Comparison of commercial probe labeling kits for microarray: Towards quality assurance and consistency of reactions

Lynch, Jessica; deSilva, C.J.S.; Peeva, Violet K.; Swanson, Nigel

doi:10.1016/j.ab.2006.04.052

Cited by 6 publications

(3 citation statements)

References 26 publications

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“…Most experiments rely on detection of a fluorescent signal to identify these interactions. In protein binding experiments, for example, the target protein is labeled and then applied to the biochip array, after which analysis with a flatbed scanner identifies those spots that have retained the soluble protein (40,73). Similarly, the identification of molecules in an array that are substrates for an enzyme can be performed using fluorescently labeled antibodies that bind the product (74,75).…”

Section: Detection Methodsmentioning

confidence: 99%

Combining Self-Assembled Monolayers and Mass Spectrometry for Applications in Biochips

Gurard-Levin

Mrksich

2008

Annual Rev. Anal. Chem.

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Biochip arrays have enabled the massively parallel analysis of genomic DNA and hold great promise for application to the analysis of proteins, carbohydrates, and small molecules. Surface chemistry plays an intrinsic role in the preparation and analysis of biochips by providing functional groups for immobilization of ligands, providing an environment that maintains activity of the immobilized molecules, controlling nonspecific interactions of analytes with the surface, and enabling detection methods. This review describes recent advances in surface chemistry that enable quantitative assays of a broad range of biochemical activities. The discussion emphasizes the use of self-assembled monolayers of alkanethiolates on gold as a structurally well-defined and synthetically flexible platform for controlling the immobilization and activity of molecules in an array. The review also surveys recent methods of performing label-free assays, and emphasizes the use of matrix-assisted laser desorption/ionization mass spectrometry to directly observe molecules attached to the self-assembled monolayers.

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Section: Detection Methodsmentioning

confidence: 99%

Combining Self-Assembled Monolayers and Mass Spectrometry for Applications in Biochips

Gurard-Levin

Mrksich

2008

Annual Rev. Anal. Chem.

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“…Equal amounts of total RNA from each sample of one treatment group were combined to give about 100 mg total of which 16 μg was used for probe-labeling with the SuperScript indirect cDNA labeling system (Invitrogen) [25]. Probes were hybridized to mouse whole-genome 4x44K oligo microarrays (Agilent Technologies) following the manufacturer’s instructions.…”

Section: Methodsmentioning

confidence: 99%

Identification of serum insulin-like growth factor binding protein 1 as diagnostic biomarker for early-stage alcohol-induced liver disease

Doiron

Patterson

et al. 2013

J Transl Med

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BackgroundAlcohol consumption is a major cause of liver disease in humans. The use and monitoring of biomarkers associated with early, pre-clinical stages of alcohol-induced liver disease (pre-ALD) could facilitate diagnosis and treatment, leading to improved outcomes.MethodsWe investigated the pathological, transcriptomic and protein changes in early stages of pre-ALD in mice fed the Lieber-Decarli liquid diet with or without alcohol for four months to identify biomarkers for the early stage of alcohol induced liver injury. Mice were sampled after 1, 2 and 4 months treatment.ResultsPathological examination revealed a modest increase in fatty liver changes in alcohol-treated mice. Transcriptomics revealed gene alterations at all time points. Most notably, the Igfbp1 (Insulin-Like Growth Factor Binding Protein 1) was selected as the best candidate gene for early detection of liver damage since it showed early and continuously enhanced induction during the treatment course. Consistent with the microarray data, both Igfbp1mRNA expression in the liver tissue and the IGFBP1 serum protein levels showed progressive and significant increases over the course of pre-ALD development.ConclusionsThe results suggest that in conjunction with other tests, serum IGFBPI protein could provide an easily measured biomarker for early detection of alcohol-induced liver injury in humans.

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“…Fluorescently labeled targets are in general prepared using one of the many commercially available kits [114] or following standardized labeling protocols [21]. Incorporation of the fluorescently labeled nucleotides occurs during enzymatic amplification of the nucleic acids (e.g.…”

Section: Labeling Of the Targetsmentioning

confidence: 99%

Introduction to Microarray‐Based Detection Methods

Schrenzel

Kostić²,

Bodrossy

et al. 2009

Detection of Highly Dangerous Pathogens

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Microarrays consist of an orderly arrangement of probes (oligonucleotides, DNA fragments, proteins, sugars or lectins) attached to a solid surface. The main advantages of microarray technology are high throughput, parallelism, miniaturization, speed and automation. Despite the fact that microarray analysis is a relatively novel technology, with the publication of the first microarray studies in 1995 [101,152], it is now broadly applied and the milestone of nearly 5000 published microarray papers was recorded in 2004 [80]. The scientific and technological background discussed here will be limited to DNA microarrays, excluding the new evolving fields of protein microarrays and glycomics [140].Analogous to antigen-antibody interactions on immunoarrays, DNA microarrays rely on sequence complementarity of the two strands. They put in practice the fundamentals of complementary base-pairing (hybridization) that were first described by Ed Southern [162]. In general, the strategy of microarray hybridization is reversed to that of a standard dot-blot, leading to recurring confusion in the nomenclature. Therefore, it has been suggested to describe tethered nucleic acid as the probe and free nucleic acid as the target [134].Earlier studies on duplex melting and reformation, carried out on DNA solutions, have provided the basic knowledge about the reaction kinetics. Furthermore, a method for computational determination of the melting point as a function of nucleic acid composition and salt concentration was established [6,148,149]. Much of the pioneering work can be linked to the use of nitrocellulose membranes [69], dot-blots [84] and Southern blots [162]. Development of cDNA or oligonucleotide arrays was possible by combined innovations in micro-engineering, molecular biology [33,120,123,156,163,164] and bioinformatics [59]. The real breakthrough in microarray technology was initiated by two key innovations: the use of non-porous solid supports (such as glass and silicon) and the development of methods for highdensity synthesis of oligonucleotides directly onto the microarray surface [59].

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Comparison of commercial probe labeling kits for microarray: Towards quality assurance and consistency of reactions

Cited by 6 publications

References 26 publications

Combining Self-Assembled Monolayers and Mass Spectrometry for Applications in Biochips

Combining Self-Assembled Monolayers and Mass Spectrometry for Applications in Biochips

Identification of serum insulin-like growth factor binding protein 1 as diagnostic biomarker for early-stage alcohol-induced liver disease

Introduction to Microarray‐Based Detection Methods

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