Electrokinetic Concentration of DNA Polymers in Nanofluidic Channels

Stein, Derek; Deurvorst, Zeno; Heyden, Frank H. J. van der; Koopmans, Wiepke J. A.; Gabel, Alan; Dekker, Cees

doi:10.1021/nl902228p

Cited by 73 publications

(77 citation statements)

References 42 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…It is based on the fact that the velocities of EO and EP are opposite for DNA, inducing an enhancement of DNA concentration at the location where the velocities of EO and EP are of the same magnitude. Stein et al 18 found DNA aggregation in nanochannels by using similar method of force balancing. However, it is very difficult to create a condition in which EO mobility and EP mobility are exactly identical in magnitude.…”

Section: Introductionmentioning

confidence: 99%

On-chip DNA preconcentration in different media conductivities by electrodeless dielectrophoresis

Hui

et al. 2015

Biomicrofluidics

View full text Add to dashboard Cite

Electrodeless dielectrophoresis is the best choice to achieve preconcentration of nanoparticles and biomolecules due to its simple, robust, and easy implementation. We designed a simple chip with microchannels and nano-slits in between and then studied the trapping of DNA in high conductive medium and low conductive medium, corresponding to positive and negative dielectrophoresis (DEP), respectively. It is very important to investigate the trapping in media with different conductivities since one always has to deal with the sample solutions with different conductivities. The trapping process was analyzed by the fluorescent intensity changes. The results showed that DNA could be trapped at the nano-slit in both high and low conductive media in a lower electric field strength (10 V/cm) compared to the existing methods. This is a significant improvement to suppress the Joule heating effect in DEP related experiments. Our work may give insight to researchers for DNA trapping by a simple and low cost device in the Lab-on-a-Chip system. V C 2015 AIP Publishing LLC. [http://dx

show abstract

Section: Introductionmentioning

confidence: 99%

On-chip DNA preconcentration in different media conductivities by electrodeless dielectrophoresis

Hui

et al. 2015

Biomicrofluidics

View full text Add to dashboard Cite

show abstract

“…To alleviate these limitations, various techniques have been reported in a form of miniaturized system. [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16][17] The conventional way to enhance the sensitivity of detection is to increase the copy number of DNA by the chemical amplification through polymerase chain reaction ͑PCR͒. [1][2][3] However, various components are necessary in PCR chemistry, such as enzymes and primers as well as precise temperature control.…”

Section: Introductionmentioning

confidence: 99%

“…[4][5][6][7][8][9][10][11][12][13][14][15][16][17] Sample preconcentration exploits various sample characteristics, including electric charge, size, mobility, and affinity. [4][5][6][7][8][9][10][11][12][13][14][15][16][17] DNA has the unique property of having a uniform charge to size ratio, making charge selective preconcentration efficient. Among the preconcentration techniques using the electric property of DNA, the electrokinetic trapping technique has received much attention due to its high sensitivity and easy miniaturization.…”

Section: Introductionmentioning

confidence: 99%

“…Electrokinetic trapping usually utilizes a charged nanochannel ͑or nanoporous membrane͒ between microchannels, allowing for enrichment of counterions along the structure while excluding coions. [11][12][13][14][15][16][17] The local electric field gradient and concentration polarization are induced when an electric field is applied across the charged nanochannel so that sample preconcentration can be achieved. 17 The electrokinetic trap-ping technique does not suffer from overall device size, since the preconcentration occurs in the immediate proximity of the ion depleted boundary, and has shown a high efficiency for concentrating charged biomolecules.…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Optofluidic in situ maskless lithography of charge selective nanoporous hydrogel for DNA preconcentration

Kim

et al. 2010

Biomicrofluidics

View full text Add to dashboard Cite

An optofluidic maskless photopolymerization process was developed for in situ negatively charged nanoporous hydrogel ͓poly-AMPS ͑2-acrylamido-2-methyl-1-propanesulfonic acid͔͒ fabrication. The optofluidic maskless lithography system, which combines a high power UV source and digital mirror device, enables fast polymerization of arbitrary shaped hydrogels in a microfluidic device. The poly-AMPS hydrogel structures were positioned near the intersections of two microchannels, and were used as a cation-selective filter for biological sample preconcentration. Preconcentration dynamics as well as the fabricated polymer shape were analyzed in three-dimensions using fluorescein sample and a confocal microscope. Finally, single-stranded DNA preconcentration was demonstrated for polymerase chain reaction-free signal enhancement.

show abstract

“…10 Previous work has also used single molecule fluorescence for hydrodynamic studies in nanochannels. 11 In this paper, we demonstrate simultaneous ionic current and fluorescent detection of DNA translocation through glass nanocapillaries. These have been shown to be an alternative to traditional solid state nanopores.…”

mentioning

confidence: 99%

Studying DNA translocation in nanocapillaries using single molecule fluorescence

Thacker

Ghosal

Hernández‐Ainsa

et al. 2012

Applied Physics Letters

View full text Add to dashboard Cite

We demonstrate simultaneous measurements of DNA translocation into glass nanopores using ionic current detection and fluorescent imaging. We verify the correspondence between the passage of a single DNA molecule through the nanopore and the accompanying characteristic ionic current blockage. By tracking the motion of individual DNA molecules in the nanocapillary perpendicular to the optical axis and using a model, we can extract an effective mobility constant for DNA in our geometry under high electric fields. Where nanopores have been combined with single molecule fluorescence, this has been done with the aim of developing alternative DNA sequencing techniques. 10 Previous work has also used single molecule fluorescence for hydrodynamic studies in nanochannels. 11 In this paper, we demonstrate simultaneous ionic current and fluorescent detection of DNA translocation through glass nanocapillaries. These have been shown to be an alternative to traditional solid state nanopores. 12 We have extended this system by combining ionic current detection with single molecule fluorescence imaging and have shown by direct visual observation that the drop in ionic current does in fact correspond to the transient blockade of the pore by the DNA molecule. By tracking the movement of the k DNA molecules into the nanocapillary, we are also able to extract an effective mobility constant for long DNA molecules.Figure 1(a) shows a schematic of the custom built setup for combined fluorescence and ionic current detection. As described previously, 12 a nanocapillary is produced from quartz capillaries of outer diameter 0.5 mm and inner diameter 0.2 mm (Sutter) using a commercial laser puller (Sutter, P2000). This is assembled into a polydimethylsiloxane (PDMS) chip where it connects two reservoirs filled with an electrolyte solution. For the experiments described in this paper, we use 100 mM KCl in 100 mM citrate buffer at pH 4.6.The Ag/AgCl electrode within the nanocapillary is held at a constant positive potential with reference to the ground electrode in the reservoir surrounding the nanocapillary. An amplifier (HEKA, EPC 800) detects the ionic current flowing through the nanocapillary at a bandwidth of 5 kHz. Negatively charged DNA translocates into the nanocapillary which results in characteristic blockades in the ionic current. The I-V curve for the nanocapillary (diameter $ 50 nm) used for all experiments described in this paper is shown in Figure 1(a).The k DNA stock solution (Fermentas, 0.3 mg/ml, 48 502 bp) is diluted to 10 pM in the buffer solution and incubated with 50 nM solution of the DNA intercalating dye SYTOX Orange (Invitrogen), following a protocol described in Yan et al. 13 to obtain a dye:DNA base pair ratio of $1:10. The dye molecules are excited by emissions from a 532 nm laser (Laser Quantum) operating at <5 mW. A long pass dichroic mirror at 532 nm (Semrock Filters) directs the excitation light to the rear of a 60Â objective (UPLSAPO NA ¼ 1.2, Olympus). The fluorescence emission from the dye molecules is coll...

show abstract

Electrokinetic Concentration of DNA Polymers in Nanofluidic Channels

Cited by 73 publications

References 42 publications

On-chip DNA preconcentration in different media conductivities by electrodeless dielectrophoresis

On-chip DNA preconcentration in different media conductivities by electrodeless dielectrophoresis

Optofluidic in situ maskless lithography of charge selective nanoporous hydrogel for DNA preconcentration

Studying DNA translocation in nanocapillaries using single molecule fluorescence

Contact Info

Product

Resources

About