
Zalewski DR, Schlautmann S, Schasfoort RBM, Gardeniers HJGE (2008) Electrokinetic sorting and collection of fractions for preparative capillary electrophoresis on a chip. Lab Chip 8:801–809
Acknowledgments
The authors gratefully acknowledge Hokkaido University for chip fabrication. This work was supported by State Key Laboratory of Urban Water Resource and Environment (Harbin Institute of Technology) (No. 2011TS02).
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Sun, K., Li, Z., You, S. et al. Spatiotemporal fractionation of two DNA fragments by microfluidic devices. Microfluid Nanofluid 19, 291–298 (2015). https://doi.org/10.1007/s10404-014-1523-7
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10404-014-1523-7