title: Ultrafast DNA sequencing on a microchip by a hybrid separation mechanism that gives 600 bases in 6.5 minutes.
abstract: To realize the immense potential of large-scale genomic sequencing after the completion of the second human genome (Venter's), the costs for the complete sequencing of additional genomes must be dramatically reduced. Among the technologies being developed to reduce sequencing costs, microchip electrophoresis is the only new technology ready to produce the long reads most suitable for the de novo sequencing and assembly of large and complex genomes. Compared with the current paradigm of capillary electrophoresis, microchip systems promise to reduce sequencing costs dramatically by increasing throughput, reducing reagent consumption, and integrating the many steps of the sequencing pipeline onto a single platform. Although capillary-based systems require approximately 70 min to deliver approximately 650 bases of contiguous sequence, we report sequencing up to 600 bases in just 6.5 min by microchip electrophoresis with a unique polymer matrix/adsorbed polymer wall coating combination. This represents a two-thirds reduction in sequencing time over any previously published chip sequencing result, with comparable read length and sequence quality. We hypothesize that these ultrafast long reads on chips can be achieved because the combined polymer system engenders a recently discovered "hybrid" mechanism of DNA electromigration, in which DNA molecules alternate rapidly between repeating through the intact polymer network and disrupting network entanglements to drag polymers through the solution, similar to dsDNA dynamics we observe in single-molecule DNA imaging studies. Most importantly, these results reveal the surprisingly powerful ability of microchip electrophoresis to provide ultrafast Sanger sequencing, which will translate to increased system throughput and reduced costs.
authors.affiliation: Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA.
authors.forename: Christopher P
authors.initials: CP
authors.lastname: Fredlake
authors.forename: Daniel G
authors.initials: DG
authors.lastname: Hert
authors.forename: Cheuk-Wai
authors.initials: CW
authors.lastname: Kan
authors.forename: Thomas N
authors.initials: TN
authors.lastname: Chiesl
authors.forename: Brian E
authors.initials: BE
authors.lastname: Root
authors.forename: Ryan E
authors.initials: RE
authors.lastname: Forster
authors.forename: Annelise E
authors.initials: AE
authors.lastname: Barron
mesh_terms: D004247:DNA / Q000032:analysis; D004277:DNA, Single-Stranded / Q000737:chemistry; D046209:Electrophoresis, Microchip / Q000295:instrumentation* / Q000379:methods*; D004867:Equipment Design; D015894:Genome, Human; D006801:Humans; D018715:Microscopy, Video / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D011108:Polymers / Q000737:chemistry; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA / Q000295:instrumentation* / Q000379:methods*; D013997:Time Factors
chemical_list: D004277:DNA, Single-Stranded; D011108:Polymers; D004247:DNA