Self-Associating Block Copolymer Networks for Microchip Electrophoresis Provide Enhanced DNA Separation via “Inchworm” Chain Dynamics

Chiesl, Thomas N.; Putz, Karl W.; Babu, Meena; Mathias, Patrick C.; Shaikh, Kashan; Goluch, Edgar D.; Liu, Chang; Barron, Annelise E.

doi:10.1021/ac060193u

Cited by 23 publications

(27 citation statements)

References 31 publications

(50 reference statements)

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“…Since this conventional determination assumed that a polymer solution would be a flexible polymer in a good solvent, it is difficult to determine an accurate mesh size for semiflexible and rigid polymer solutions. Additionally this conventional determination is inadequate for the mixture of the different kinds of polymers [12], a self-associating block copolymer [13], and a lyotropic polymer liquid crystal [14], because the approach required the detail physical characterization of these polymers. The direct determination of polymer mesh size is desirable.…”

Section: Introductionmentioning

confidence: 99%

Dynamic light‐scattering measurement of sieving polymer solutions for protein separation on SDS CE

et al. 2009

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We evaluated the mesh size and homogeneity of polymer network by dynamic light scattering and discussed the relationship between the physical properties of polymer network and the protein separation behavior by capillary polymer electrophoresis. We compared three kinds of sieving polymers in solutions with a wide range of molecular weights and concentrations: polyacrylamide and polyethylene oxide as flexible polymers, and hydroxyethyl cellulose as a semiflexible polymer. We found that the mobility of protein was dominated primarily by the mesh size xi, irrespective of the type of sieving polymers, and the peak spacing between protein peaks increased drastically in the range of xi<10 nm, where the mobility also decreased. And the peak widths were dependent on the molecular species of sieving polymers and their homogeneity of polymer network. We proposed that a polymer network with a homogenous mesh size of less than 10 nm is the best sieving medium for separation of the proteins in the molecular weight range 14,300-97,200 Da from the view point of the resolution in protein separation.

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Section: Introductionmentioning

confidence: 99%

Dynamic light‐scattering measurement of sieving polymer solutions for protein separation on SDS CE

et al. 2009

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“…Current technology allows for rapid ssDNA separations at the capillary or microchip scale with minimal sample requirements and high resolution [1][2][3]. These separations generally employ chemical or physical sieving gels to achieve separations based on the length of the DNA fragment, as in DNA sequencing.…”

Section: Introductionmentioning

confidence: 99%

Guanosine gel for sequence‐dependent separation of polymorphic ssDNA

et al. 2007

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The separation of fluorescent-labeled ssDNA fragments of equal length based on differences in sequence was achieved through the use of guanosine gels (G-gels) formed by guanosine-5'-monophosphate (GMP) in capillary gel electrokinetic chromatography (CGEKC) with LIF detection. Baseline resolution was achieved for homodimers and homopentamers of A, T, and C. G-gel CGEKC provided better resolution than CZE, MEKC, or a sieving gel in CGE. Resolution improved with increasing GMP, indicating that the interaction is linked to structural organization of the G-gel. Fluorescence intensity and anisotropy show that the order of interaction with G-gels is T>C>A. We then investigated four conformationally similar, polymorphic 76-mers with A/G substitutions that are utilized in forensic DNA typing. Resolution was achieved by CGEKC but not CZE or CGE. In CGEKC, the negatively charged G-gels and oligonucleotides electromigrate toward the positive inlet while being driven by EOF to the negative outlet. The net forward velocity is the greatest for oligonucleotides most closely associated with the slower, more cumbersome G-gel network. For the 76-mers, resolution increases with increasing difference in guanosine content between strands and, for a given difference, with increasing total guanosines in the strands.

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“…Lambda DNA (Invitrogen) fluorescently labeled with YOYO-1 (Molecular Probes) was visualized during microchannel electrophoresis using a homebuilt system described previously (47). Briefly, the imaging system consists of an inverted epifluorescence microscope outfitted with a ϫ100-N.A.…”

Section: Methodsmentioning

confidence: 99%

Ultrafast DNA sequencing on a microchip by a hybrid separation mechanism that gives 600 bases in 6.5 minutes

Fredlake

Hert

Kan

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

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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 Ϸ70 min to deliver Ϸ650 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 reptating 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.DNA separation mechanism ͉ microchip electrophoresis ͉ entangled polymer solution ͉ DNA imaging

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Self-Associating Block Copolymer Networks for Microchip Electrophoresis Provide Enhanced DNA Separation via “Inchworm” Chain Dynamics

Cited by 23 publications

References 31 publications

Dynamic light‐scattering measurement of sieving polymer solutions for protein separation on SDS CE

Dynamic light‐scattering measurement of sieving polymer solutions for protein separation on SDS CE

Guanosine gel for sequence‐dependent separation of polymorphic ssDNA

Ultrafast DNA sequencing on a microchip by a hybrid separation mechanism that gives 600 bases in 6.5 minutes

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