A microarray is a
multiplex
Multiplex may refer to:
Science and technology
* Multiplex communication, combining many signals into one transmission circuit or channel
** Multiplex (television), a group of digital television or radio channels that are combined for broadcast
* ...
lab-on-a-chip
A lab-on-a-chip (LOC) is a device that integrates one or several laboratory functions on a single integrated circuit (commonly called a "chip") of only millimeters to a few square centimeters to achieve automation and high-throughput screening. ...
. Its purpose is to simultaneously detect the expression of thousands of biological interactions. It is a two-dimensional array on a
solid substrate—usually a
glass slide or
silicon thin-film cell—that
assay
An assay is an investigative (analytic) procedure in laboratory medicine, mining, pharmacology, environmental biology and molecular biology for qualitatively assessing or quantitatively measuring the presence, amount, or functional activity ...
s (tests) large amounts of
biological material using
high-throughput screening
High-throughput screening (HTS) is a method for scientific discovery especially used in drug discovery and relevant to the fields of biology, materials science and chemistry. Using robotics, data processing/control software, liquid handling device ...
miniaturized, multiplexed and parallel processing and detection methods. The concept and methodology of microarrays was first introduced and illustrated in
antibody microarray
An antibody microarray (also known as antibody array) is a specific form of protein microarray. In this technology, a collection of captured antibodies are spotted and fixed on a solid surface such as glass, plastic, membrane, or silicon chip, an ...
s (also referred to as
antibody matrix
An antibody microarray (also known as antibody array) is a specific form of protein microarray. In this technology, a collection of captured antibodies are spotted and fixed on a solid surface such as glass, plastic, membrane, or silicon chip, an ...
) by
Tse Wen Chang in 1983 in a scientific publication
and a series of patents. The "
gene chip
A DNA microarray (also commonly known as a DNA chip or biochip) is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure the Gene expression, expression levels of large numbers of genes simu ...
" industry started to grow significantly after the 1995 ''
Science Magazine'' article by the Ron Davis and Pat Brown labs at Stanford University. With the establishment of companies, such as
Affymetrix
Affymetrix is now Applied Biosystems, a brand of DNA microarray products sold by Thermo Fisher Scientific that originated with an American biotechnology research and development and manufacturing company of the same name. The Santa Clara, Calif ...
,
Agilent, Applied Microarrays, Arrayjet,
Illumina, and others, the technology of
DNA microarray
A DNA microarray (also commonly known as a DNA chip or biochip) is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or t ...
s has become the most sophisticated and the most widely used, while the use of protein, peptide and carbohydrate microarrays is expanding.
Types of microarrays include:
*
DNA microarray
A DNA microarray (also commonly known as a DNA chip or biochip) is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or t ...
s, such as cDNA microarrays, oligonucleotide microarrays, BAC microarrays and SNP microarrays
*
MMChips, for surveillance of microRNA populations
*
Protein microarray
A protein microarray (or protein chip) is a high-throughput method used to track the interactions and activities of proteins, and to determine their function, and determining function on a large scale. Its main advantage lies in the fact that larg ...
s
*
Peptide microarray
A peptide microarray (also commonly known as peptide chip or peptide epitope microarray) is a collection of peptides displayed on a solid surface, usually a glass or plastic chip. Peptide chips are used by scientists in biology, medicine and pharm ...
s, for detailed analyses or optimization of
protein–protein interaction
Protein–protein interactions (PPIs) are physical contacts of high specificity established between two or more protein molecules as a result of biochemical events steered by interactions that include electrostatic forces, hydrogen bonding and t ...
s
*
Tissue microarray
Tissue microarrays (also TMAs) consist of Paraffin wax, paraffin blocks in which up to 1000 separate Biological tissue, tissue cores are assembled in array fashion to allow multiplex (assay), multiplex Histology, histological analysis.
History ...
s
*
Cellular microarray
A cellular microarray (or cell microarray) is a laboratory tool that allows for the multiplex interrogation of living cells on the surface of a solid support. The support, sometimes called a "chip", is spotted with varying materials, such as anti ...
s (also called transfection microarrays)
*
Chemical compound microarray A chemical compound microarray is a collection of organic chemical compounds spotted on a solid surface, such as glass and plastic. This microarray format is very similar to DNA microarray, protein microarray and antibody microarray. In chemical g ...
s
*
Antibody microarray
An antibody microarray (also known as antibody array) is a specific form of protein microarray. In this technology, a collection of captured antibodies are spotted and fixed on a solid surface such as glass, plastic, membrane, or silicon chip, an ...
s
*
Glycan array Glycan arrays, like that offered by the Consortium for Functional Glycomics (CFG), National Center for Functional Glycomics (NCFG) and Z Biotech, contain carbohydrate compounds that can be screened with lectins, antibodies or cell receptors to de ...
s (carbohydrate arrays)
*
Phenotype microarrays
*
Reverse phase protein lysate microarray
A reverse phase protein lysate microarray (RPMA) is a protein microarray designed as a dot-blot platform that allows measurement of protein expression levels in a large number of biological samples simultaneously in a quantitative manner when hig ...
s, microarrays of lysates or serum
* Interferometric reflectance imaging sensor (
IRIS)
People in the field of CMOS biotechnology are developing new kinds of microarrays. Once fed
magnetic nanoparticles
Magnetic nanoparticles (MNPs) are a class of nanoparticle that can be manipulated using magnetic fields. Such particles commonly consist of two components, a magnetic material, often iron, nickel and cobalt, and a chemical component that has func ...
, individual cells can be moved independently and simultaneously on a microarray of magnetic coils. A microarray of
nuclear magnetic resonance
Nuclear magnetic resonance (NMR) is a physical phenomenon in which nuclei in a strong constant magnetic field are disturbed by a weak oscillating magnetic field (in the near field) and respond by producing an electromagnetic signal with a ...
microcoils is under development.
Fabrication and operation of microarrays
A large number of technologies underlie the microarray platform, including the material substrates, spotting of biomolecular arrays, and the microfluidic packaging of the arrays. Microarrays can be categorized by how they physically isolate each element of the array, by spotting (making small physical wells), on-chip synthesis (synthesizing the target DNA probes adhered directly on the array), or bead-based (adhering samples to barcoded beads randomly distributed across the array).
Production process
The initial publication on microarray production process dates back to 1995, when 48
cDNAs of a plant were printed on glass slide typically used for light microscopy, modern microarrays on the other hand include now thousands of probes and different carriers with coatings. The fabrication of the microarray requires both biological and physical information, including sample libraries, printers, and slide substrates. Though all procedures and solutions always dependent on the fabrication technique employed. The basic principle of the microarray is the printing of small stains of solutions containing different species of the probe on a slide several thousand times.
Modern printers are
HEPA-filtered and have controlled humidity and temperature surroundings, which is typically around 25°C, 50% humidity. Early microarrays were directly printed onto the surface by using printer pins which deposit the samples in a user-defined pattern on the slide. Modern methods are faster, generate less cross-contamination, and produce better spot morphology. The surface to which the probes are printed must be clean, dust free and hydrophobic, for high-density microarrays. Slide coatings include poly-L-lysine, amino silane, epoxy and others, including manufacturers solutions and are chosen based on the type of sample used. Ongoing efforts to advance microarray technology aim to create uniform, dense arrays while reducing the necessary volume of solution and minimizing contamination or damage.
For the manufacturing process, a sample library which contains all relevant information is needed. In the early stages of microarray technology, the sole sample used was DNA
Deoxyribonucleic acid (; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of al ...
, obtained from commonly available clone libraries and acquired through DNA
Deoxyribonucleic acid (; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of al ...
amplification via bacterial vectors. Modern approaches do not include just DNA
Deoxyribonucleic acid (; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of al ...
as a sample anymore, but also proteins, antibodies, antigens, glycans, cell lysates and other small molecules. All samples used are presynthesized, regularly updated, and more straightforward to maintain. Array fabrication techniques include contact printing, lithography, non-contact and cell free printing. [
]
Contact printing
Contact printing microarray include Pin printing, microstamping or flow printing. Pin printing is the oldest and still widest adopted methodology in DNA
Deoxyribonucleic acid (; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of al ...
microarray contact printing. This technique uses pin types like solid pins, split or quill pins to load and deliver the sample solution directly on solid microarray surfaces. Microstamping offers an alternative to the commonly used pin printing and is also referred as soft lithography
Lithography () is a planographic method of printing originally based on the miscibility, immiscibility of oil and water. The printing is from a stone (lithographic limestone) or a metal plate with a smooth surface. It was invented in 1796 by ...
, which in theory covers different, related pattern transfer technologies using patterned polymer monolithic substrates, the most prominent being microstamping. In contrast to pin printing, microstamping is a more parallel deposition method with less individuality. Certain stamps are loaded with reagents and printed with these reagent solutions identically.
Lithography
Lithography
Lithography () is a planographic method of printing originally based on the miscibility, immiscibility of oil and water. The printing is from a stone (lithographic limestone) or a metal plate with a smooth surface. It was invented in 1796 by ...
combines various methods like Photolithography, Interference lithography, laser writing, electron-beam and Dip pen. The most widely used and researched method remains Photolithography, in which photolithographic masks are used to target specific nucleotides to the surface. UV light is passed through the mask that acts as a filter to either transmit or block the light from the chemically protected microarray surface. If the UV light has been blocked, the area will remain protected from the addition of nucleotides, whereas in areas which were exposed to UV light, further nucleotides can be added. With this method high-quality custom arrays can be produced with a very high density of DNA
Deoxyribonucleic acid (; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of al ...
features by using a compact device with few moving parts.
Non contact
Non-contact printing methods vary from Photochemistry
Photochemistry is the branch of chemistry concerned with the chemical effects of light. Generally, this term is used to describe a chemical reaction caused by absorption of ultraviolet (wavelength from 100 to 400 Nanometre, nm), visible ligh ...
-based printing, Electro-printing and droplet dispensing. In contrast to the other methods, non-contact printing does not involve contact between the surface and the stamp, pin, or other used dispenser. The main advantages are reduced contamination, lesser cleaning and higher throughput which increases steadily. Many of the methods are able to load the probes in parallel, allowing multiple arrays to be produced simultaneously.[
]
Cell free
In cell free systems, the transcription and translation are carried out in situ, which makes the cloning and expression of proteins in host cells obsolete, because no intact cells are needed. The molecule of interest is directly synthesized onto the surface of a solid area. These assays allow high-throughput analysis in a controlled environment without inferences associated with intact cells.
See also
* Microarray databases A microarray database is a repository containing microarray gene expression data. The key uses of a microarray database are to store the measurement data, manage a searchable index, and make the data available to other applications for analysis and ...
* Microarray analysis techniques
Microarray analysis techniques are used in interpreting the data generated from experiments on DNA (Gene chip analysis), RNA, and protein microarrays, which allow researchers to investigate the expression state of a large number of genesin many cas ...
* DNA Microarray
A DNA microarray (also commonly known as a DNA chip or biochip) is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or t ...
* Biochip
Notes
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