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Another, more specific application: Crop specific chips, crop breeding, seedling screening for breeding program efficiency. From Rasheed et al 2017. |
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In ''oligonucleotide microarrays'', the probes are short sequences designed to match parts of the sequence of known or predicted [[open reading frame]]s. Although oligonucleotide probes are often used in "spotted" microarrays, the term "oligonucleotide array" most often refers to a specific technique of manufacturing. Oligonucleotide arrays are produced by printing short oligonucleotide sequences designed to represent a single gene or family of gene splice-variants by [[oligonucleotide synthesis|synthesizing]] this sequence directly onto the array surface instead of depositing intact sequences. Sequences may be longer (60-mer probes such as the [[Agilent]] design) or shorter (25-mer probes produced by [[Affymetrix]]) depending on the desired purpose; longer probes are more specific to individual target genes, shorter probes may be spotted in higher density across the array and are cheaper to manufacture.
One technique used to produce oligonucleotide arrays include [[photolithographic]] synthesis (Affymetrix) on a silica substrate where light and light-sensitive masking agents are used to "build" a sequence one nucleotide at a time across the entire array.<ref name="Affy PNAS Paper">{{cite journal|author=Pease AC|author2=Solas D|author3=Sullivan EJ|author4=Cronin MT|author5=Holmes CP|author6=Fodor SP|date= 1994|title=Light-generated oligonucleotide arrays for rapid DNA sequence analysis|journal=PNAS|volume=91|pages=5022–5026|pmid=8197176|doi=10.1073/pnas.91.11.5022|issue=11|pmc=43922|bibcode=1994PNAS...91.5022P|doi-access=free}}</ref> Each applicable probe is selectively "unmasked" prior to bathing the array in a solution of a single nucleotide, then a masking reaction takes place and the next set of probes are unmasked in preparation for a different nucleotide exposure. After many repetitions, the sequences of every probe become fully constructed. More recently, Maskless Array Synthesis from NimbleGen Systems has combined flexibility with large numbers of probes.<ref name="NimbleGen Genome Res Paper">{{cite journal|author=Nuwaysir EF|author2=Huang W|author3=Albert TJ|author4=Singh J|author5=Nuwaysir K|author6=Pitas A|author7=Richmond T|author8=Gorski T|author9=Berg JP|author10=Ballin J|author11=McCormick M|author12=Norton J|author13=Pollock T|author14=Sumwalt T|author15=Butcher L|author16=Porter D|author17=Molla M|author18=Hall C|author19=Blattner F|author20=Sussman MR|author21=Wallace RL|author22=Cerrina F|author23=Green RD|date= 2002|title=Gene Expression Analysis Using Oligonucleotide Arrays Produced by Maskless Photolithography|journal=Genome Res|volume=12|pages=1749–1755|pmid=12421762|doi=10.1101/gr.362402|issue=11|pmc=187555}}</ref>
=== Two-channel vs. one-channel detection ===
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