Fabrication of DNA Polymer Brush Arrays by Destructive Micropatterning and Rolling‐Circle Amplification

Barbee, Kristopher D.; Chandrangsu, Matt; Huang, Xiaoxia

doi:10.1002/mabi.201000373

Cited by 19 publications

(18 citation statements)

References 51 publications

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“…Consequently, RCA is well suited to solid-phase formats such as microarrays for generating localized signals at specific locations, and this distinctive property of RCA should allow many assays to be performed simultaneously (multiplexing) without interference. 9 To our knowledge, the most commonly used surfaces for RCA are glass [9][10][11][12] and nanoparticles. [13][14][15][16] An attractive alternative substrate for biochip application, porous silicon (pSi), previously reported by us in protein micoarrays, 17,18 is employed here in RCA.…”

Section: Introductionmentioning

confidence: 99%

DNA microarray fabricated on poly(acrylic acid) brushes-coated porous silicon by in situ rolling circle amplification

Wang

Jia

Jiang

et al. 2012

Analyst

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Microarrays hold considerable promise in large-scale biology on account of their analytical, massive and parallel nature. In a step toward further enabling such a capability, we describe the application of rolling circle amplification (RCA) for a sensitive and multiplex detection of nucleic acid targets on oligonucleotide-conjugated polymer brushes covalently grown from porous silicon. Both RCA and polymer brushes have been taken to increase the loading quantity of target molecules and thus improve the detection sensitivity without loss of multiplexing. Besides, polymer brushes were employed to protect porous silicon and to provide biologically simulated environments, making the attached biomolecules maintain bioactivity. This approach can reach a detection limit of 0.1 nM target analytes and three orders of magnitude dynamic range of 0.1-100 nM, with a fluorescence scanner. A two-colour DNA microarray was achieved via RCA of two kinds of circular DNA targets on one chip simultaneously. The porous silicon chip-based RCA technique is promising for the multiplex detection of deoxynucleic acids on microarrays.

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Section: Introductionmentioning

confidence: 99%

DNA microarray fabricated on poly(acrylic acid) brushes-coated porous silicon by in situ rolling circle amplification

Wang

Jia

Jiang

et al. 2012

Analyst

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“…Glass coverslips are processed, 14 functionalized with poly-(dT) 50 (detail in the Supporting Information), then assembled onto a flow cell consisting of nine 40 mm × 2 mm × 100 μm channels cut from double-side adhesive silicone tape, and attached to an anodized aluminum or stainless steel plate with 1 mm holes drilled for fluidic connections. The modular flow cell is mounted into an aluminum encasement block of a temperature control unit comprised of thermoelectric modules sandwiched between the block and a liquid-cooled aluminum heatsink, which is designed to mount on a motorized XY microscope stage.…”

mentioning

confidence: 99%

Measurement of DNA Polymerase Incorporation Kinetics of Dye-Labeled Nucleotides Using Total Internal Reflection Fluorescence Microscopy

Walsh¹,

Roller²,

Ko³

et al. 2015

Biochemistry

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We report a method for the rapid and automated measurements of the incorporation kinetics of fluorescent dye-labeled nucleotides by DNA polymerases without using stopped-flow and quench-flow methods. Total internal reflection fluorescence microscopy is used to monitor the incorporation of fluorescently labeled nucleotides by DNA polymerase into surface-bound primed DNA templates, and a microfluidic system is used to perform the reactions. We successfully demonstrated the method using Bst DNA polymerase and a set of coumarin-labeled nucleotides. Our method allows the rapid acquisition of polymerase kinetics for implementing and improving DNA sequencing technologies that rely on labeled nucleotides and DNA polymerases.

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“…After assembly into a microfluidic chip, the DNA brushes were synthesized on the oligonucleotide array by rollingcircle DNA amplification. Barbee discussed various applications for these arrays [156].…”

Section: Lateral Flow Strip Through Dual Immunoreactionsmentioning

confidence: 99%

Isothermal Amplification and Quantification of Nucleic Acids and its Use in Microsystems

Tröger¹,

Niemann²,

Gärtig³

et al. 2015

J Nanomed Nanotechnol

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Nucleic acid amplification technologies (NAATs) offer the most sensitive tests in the clinical laboratory. These techniques are used as a powerful tool for screening and diagnosis of infectious diseases. Isothermal methods, as an alternative to polymerase chain reaction (PCR), require no thermocycling machine and can mostly be performed with reduced time, high throughput, and accurate and reliable results.However, current molecular diagnostic approaches generally need manual analysis by qualified and experienced personal which is a highly complex, time-consuming and labor-intensive task. Thus, the demand for simpler, miniaturized systems and assays for pathogen detection is steadily increasing. Microfluidic platforms and lab-on-a-chip devices have many advantages such as small sample volume, portability and rapid detection time and enable point-of-care diagnosis.In this article, we review several isothermal amplification methods and their implementation in microsystems in relation to quantification of nucleic acids. miniaturized systems can be diverse. The majority of publications are focussed on clinical diagnostics including foodborne organisms for environmental monitoring [10][11][12]. In case of an infectious disease, cultivation and phenotypic characterization are still the standard methods of microbiologists which need days up to weeks to obtain a diagnostic result. Hence, scientists started to make use of nucleic acid amplification methods to accelerate the analysis. The most widespread and well known technique for this purpose is the polymerase chain reaction (PCR) [10,13], which exploits the activity of the DNA polymerase. The method is based on a thermal cycling process consisting of repeated cycles of heating and cooling steps allowing for DNA melting, sequence specific primer binding and enzymatic amplification of the target nucleic acid. The quantitative assessment of target copies is possible by using a real-time PCR approach, where a concentration dependent signal (e.g. fluorescence) increases over time [14]. The latter enables the user to easily assess the pathogen load of patient samples [15][16][17][18]. Since the first example of a PCR on a miniaturized system in 1994 [19,20], numerous devices were presented, which integrate not just the amplification, but also sample preparation and detection steps [9,[21][22][23][24][25][26][27][28]. Just a few of those microsystems have reached the market so far, but some have shown a fascinating potential to replace the classical laboratory-oriented state-of-the art [29][30][31][32][33]. setups has been shown to obtain a similar result [34]. A smaller heat capacity allows for rapid changes in temperature beneficial for the PCR time as well as a higher parallelism of multiple genetic samples [34].However, a major drawback of the integration of PCR to microsystems is the necessity of sophisticated instrumentation. The reaction requires a thermal cycling instrumentation, space and considerable expertise [35]. Therefore, isothermal reactions for the ta...

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Fabrication of DNA Polymer Brush Arrays by Destructive Micropatterning and Rolling‐Circle Amplification

Cited by 19 publications

References 51 publications

DNA microarray fabricated on poly(acrylic acid) brushes-coated porous silicon by in situ rolling circle amplification

DNA microarray fabricated on poly(acrylic acid) brushes-coated porous silicon by in situ rolling circle amplification

Measurement of DNA Polymerase Incorporation Kinetics of Dye-Labeled Nucleotides Using Total Internal Reflection Fluorescence Microscopy

Isothermal Amplification and Quantification of Nucleic Acids and its Use in Microsystems

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