Editing Microarray

{{Short description|Small-scale two-dimensional array of samples on a solid support}}
{{Redirect|Microarrays|the journal|Microarrays (journal)}}
[[File:Venn Diagram for bioMEMS, LOC, and MTAS.svg|right|thumb|upright=2|A [[Venn diagram]] outlining and contrasting some aspects of the fields of [[bio-MEMS]], [[lab-on-a-chip]], [[Total analysis system|μTAS]]]]
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A '''microarray''' is a [[multiplex (assay)|multiplex]] [[lab-on-a-chip]].<ref>{{Cite journal |last1=Carroll |first1=Gregory T. |last2=Wang |first2=Denong |last3=Turro |first3=Nicholas J. |last4=Koberstein |first4=Jeffrey T. |date=2008 |title=Photons to illuminate the universe of sugar diversity through bioarrays |journal=Glycoconjugate Journal |language=en |volume=25 |issue=1 |pages=5–10 |doi=10.1007/s10719-007-9052-1 |issn=0282-0080 |pmc=7088275 |pmid=17610157}}</ref> Its purpose is to simultaneously detect the expression of thousands of biological interactions. It is a two-dimensional array on a [[Substrate (materials science)|solid substrate]]—usually a [[glass slide]] or [[silicon thin-film cell]]—that [[assay]]s (tests) large amounts of [[biotic material|biological material]] using [[high-throughput screening]] miniaturized, multiplexed and parallel processing and detection methods. The concept and methodology of microarrays was first introduced and illustrated in [[antibody microarray]]s (also referred to as [[antibody matrix]]) by [[Tse Wen Chang]] in 1983 in a scientific publication<ref name="pmid6606681">{{cite journal |doi=10.1016/0022-1759(83)90318-6 |title=Binding of cells to matrixes of distinct antibodies coated on solid surface |year=1983 |last1=Tse-Wen Chang |journal=Journal of Immunological Methods |volume=65 |pages=217–23 |pmid=6606681 |first1=TW |issue=1–2}}</ref> and a series of patents.<ref>{{cite patent |country=US |number=4591570 |status=patent |title=Matrix of antibody-coated spots for determination of antigens |pubdate= |gdate= |fdate= |pridate= |inventor= |invent1= |invent2= |assign1= |assign2= |class= |url=}}</ref><ref>{{cite patent |country=US |number=4829010 |status=patent |title=Immunoassay device enclosing matrixes of antibody spots for cell determinations |pubdate= |gdate= |fdate= |pridate= |inventor= |invent1= |invent2= |assign1= |assign2= |class= |url=}}</ref><ref>{{cite patent |country=US |number=5100777 |status=patent |title=Antibody matrix device and method for evaluating immune status |pubdate= |gdate= |fdate= |pridate= |inventor= |invent1= |invent2= |assign1= |assign2= |class= |url=}}</ref> The "[[gene chip]]" industry started to grow significantly after the 1995 ''[[Science Magazine]]'' article by the Ron Davis and Pat Brown labs at Stanford University.<ref>{{cite journal |doi=10.1126/science.270.5235.467 |title=Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA Microarray |year=1995 |last1=Schena |first1=M. |last2=Shalon |first2=D. |last3=Davis |first3=R. W. |last4=Brown |first4=P. O. |journal=Science |volume=270 |issue=5235 |pages=467–70 |pmid=7569999|bibcode=1995Sci...270..467S |s2cid=6720459 }}</ref> With the establishment of companies, such as [[Affymetrix]], [[Agilent]], Applied Microarrays, Arrayjet, [[Illumina (company)|Illumina]], and others, the technology of [[DNA microarray]]s has become the most sophisticated and the most widely used, while the use of protein, peptide and carbohydrate microarrays<ref>{{cite journal |doi=10.1002/pmic.200600478 |title=Photogenerated glycan arrays identify immunogenic sugar moieties of Bacillus anthracis exosporium |year=2007 |journal=Proteomics |volume=7 |issue=2 |pages=180–184|pmid=17205603 | last1 = Wang | first1 = D | last2 = Carroll | first2 = GT | last3 = Turro | first3 = NJ | last4 = Koberstein | first4 = JT | last5 = Kovác | first5 = P | last6 = Saksena | first6 = R | last7 = Adamo | first7 = R | last8 = Herzenberg | first8 = LA | last9 = Herzenberg | first9 = LA | last10 = Steinman | first10 = L|s2cid=21145793 | doi-access = free }}</ref> is expanding.

Types of microarrays include:
* [[DNA microarray]]s, such as cDNA microarrays, oligonucleotide microarrays, BAC microarrays and SNP microarrays
* [[MMChip]]s, for surveillance of microRNA populations
* [[Protein microarray]]s
* [[Peptide microarray]]s, for detailed analyses or optimization of [[protein–protein interaction]]s
* [[Tissue microarray]]s
* [[Cellular microarray]]s (also called transfection microarrays)
* [[Chemical compound microarray]]s
* [[Antibody microarray]]s
* [[Glycan array]]s (carbohydrate arrays)
* [[Phenotype microarray]]s
* [[Reverse phase protein lysate microarray]]s, microarrays of lysates or serum
* Interferometric reflectance imaging sensor ([[IRIS (Biosensor)|IRIS]])

People in the field of CMOS biotechnology are developing new kinds of microarrays. Once fed [[magnetic nanoparticles]], individual cells can be moved independently and simultaneously on a microarray of magnetic coils. A microarray of [[nuclear magnetic resonance]] microcoils is under development.<ref>{{cite journal |doi=10.1109/N-SSC.2007.4785650 |title=The silicon that Moves and Feels Small Living Things |year=2007 |last1=Ham |first1=Donhee |last2=Westervelt |first2=Robert M. |journal=IEEE Solid-State Circuits Newsletter |volume=12 |issue=4 |pages=4–9|s2cid=35867338 }}</ref>

==Fabrication and operation of microarrays==
A large number of technologies underlie the microarray platform, including the material substrates,<ref>{{cite journal | doi=10.1016/j.bios.2020.112279 | title=Immunoassays on thiol-ene synthetic paper generate a superior fluorescence signal |year=2020 |journal=Biosensors and Bioelectronics | last1 = Guo | first1 = W | last2 = Vilaplana | first2 = L | last3 = Hansson | first3 = J | last4 = Marco | first4 = P| last5 = van der Wijngaart | first5 = W | volume=163 | page=112279 | pmid=32421629 | hdl=10261/211201 | s2cid=218688183 | hdl-access = free }}</ref> spotting of biomolecular arrays,<ref>{{cite journal |doi=10.1080/07388550600978358 |pmid=17095434 |title=Bio-Microarray Fabrication Techniques—A Review |year=2008 |author= Barbulovic-Nad|display-authors=etal| journal=Critical Reviews in Biotechnology |volume=26 |issue=4 |pages=237–259|citeseerx=10.1.1.661.6833 |s2cid=13712888 }}</ref> and the microfluidic packaging of the arrays.<ref>{{cite journal |doi=10.1039/C7LC00652G |title=Thiol–ene–epoxy thermoset for low-temperature bonding to biofunctionalized microarray surfaces |year=2017 |author= Zhou|display-authors=etal| journal=Lab Chip |volume=17 |issue=21 |pages=3672–3681|pmid=28975170 }}</ref> 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).<ref>{{cite book |last1= Dufva |first1= M|title= DNA Microarrays for Biomedical Research|date= 2008 |chapter= Fabrication of DNA Microarray|chapter-url=https://link.springer.com/protocol/10.1007/978-1-59745-538-1_5 |series=Methods in Molecular Biology |volume= 529 |pages= 63–79|doi= 10.1007/978-1-59745-538-1_5 |pmid= 19381969|isbn= 978-1-934115-69-5|access-date= 30 September 2022}}</ref>

=== Production process ===
The initial publication on microarray production process dates back to 1995, when 48 [[Complementary DNA|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.<ref name=":0">{{Citation |last1=Petersen |first1=David W. |url=http://dx.doi.org/10.1007/978-0-387-39978-2_1 |pages=1–11 |access-date=2023-05-18 |place=New York, NY |publisher=Springer New York |isbn=978-0-387-39977-5 |last2=Kawasaki |first2=Ernest S.|title=Microarray Technology and Cancer Gene Profiling |chapter=Manufacturing of Microarrays |series=Advances in Experimental Medicine and Biology |year=2007 |volume=593 |doi=10.1007/978-0-387-39978-2_1 |pmid=17265711 }}</ref>

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.<ref name=":0" /><ref name=":1">{{Cite journal |last1=Barbulovic-Nad |first1=Irena |last2=Lucente |first2=Michael |last3=Sun |first3=Yu |last4=Zhang |first4=Mingjun |last5=Wheeler |first5=Aaron R. |last6=Bussmann |first6=Markus |date=January 2006 |title=Bio-Microarray Fabrication Techniques—A Review |url=http://dx.doi.org/10.1080/07388550600978358 |journal=Critical Reviews in Biotechnology |volume=26 |issue=4 |pages=237–259 |doi=10.1080/07388550600978358 |pmid=17095434 |s2cid=13712888 |issn=0738-8551}}</ref>

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]], obtained from commonly available clone libraries and acquired through [[DNA]] amplification via bacterial vectors. Modern approaches do not include just [[DNA]] 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. <ref name=":1" />

==== Contact printing ====
Contact printing microarray include Pin printing, microstamping or flow printing. Pin printing is the oldest and still widest adopted methodology in [[DNA]] 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]], 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.<ref name=":2">{{Cite journal |last1=Romanov |first1=Valentin |last2=Davidoff |first2=S. Nikki |last3=Miles |first3=Adam R. |last4=Grainger |first4=David W. |last5=Gale |first5=Bruce K. |last6=Brooks |first6=Benjamin D. |date=2014 |title=A critical comparison of protein microarray fabrication technologies |url=http://dx.doi.org/10.1039/c3an01577g |journal=The Analyst |volume=139 |issue=6 |pages=1303–1326 |doi=10.1039/c3an01577g |pmid=24479125 |bibcode=2014Ana...139.1303R |issn=0003-2654}}</ref>

==== Lithography ====
[[Lithography]] 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. [[Ultraviolet|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 [[Ultraviolet|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]] features by using a compact device with few moving parts.<ref>{{Cite journal |last1=Miller |first1=Melissa B. |last2=Tang |first2=Yi-Wei |date=October 2009 |title=Basic Concepts of Microarrays and Potential Applications in Clinical Microbiology |url=http://dx.doi.org/10.1128/cmr.00019-09 |journal=Clinical Microbiology Reviews |volume=22 |issue=4 |pages=611–633 |doi=10.1128/cmr.00019-09 |pmid=19822891 |pmc=2772365 |s2cid=5865637 |issn=0893-8512}}</ref><ref>{{Cite journal |last1=Sack |first1=Matej |last2=Hölz |first2=Kathrin |last3=Holik |first3=Ann-Katrin |last4=Kretschy |first4=Nicole |last5=Somoza |first5=Veronika |last6=Stengele |first6=Klaus-Peter |last7=Somoza |first7=Mark M. |date=2016-03-02 |title=Express photolithographic DNA microarray synthesis with optimized chemistry and high-efficiency photolabile groups |journal=Journal of Nanobiotechnology |volume=14 |issue=1 |page=14 |doi=10.1186/s12951-016-0166-0 |pmid=26936369 |pmc=4776362 |issn=1477-3155 |doi-access=free }}</ref>

==== Non contact ====
Non-contact printing methods vary from [[Photochemistry]]-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.<ref name=":1" /><ref name=":2" />

==== 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.<ref>{{Cite journal |last1=Chandra |first1=Harini |last2=Srivastava |first2=Sanjeeva |date=2009-12-01 |title=Cell-free synthesis-based protein microarrays and their applications |url=http://dx.doi.org/10.1002/pmic.200900462 |journal=Proteomics |volume=10 |issue=4 |pages=717–730 |doi=10.1002/pmic.200900462 |pmid=19953547 |s2cid=22007600 |issn=1615-9853}}</ref>

==See also==
* [[Microarray databases]]
* [[Microarray analysis techniques]]
* [[DNA microarray|DNA Microarray]]
* [[Biochip]]

==Notes==
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[[Category:Microarrays| ]]