MICROARRAY

In the past few years a new approach has emerged designed to asses differences in gene expressions between various cell types or the same cells treated in different fashions. Thus technology referred to as Micro-array technology or gene profiling has the ability to rapidly and reliably scan large numbers of different mRNAs.

DNA microarray flash animation..
http://www.bio.davidson.edu/Courses/genomics/chip/chip.html

Types of microarrays include:

• DNA microarrays, such as cDNA microarrays, oligonucleotide microarrays and SNP microarrays
• MMChips, for surveillance of microRNA populations
• Protein microarrays
• Tissue microarrays
• Cellular microarrays
• Chemical compound microarrays
• Antibody microarrays
• Carbohydrate arrays (glycoarrays)

A microarray

is a multiplex lab-on-a-chip. It is a 2D array on a solid substrate (usually a glass slide or silicon thin-film cell) that assays large amounts of biological material using high-throughput screening methods.

The principle is simple and is derived from what we already know about RNA and DNA hybridization.

mRNA is isolated from the given DNA synthesis is initiated the first strand of cDNA is labeled with the tag. This forms a pool of target sequences.

The next step is to hybridize the labelled cDNA to a microarray.

There are many microarrays commercially available, which fall mainly into two classes ;those composed of cDNA and those composed of oligosaccharides.

Microarrays of cDNA are ,as the name suggests ,a collection of cDNA that have been arranged ,or arrayed on a solid substrate in defined locations.

The substrate varies but usually is a nylon membrane or a glass slide.

If a very small amount of cDNA is used, the spots of cDNA arranged on the substrate can be as small as 100-300 mm in size;it is relatively simple to array as many as 30,ooo cDNA on microscopic slide.

The actual process of arraying the cDNA is usually accomplished using robotics.

Th cDNAs are most frequently obtained from available cDNA libraries and in some cases, are PCR products amplified from the cDNA library using primers specific for certain known genes.

The oligosaharide arrays are usually a collection of oligos 20-25 nucleotides long.

The advantage of this type of array is that one only needs a sequences of genes of interest.No cDNA library is needed.

However the cost of assembling such a array is high, since the oligos have to be made and then spotted on to the filter or glass slide.

Another problem with this approach is ,depending upon the length of the oligo, there can be a degree of non specific hybridization that hinders the final analysis of the data.

This problem can be avoided by making longer oligos-which further increases the cost. For these reasons, oligo arrays are used most often by large pharmaceutical or biotechnology companies.

Uses and types

Many types of array exist and the broadest distinction is whether they are spatially arranged on a surface or on coded beads:

• The traditional solid-phase array is a collection of orderly microscopic "spots", called features, each with a specific probe attached to a solid surface, such as glass, plastic or silicon biochip (commonly known gene chip, genome chip, DNA chip or gene array). Thousands of them can be placed in known locations on a single DNA microarray.
• The alternative bead array is a collection of microscopic polystyrene beads, each with a specific probe and a ratio of two or more dyes, which do not interfere with the fluorescent dyes used on the target sequence.

DNA microarrays can be used to detect DNA (as in comparative genomic hybridization), or detect RNA (most commonly as cDNA after reverse transcription) that may or may not be translated into proteins. The process of measuring gene expression via cDNA is called expression analysis or expression profiling.

Application or technology	Synopsis
Gene expression profiling	In an mRNA or gene expression profiling experiment the expression levels of thousands of genes are simultaneously monitored to study the effects of certain treatments, diseases, and developmental stages on gene expression. For example, microarray-based gene expression profiling can be used to identify genes whose expression is changed in response to pathogens or other organisms by comparing gene expression in infected to that in uninfected cells or tissues.
Comparative genomic hybridization	Assessing genome content in different cells or closely related organisms.
GeneID	Small microarrays to check IDs of organisms in food and feed (like GMO ), mycoplasms in cell culture, or pathogens for disease detection, mostly combiningPCR and microarray technology.
Chromatin immunoprecipitation on Chip	DNA sequences bound to a particular protein can be isolated by immunoprecipitating that protein (ChIP), these fragments can be then hybridized to a microarray (such as a tiling array) allowing the determination of protein binding site occupancy throughout the genome. Example protein to immunoprecipitate are histone modifications (H3K27me3, H3K4me2, H3K9me3, etc), Polycomb-group protein (PRC2:Suz12, PRC1:YY1) and trithorax-group protein (Ash1) to study the epigenetic landscape or RNA Polymerase II to study the transcription landscape.
SNP detection	Identifying single nucleotide polymorphism among alleles within or between populations. Several applications of microarrays make use of SNP detection, includingGenotyping, forensic analysis, measuring predisposition to disease, identifying drug-candidates, evaluating germline mutations in individuals or somatic mutations in cancers, assessing loss of heterozygosity, or genetic linkage analysis.
Alternative splicingdetection	An 'exon junction array design uses probes specific to the expected or potential splice sites of predicted exons for a gene. It is of intermediate density, or coverage, to a typical gene expression array (with 1-3 probes per gene) and a genomic tiling array (with hundreds or thousands of probes per gene). It is used to assay the expression of alternative splice forms of a gene. Exon arrays have a different design, employing probes designed to detect each individual exon for known or predicted genes, and can be used for detecting different splicing isoforms.
Fusion genesmicroarray	A Fusion gene microarray can detect fusion transcripts, e.g. from cancer specimens. The principle behind this is building on the alternative splicing microarrays. The oligo design strategy enables combined measurements of chimeric transcript junctions with exon-wise measurements of individual fusion partners.
Tiling array	Genome tiling arrays consist of overlapping probes designed to densely represent a genomic region of interest, sometimes as large as an entire human chromosome. The purpose is to empirically detect expression of transcripts or alternatively splice forms which may not have been previously known or predicted.

Biotechnology trends

Biotechnology draws on the pure biological sciences (genetics, microbiology, animal cell culture, molecular biology, biochemistry,embryology, cell biology) and in many instances is also dependent on knowledge and methods from outside the sphere of biology (chemical engineering, bioprocess engineering, information technology, biorobotics). Conversely, modern biological sciences (including even concepts such as molecular ecology) are intimately entwined and dependent on the methods developed through biotechnology and what is commonly thought of as the life sciences industry.