Exploiting the benefits of miniaturization for the enhancement of DNA microarrays

Vanderhoeven, Johan; Pappaert, Kris; Dutta, Binita; Vanhummelen, Paul; Baron, Gino V.; Desmet, Gert

doi:10.1002/elps.200406116

Cited by 15 publications

(23 citation statements)

References 17 publications

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“…This correlation was applied because of evidence that the diffusion coefficients of relatively small ssDNA oligomers are not substantially different from those of doublestranded DNA oligomers of the same size (33). Based on a survey of multiple data (30) the dissociation constant K D was chosen such that the solid phase hybridization value was three orders of magnitude larger than the bulk solution value; for this system the constant was chosen to be K D ϭ 10 Ϫ7 M, consistent with data in a recent study (34). The one adjustable parameter in the model is the forward rate constant k 1 , because this kinetic solid-phase hybridization rate constant has not been measured for this specific system.…”

Section: P-labeled Radiometric Assay Of Both Dna Surface Density Andmentioning

confidence: 96%

Array feature size influences nucleic acid surface capture in DNA microarrays

Dandy¹,

Grainger

2007

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

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Analyte affinity capture by surface-immobilized diagnostic agents is a routinely used assay format for profiling numerous medically and technologically important target analytes. These assays suffer from numerous performance limitations, including sensitivity and rapidity. Assay miniaturization is advocated to improve surfacecapture performance, specifically exploiting the inverse relationship between analyte flux and capture feature size under mass transfer-limiting capture conditions that characterize many such assay formats. Reduced capture feature sizes, e.g., microarrays, are proposed to overcome mass transfer limitations, yet this is difficult to achieve across several size scales. This study validates certain advantages advocated for capture spot miniaturization using a rationale to understand surface capture miniaturization strategies. Experimentally derived immobilized ligand and target capture densities as a function of microspot size for DNA oligomers immobilized on model gold substrates are compared directly with theoretical analysis, validating the hypothesis that miniaturization yields many practical assay advantages. Specifically, results show that transitions from assay mass transfer limiting to kinetically limiting conditions as feature size decreases identify an optimal microspot size range for a specific bioassay system. Analytical advantages realized from such assay miniaturization are more uniform target-spot coverage and substantially increased rate of capture (hybridization), increasing assay signal and rapidity.bioassay ͉ mass transport ͉ miniaturization N ew strategies to improve bioanalytical methods, clinical assay designs, diagnostic devices, and rapid screening tools for disease biomarkers, biosecurity threats, and food pathogens have nearly universally emphasized miniaturization as a route to improve performance, cost, convenience, speed-to-answer, and portability. Reducing size scales for these applications has many practical implications to the measurement of biological analytes and such assay designs. Optimal device sizing is a key design feature for assays that commonly involve affinity binding of analytes to surfaces. Surface capture microassays employ diverse affinity reagents (e.g., antibodies, aptamers, and DNA) to capture broad varieties of analytes (e.g., small molecules, peptides, proteins, nucleic acids, and pathogens). Without active transport (e.g., stirring or field-induced), all current microassay platforms suffer from severe mass transfer limitations, that is, rates of analyte transport to the assay capture surface significantly lag rates of analyte binding. This problem is particularly important in producing rapid results in DNA microassays, where resulting DNA-DNA charge-charge interactions produce complications. A long-standing yet experimentally tentative assertion is that surface capture assays benefit significantly from reduced capture feature (i.e., microarray spot) size, specifically, that these assay systems capitalize on the inverse relationship between an...

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Section: P-labeled Radiometric Assay Of Both Dna Surface Density Andmentioning

confidence: 96%

Array feature size influences nucleic acid surface capture in DNA microarrays

Dandy¹,

Grainger

2007

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

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“…The present study has been set up to verify whether the DNA hybridization enhancement realized for a simplified sample (containing only three matching and three nonmatching probes) in [19] by a combination of a hybridization chamber reduction (allowing to increase the sample concentration under constant DNA mass conditions) and a convective shear-driven flow transport, can still be achieved for a complex sample of mouse lung and testis total RNA. Another aim of the study was to verify how the rotating microchamber system would perform in comparison with two conventional hybridization techniques (the diffusion-driven coverslip system and a commercial pump-around system), applying the same amount of genetic material to each system.…”

Section: Introductionmentioning

confidence: 98%

“…The study in [19] showed that, in comparison with diffusion-driven hybridizations under a coverslip, the combination of the shear-driven flow transport and a reduced volume microchamber significantly enhances the hybridization on microarrays. The gain in final hybridization was nearly inversely proportional to the applied sample volume reduction (keeping the amount of dry DNA mass constant).…”

Section: Introductionmentioning

confidence: 98%

“…Comparing hybridizations on the same microchamber, with and without rotational transport, it was shown that the advantage of the applied shear-driven convective transport method only relates to the rate with which the final equilibrium is achieved and not to its value. The final equilibrium spot intensity, which in diffusion-driven conditions is normally reached only after overnight incubation, was always reached must faster (typically in about 1-2 h for a 330 bp polA-probe [19]) due to the convective transport.…”

Section: Introductionmentioning

confidence: 99%

“…Our group previously reported the use of a rotating disk flow system [7,19] wherein convection of the sample is achieved by applying the shear-driven flow principle [20,21] in a rotating circular microchamber. The shear-driven flow principle relies on the dragging effect of a moving channel or chamber wall and therefore does not exhibit any of the pressure-drop or Joule-heating limitations on the fluid velocity noticed in pressure and electrically driven transport enhancement methods.…”

Section: Introductionmentioning

confidence: 99%

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Development of capillary electrophoresis methods for quantitative determination of taurine in vehicle system and biological media

et al. 2006

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In the present study, we demonstrate the benefits of a shear-driven rotating microchamber system for the enhancement of microarray hybridizations, by comparing the system with two commonly used hybridization techniques: purely diffusion-driven hybridization under coverslip and hybridization using a fully automated hybridization station, in which the sample is pumped in an oscillating manner. Starting from the same amount of DNA for the three different methods, a series of hybridization experiments using mouse lung and testis DNA is presented to demonstrate these benefits. The gain observed using the rotating microchamber is large: both in terms of analysis speed (up to tenfold increase) and in final spot intensity (up to sixfold increase). The gain is due to the combined effect of the hybridization chamber miniaturization (leading to a sample concentration increase if comparing iso-mass conditions) and the transport enhancement originating from the rotational shear-driven flow induced by the rotation of the chamber bottom wall.

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Integrated Microfluidic Systems for DNA Analysis

et al. 2011

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The potential utility of genome-related research in terms of evolving basic discoveries in biology has generated widespread use of DNA diagnostics and DNA forensics and driven the accelerated development of fully integrated microfluidic systems for genome processing. To produce a microsystem with favorable performance characteristics for genetic-based analyses, several key operational elements must be strategically chosen, including device substrate material, temperature control, fluidic control, and reaction product readout. As a matter of definition, a microdevice is a chip that performs a single processing step, for example microchip electrophoresis. Several microdevices can be integrated to a single wafer, or combined on a control board as separate devices to form a microsystem. A microsystem is defined as a chip composed of at least two microdevices. Among the many documented analytical microdevices, those focused on the ability to perform the polymerase chain reaction (PCR) have been reported extensively due to the importance of this processing step in most genetic-based assays. Other microdevices that have been detailed in the literature include those for solid-phase extractions, microchip electrophoresis, and devices composed of DNA microarrays used for interrogating DNA primary structure. Great progress has also been made in the areas of chip fabrication, bonding and sealing to enclose fluidic networks, evaluation of different chip substrate materials, surface chemistries, and the architecture of reaction conduits for basic processing steps such as mixing. Other important elements that have been developed to realize functional systems include miniaturized readout formats comprising optical or electrochemical transduction and interconnect technologies. These discoveries have led to the development of fully autonomous and functional integrated systems for genome processing that can supply "sample in/answer out" capabilities. In this chapter, we focus on microfluidic systems that are composed of two or more microdevices directed toward DNA analyses. Our discussions will primarily be focused on the integration of various processing steps with microcapillary electrophoresis (μCE) or microarrays. The advantages afforded by fully integrated microfluidic systems to enable challenging applications, such as single-copy DNA sequencing, single-cell gene expression analysis, pathogen detection, and forensic DNA analysis in formats that provide high throughput and point-of-analysis capabilities will be discussed as well.

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Exploiting the benefits of miniaturization for the enhancement of DNA microarrays

Cited by 15 publications

References 17 publications

Array feature size influences nucleic acid surface capture in DNA microarrays

Array feature size influences nucleic acid surface capture in DNA microarrays

Development of capillary electrophoresis methods for quantitative determination of taurine in vehicle system and biological media

Integrated Microfluidic Systems for DNA Analysis

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