Molecular interactions on microarrays

Southern, Edwin M.; Mir, Kalim U.; Shchepinov, Mikhail S.

doi:10.1038/4429

Cited by 701 publications

(498 citation statements)

References 35 publications

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“…Microarray-based expression profile technology is based on hybridisation methods first employed nearly 30 years ago (Southern et al, 1999). RNA from cells are reverse transcribed into cDNAs, which are then fluorescently or radioactively labelled and used to probe a predetermined set of DNAs.…”

Section: Microarray Technologymentioning

confidence: 99%

Expression profiling of small cellular samples in cancer: less is more

Glanzer

Eberwine

2004

Br J Cancer

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Section: Microarray Technologymentioning

confidence: 99%

Expression profiling of small cellular samples in cancer: less is more

Glanzer

Eberwine

2004

Br J Cancer

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“…These spacers are used to reduce steric hindrance caused by oligonucleotide packing at the substrate surface that makes bases near the surface less accessible for hybridization. It has previously been shown that hybridization efficiency can be increased two orders of magnitude by including such spacer arms (Southern et al, 1999). Immediately after arraying, the surfaces are put in a humid chamber at 37°C for 6-24 h. To prevent nonspecific adhesion of sample DNA and of the magnetic beads to the unmodified areas of the gold surface, the arrayed surfaces are also treated with thiolated PEG (O-(2-mercaptoethyl)-o%-methyl-polyethylene glycol 5000, 10 mg/ml in deionized water for 1 h at room temperature).…”

Section: Dna Patterning and Hybridization Assaymentioning

confidence: 99%

The BARC biosensor applied to the detection of biological warfare agents

Edelstein¹

2000

Biosensors and Bioelectronics

417

154

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“…Glass is preferable as it enables the use of small reaction volumes, permitting a greater number of probes to be applied in a smaller space with low autofluorescence, allowing the simultaneous application of paired fluorophores to a single sample. 13,14 Oligonucleotides of cDNA, typically 20-25 base pairs long, are spotted mechanically onto a silane-coated slide or are synthesized in loco. 15 For analysis using a cDNA microarray it was formerly imperative to employ specific sets of tissue-appropriate cDNA probes generated from the mRNA derived from relevant clones.…”

Section: Molecular Adjuncts To Diagnosis: the Microarraymentioning

confidence: 99%

The future of dermatopathology

Crowson

2006

Modern Pathology

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Of the major issues that dermatopathology will face in the immediate future, two powerful challenges loom large. The first is the application of novel nondestructive imaging technologies to in vivo diagnosis in humans. The second is the application of molecular technologies to a diagnostic arena which formerly belonged exclusively to the light microscopist. The first to be considered in this context is the application of near infrared spectroscopy to the noninvasive in vivo diagnosis of neoplastic skin disease. The second will be a discussion of application, methodology and the current state of the art in microarray technologies as they apply to neoplastic dermatopathology and, in particular, the diagnosis and prognostication of melanoma. Modern Pathology (2006) 19, S155-S163. doi:10.1038/modpathol.3800513Keywords: in vivo microscope; tissue microarray; basal cell carcinoma; infrared spectroscopy Noninvasive assessment of skin lesions by near infrared (IR) spectroscopyIn the late 1990s, working with Dr Laura McIntosh and colleagues at the National Research Council of Canada, the University of Manitoba, Central Medical Laboratories and the Misericordia General Hospital in Winnipeg, Canada, we designed and patented a noninvasive tool for the diagnosis of skin tumors using visible and near IR spectroscopy in the 400-2500 nm size wavelength range. 1-5 Initially, we excised neoplasms, and processed them in the fresh state with sections for formaldehyde fixation and paraffin embedding matched to tissue elements snap frozen in liquid nitrogen and stored at À801F. Thick sections from the frozen tissue elements were interrogated by mid-IR wavelength light (Figure 1). The transmitted light generated significant spectral differences; water, hemoglobin, cytochromes, lipids and proteins all absorb light at specific frequencies ( Figure 2). In particular, the mid-IR range is rich with information about proteins including in the context of collagen and RNA. When analyzed by a sophisticated leave-one-out hierarchical classification algorithm, distinction between microanatomic compartments of the skin could be made (Figure 3). Using this methodology, we were able with an accuracy of 90-95% to distinguish basal cell carcinoma (BCC) from melanocytic nevi, seborrheic keratoses and squamous cell carcinomata in vitro. Melanocytic nevi could be subdivided into banal vs dysplastic nevi based upon their spectral differences and melanomas could be separately recognized as well. Furthermore, the different types of lesion were shown to have distinct mid-IR signatures when compared to adjacent normal epidermal and dermal compartments.Unfortunately, the diagnostic potential of mid-IR spectroscopy for in vivo applications is limited, as complete absorption of mid-IR light occurs with samples greater than 10-15 mm in thickness. In contrast, near-IR light scatters to a much greater extent than it absorbs and in consequence, tissues are relatively transparent in the near-IR region which permits the examination of larger tissue volumes and led to...

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Molecular interactions on microarrays

Cited by 701 publications

References 35 publications

Expression profiling of small cellular samples in cancer: less is more

Expression profiling of small cellular samples in cancer: less is more

The BARC biosensor applied to the detection of biological warfare agents

The future of dermatopathology

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