Microarrays assembled in microfluidic chips fabricated from poly(methyl methacrylate) for the detection of low-abundant DNA mutations.
Identifieur interne : 002465 ( PubMed/Corpus ); précédent : 002464; suivant : 002466Microarrays assembled in microfluidic chips fabricated from poly(methyl methacrylate) for the detection of low-abundant DNA mutations.
Auteurs : Yun Wang ; Bikas Vaidya ; Hannah D. Farquar ; Wieslaw Stryjewski ; Robert P. Hammer ; Robin L. Mccarley ; Steven A. Soper ; Yu-Wei Cheng ; Francis BaranySource :
- Analytical chemistry [ 0003-2700 ] ; 2003.
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : DNA.
- chemical , genetics : DNA.
- chemical : DNA Primers, Indicators and Reagents, Polymethyl Methacrylate.
- genetics : Mutation.
- Microcomputers, Oligonucleotide Array Sequence Analysis, Reverse Transcriptase Polymerase Chain Reaction.
Abstract
Low-density arrays were assembled into microfluidic channels hot-embossed in poly(methyl methacrylate) (PMMA) to allow the detection of low-abundant mutations in gene fragments (K-ras) that carry point mutations with high diagnostic value for colorectal cancers. Following spotting, the chip was assembled with a cover plate and the array accessed using microfluidics in order to enhance the kinetics associated with hybridization. The array was configured with zip code sequences (24-mers) that were complementary to sequences present on the target. The hybridization targets were generated using an allele-specific ligase detection reaction (LDR), in which two primers (discriminating primer that carriers the complement base to the mutation being interrogated and a common primer) that flank the point mutation and were ligated joined together) only when the particular mutation was present in the genomic DNA. The discriminating primer contained on its 5'-end the zip code complement (directs the LDR product to the appropriate site of the array), and the common primer carried on its 3' end a fluorescent dye (near-IR dye IRD-800). The coupling chemistry (5'-amine-containing oligonucleotide tethered to PMMA surface) was optimized to maximize the loading level of the zip code oligonucleotide, improve hybridization sensitivity (detection of low-abundant mutant DNAs in high copy numbers of normal sequences), and increase the stability of the linkage chemistry to permit re-interrogation of the array. It was found that microfluidic addressing of the array reduced the hybridization time from 3 h for a conventional array to less than 1 min. In addition, the coupling chemistry allowed reuse of the array > 12 times before noticing significant loss of hybridization signal. The array was used to detect a point mutation in a K-ras oncogene at a level of 1 mutant DNA in 10,000 wild-type sequences.
DOI: 10.1021/ac020683w
PubMed: 12641233
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pubmed:12641233Le document en format XML
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Farquar</name></author><author><name sortKey="Stryjewski, Wieslaw" sort="Stryjewski, Wieslaw" uniqKey="Stryjewski W" first="Wieslaw" last="Stryjewski">Wieslaw Stryjewski</name></author><author><name sortKey="Hammer, Robert P" sort="Hammer, Robert P" uniqKey="Hammer R" first="Robert P" last="Hammer">Robert P. Hammer</name></author><author><name sortKey="Mccarley, Robin L" sort="Mccarley, Robin L" uniqKey="Mccarley R" first="Robin L" last="Mccarley">Robin L. Mccarley</name></author><author><name sortKey="Soper, Steven A" sort="Soper, Steven A" uniqKey="Soper S" first="Steven A" last="Soper">Steven A. Soper</name></author><author><name sortKey="Cheng, Yu Wei" sort="Cheng, Yu Wei" uniqKey="Cheng Y" first="Yu-Wei" last="Cheng">Yu-Wei Cheng</name></author><author><name sortKey="Barany, Francis" sort="Barany, Francis" uniqKey="Barany F" first="Francis" last="Barany">Francis Barany</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2003">2003</date><idno type="RBID">pubmed:12641233</idno><idno type="pmid">12641233</idno><idno type="doi">10.1021/ac020683w</idno><idno type="wicri:Area/PubMed/Corpus">002465</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002465</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Microarrays assembled in microfluidic chips fabricated from poly(methyl methacrylate) for the detection of low-abundant DNA mutations.</title><author><name sortKey="Wang, Yun" sort="Wang, Yun" uniqKey="Wang Y" first="Yun" last="Wang">Yun Wang</name><affiliation><nlm:affiliation>Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803-1804, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Vaidya, Bikas" sort="Vaidya, Bikas" uniqKey="Vaidya B" first="Bikas" last="Vaidya">Bikas Vaidya</name></author><author><name sortKey="Farquar, Hannah D" sort="Farquar, Hannah D" uniqKey="Farquar H" first="Hannah D" last="Farquar">Hannah D. Farquar</name></author><author><name sortKey="Stryjewski, Wieslaw" sort="Stryjewski, Wieslaw" uniqKey="Stryjewski W" first="Wieslaw" last="Stryjewski">Wieslaw Stryjewski</name></author><author><name sortKey="Hammer, Robert P" sort="Hammer, Robert P" uniqKey="Hammer R" first="Robert P" last="Hammer">Robert P. Hammer</name></author><author><name sortKey="Mccarley, Robin L" sort="Mccarley, Robin L" uniqKey="Mccarley R" first="Robin L" last="Mccarley">Robin L. Mccarley</name></author><author><name sortKey="Soper, Steven A" sort="Soper, Steven A" uniqKey="Soper S" first="Steven A" last="Soper">Steven A. Soper</name></author><author><name sortKey="Cheng, Yu Wei" sort="Cheng, Yu Wei" uniqKey="Cheng Y" first="Yu-Wei" last="Cheng">Yu-Wei Cheng</name></author><author><name sortKey="Barany, Francis" sort="Barany, Francis" uniqKey="Barany F" first="Francis" last="Barany">Francis Barany</name></author></analytic><series><title level="j">Analytical chemistry</title><idno type="ISSN">0003-2700</idno><imprint><date when="2003" type="published">2003</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>DNA (chemistry)</term><term>DNA (genetics)</term><term>DNA Primers</term><term>Indicators and Reagents</term><term>Microcomputers</term><term>Mutation (genetics)</term><term>Oligonucleotide Array Sequence Analysis</term><term>Polymethyl Methacrylate</term><term>Reverse Transcriptase Polymerase Chain Reaction</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>DNA</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>DNA Primers</term><term>Indicators and Reagents</term><term>Polymethyl Methacrylate</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Mutation</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Microcomputers</term><term>Oligonucleotide Array Sequence Analysis</term><term>Reverse Transcriptase Polymerase Chain Reaction</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Low-density arrays were assembled into microfluidic channels hot-embossed in poly(methyl methacrylate) (PMMA) to allow the detection of low-abundant mutations in gene fragments (K-ras) that carry point mutations with high diagnostic value for colorectal cancers. Following spotting, the chip was assembled with a cover plate and the array accessed using microfluidics in order to enhance the kinetics associated with hybridization. The array was configured with zip code sequences (24-mers) that were complementary to sequences present on the target. The hybridization targets were generated using an allele-specific ligase detection reaction (LDR), in which two primers (discriminating primer that carriers the complement base to the mutation being interrogated and a common primer) that flank the point mutation and were ligated joined together) only when the particular mutation was present in the genomic DNA. The discriminating primer contained on its 5'-end the zip code complement (directs the LDR product to the appropriate site of the array), and the common primer carried on its 3' end a fluorescent dye (near-IR dye IRD-800). The coupling chemistry (5'-amine-containing oligonucleotide tethered to PMMA surface) was optimized to maximize the loading level of the zip code oligonucleotide, improve hybridization sensitivity (detection of low-abundant mutant DNAs in high copy numbers of normal sequences), and increase the stability of the linkage chemistry to permit re-interrogation of the array. It was found that microfluidic addressing of the array reduced the hybridization time from 3 h for a conventional array to less than 1 min. In addition, the coupling chemistry allowed reuse of the array > 12 times before noticing significant loss of hybridization signal. The array was used to detect a point mutation in a K-ras oncogene at a level of 1 mutant DNA in 10,000 wild-type sequences.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">12641233</PMID><DateCompleted><Year>2004</Year><Month>04</Month><Day>13</Day></DateCompleted><DateRevised><Year>2019</Year><Month>07</Month><Day>17</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">0003-2700</ISSN><JournalIssue CitedMedium="Print"><Volume>75</Volume><Issue>5</Issue><PubDate><Year>2003</Year><Month>Mar</Month><Day>01</Day></PubDate></JournalIssue><Title>Analytical chemistry</Title><ISOAbbreviation>Anal. Chem.</ISOAbbreviation></Journal><ArticleTitle>Microarrays assembled in microfluidic chips fabricated from poly(methyl methacrylate) for the detection of low-abundant DNA mutations.</ArticleTitle><Pagination><MedlinePgn>1130-40</MedlinePgn></Pagination><Abstract><AbstractText>Low-density arrays were assembled into microfluidic channels hot-embossed in poly(methyl methacrylate) (PMMA) to allow the detection of low-abundant mutations in gene fragments (K-ras) that carry point mutations with high diagnostic value for colorectal cancers. Following spotting, the chip was assembled with a cover plate and the array accessed using microfluidics in order to enhance the kinetics associated with hybridization. The array was configured with zip code sequences (24-mers) that were complementary to sequences present on the target. The hybridization targets were generated using an allele-specific ligase detection reaction (LDR), in which two primers (discriminating primer that carriers the complement base to the mutation being interrogated and a common primer) that flank the point mutation and were ligated joined together) only when the particular mutation was present in the genomic DNA. The discriminating primer contained on its 5'-end the zip code complement (directs the LDR product to the appropriate site of the array), and the common primer carried on its 3' end a fluorescent dye (near-IR dye IRD-800). The coupling chemistry (5'-amine-containing oligonucleotide tethered to PMMA surface) was optimized to maximize the loading level of the zip code oligonucleotide, improve hybridization sensitivity (detection of low-abundant mutant DNAs in high copy numbers of normal sequences), and increase the stability of the linkage chemistry to permit re-interrogation of the array. It was found that microfluidic addressing of the array reduced the hybridization time from 3 h for a conventional array to less than 1 min. In addition, the coupling chemistry allowed reuse of the array > 12 times before noticing significant loss of hybridization signal. The array was used to detect a point mutation in a K-ras oncogene at a level of 1 mutant DNA in 10,000 wild-type sequences.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Wang</LastName><ForeName>Yun</ForeName><Initials>Y</Initials><AffiliationInfo><Affiliation>Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803-1804, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Vaidya</LastName><ForeName>Bikas</ForeName><Initials>B</Initials></Author><Author ValidYN="Y"><LastName>Farquar</LastName><ForeName>Hannah D</ForeName><Initials>HD</Initials></Author><Author ValidYN="Y"><LastName>Stryjewski</LastName><ForeName>Wieslaw</ForeName><Initials>W</Initials></Author><Author ValidYN="Y"><LastName>Hammer</LastName><ForeName>Robert P</ForeName><Initials>RP</Initials></Author><Author ValidYN="Y"><LastName>McCarley</LastName><ForeName>Robin L</ForeName><Initials>RL</Initials></Author><Author ValidYN="Y"><LastName>Soper</LastName><ForeName>Steven A</ForeName><Initials>SA</Initials></Author><Author ValidYN="Y"><LastName>Cheng</LastName><ForeName>Yu-Wei</ForeName><Initials>YW</Initials></Author><Author ValidYN="Y"><LastName>Barany</LastName><ForeName>Francis</ForeName><Initials>F</Initials></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>R24-CA84625</GrantID><Acronym>CA</Acronym><Agency>NCI NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013487">Research Support, U.S. Gov't, P.H.S.</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Anal Chem</MedlineTA><NlmUniqueID>0370536</NlmUniqueID><ISSNLinking>0003-2700</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D017931">DNA Primers</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D007202">Indicators and Reagents</NameOfSubstance></Chemical><Chemical><RegistryNumber>9007-49-2</RegistryNumber><NameOfSubstance UI="D004247">DNA</NameOfSubstance></Chemical><Chemical><RegistryNumber>9011-14-7</RegistryNumber><NameOfSubstance UI="D019904">Polymethyl Methacrylate</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D004247" MajorTopicYN="N">DNA</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017931" MajorTopicYN="N">DNA Primers</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D007202" MajorTopicYN="N">Indicators and Reagents</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008838" MajorTopicYN="N">Microcomputers</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D009154" MajorTopicYN="N">Mutation</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020411" MajorTopicYN="Y">Oligonucleotide Array Sequence Analysis</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019904" MajorTopicYN="N">Polymethyl Methacrylate</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020133" MajorTopicYN="N">Reverse Transcriptase Polymerase Chain Reaction</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2003</Year><Month>3</Month><Day>19</Day><Hour>4</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2004</Year><Month>4</Month><Day>14</Day><Hour>5</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2003</Year><Month>3</Month><Day>19</Day><Hour>4</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">12641233</ArticleId><ArticleId IdType="doi">10.1021/ac020683w</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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