High-Throughput Block Optical DNA Sequence Identification.
Identifieur interne : 000A59 ( PubMed/Curation ); précédent : 000A58; suivant : 000A60High-Throughput Block Optical DNA Sequence Identification.
Auteurs : Dodderi Manjunatha Sagar [États-Unis] ; Lee Erik Korshoj [États-Unis] ; Katrina Bethany Hanson [États-Unis] ; Partha Pratim Chowdhury [États-Unis] ; Peter Britton Otoupal [États-Unis] ; Anushree Chatterjee [États-Unis] ; Prashant Nagpal [États-Unis]Source :
- Small (Weinheim an der Bergstrasse, Germany) [ 1613-6829 ] ; 2018.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : DNA.
- methods : Sequence Analysis, DNA.
- Spectrophotometry, Infrared, Spectroscopy, Fourier Transform Infrared, Spectrum Analysis, Raman.
Abstract
Optical techniques for molecular diagnostics or DNA sequencing generally rely on small molecule fluorescent labels, which utilize light with a wavelength of several hundred nanometers for detection. Developing a label-free optical DNA sequencing technique will require nanoscale focusing of light, a high-throughput and multiplexed identification method, and a data compression technique to rapidly identify sequences and analyze genomic heterogeneity for big datasets. Such a method should identify characteristic molecular vibrations using optical spectroscopy, especially in the "fingerprinting region" from ≈400-1400 cm-1 . Here, surface-enhanced Raman spectroscopy is used to demonstrate label-free identification of DNA nucleobases with multiplexed 3D plasmonic nanofocusing. While nanometer-scale mode volumes prevent identification of single nucleobases within a DNA sequence, the block optical technique can identify A, T, G, and C content in DNA k-mers. The content of each nucleotide in a DNA block can be a unique and high-throughput method for identifying sequences, genes, and other biomarkers as an alternative to single-letter sequencing. Additionally, coupling two complementary vibrational spectroscopy techniques (infrared and Raman) can improve block characterization. These results pave the way for developing a novel, high-throughput block optical sequencing method with lossy genomic data compression using k-mer identification from multiplexed optical data acquisition.
DOI: 10.1002/smll.201703165
PubMed: 29205813
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596 UCB, Boulder, CO, 80303, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Chemical and Biological Engineering, University of Colorado Boulder, 596 UCB, Boulder, CO, 80303</wicri:regionArea></affiliation></author><author><name sortKey="Korshoj, Lee Erik" sort="Korshoj, Lee Erik" uniqKey="Korshoj L" first="Lee Erik" last="Korshoj">Lee Erik Korshoj</name><affiliation wicri:level="1"><nlm:affiliation>Department of Chemical and Biological Engineering, University of Colorado Boulder, 596 UCB, Boulder, CO, 80303, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Chemical and Biological Engineering, University of Colorado Boulder, 596 UCB, Boulder, CO, 80303</wicri:regionArea></affiliation></author><author><name sortKey="Hanson, Katrina Bethany" sort="Hanson, Katrina Bethany" uniqKey="Hanson K" first="Katrina Bethany" last="Hanson">Katrina Bethany Hanson</name><affiliation wicri:level="1"><nlm:affiliation>Department of Chemical and Biological Engineering, University of Colorado Boulder, 596 UCB, Boulder, CO, 80303, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Chemical and Biological Engineering, University of Colorado Boulder, 596 UCB, Boulder, CO, 80303</wicri:regionArea></affiliation></author><author><name sortKey="Chowdhury, Partha Pratim" sort="Chowdhury, Partha Pratim" uniqKey="Chowdhury P" first="Partha Pratim" last="Chowdhury">Partha Pratim Chowdhury</name><affiliation wicri:level="1"><nlm:affiliation>Department of Chemical and Biological Engineering, University of Colorado Boulder, 596 UCB, Boulder, CO, 80303, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Chemical and Biological Engineering, University of Colorado Boulder, 596 UCB, Boulder, CO, 80303</wicri:regionArea></affiliation></author><author><name sortKey="Otoupal, Peter Britton" sort="Otoupal, Peter Britton" uniqKey="Otoupal P" first="Peter Britton" last="Otoupal">Peter Britton Otoupal</name><affiliation wicri:level="1"><nlm:affiliation>Department of Chemical and Biological Engineering, University of Colorado Boulder, 596 UCB, Boulder, CO, 80303, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Chemical and Biological Engineering, University of Colorado Boulder, 596 UCB, Boulder, CO, 80303</wicri:regionArea></affiliation></author><author><name sortKey="Chatterjee, Anushree" sort="Chatterjee, Anushree" uniqKey="Chatterjee A" first="Anushree" last="Chatterjee">Anushree Chatterjee</name><affiliation wicri:level="1"><nlm:affiliation>Department of Chemical and Biological Engineering, University of Colorado Boulder, 596 UCB, Boulder, CO, 80303, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Chemical and Biological Engineering, University of Colorado Boulder, 596 UCB, Boulder, CO, 80303</wicri:regionArea></affiliation></author><author><name sortKey="Nagpal, Prashant" sort="Nagpal, Prashant" uniqKey="Nagpal P" first="Prashant" last="Nagpal">Prashant Nagpal</name><affiliation wicri:level="1"><nlm:affiliation>Department of Chemical and Biological Engineering, University of Colorado Boulder, 596 UCB, Boulder, CO, 80303, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Chemical and Biological Engineering, University of Colorado Boulder, 596 UCB, Boulder, CO, 80303</wicri:regionArea></affiliation></author></analytic><series><title level="j">Small (Weinheim an der Bergstrasse, Germany)</title><idno type="eISSN">1613-6829</idno><imprint><date when="2018" type="published">2018</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>DNA (chemistry)</term><term>Sequence Analysis, DNA (methods)</term><term>Spectrophotometry, Infrared</term><term>Spectroscopy, Fourier Transform Infrared</term><term>Spectrum Analysis, Raman</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN ()</term><term>Analyse de séquence d'ADN ()</term><term>Analyse spectrale Raman</term><term>Spectrophotométrie IR</term><term>Spectroscopie infrarouge à transformée de Fourier</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>DNA</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Spectrophotometry, Infrared</term><term>Spectroscopy, Fourier Transform Infrared</term><term>Spectrum Analysis, Raman</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ADN</term><term>Analyse de séquence d'ADN</term><term>Analyse spectrale Raman</term><term>Spectrophotométrie IR</term><term>Spectroscopie infrarouge à transformée de Fourier</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Optical techniques for molecular diagnostics or DNA sequencing generally rely on small molecule fluorescent labels, which utilize light with a wavelength of several hundred nanometers for detection. Developing a label-free optical DNA sequencing technique will require nanoscale focusing of light, a high-throughput and multiplexed identification method, and a data compression technique to rapidly identify sequences and analyze genomic heterogeneity for big datasets. Such a method should identify characteristic molecular vibrations using optical spectroscopy, especially in the "fingerprinting region" from ≈400-1400 cm<sup>-1</sup> . Here, surface-enhanced Raman spectroscopy is used to demonstrate label-free identification of DNA nucleobases with multiplexed 3D plasmonic nanofocusing. While nanometer-scale mode volumes prevent identification of single nucleobases within a DNA sequence, the block optical technique can identify A, T, G, and C content in DNA k-mers. The content of each nucleotide in a DNA block can be a unique and high-throughput method for identifying sequences, genes, and other biomarkers as an alternative to single-letter sequencing. Additionally, coupling two complementary vibrational spectroscopy techniques (infrared and Raman) can improve block characterization. These results pave the way for developing a novel, high-throughput block optical sequencing method with lossy genomic data compression using k-mer identification from multiplexed optical data acquisition.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">29205813</PMID><DateCompleted><Year>2019</Year><Month>09</Month><Day>23</Day></DateCompleted><DateRevised><Year>2019</Year><Month>09</Month><Day>23</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1613-6829</ISSN><JournalIssue CitedMedium="Internet"><Volume>14</Volume><Issue>4</Issue><PubDate><Year>2018</Year><Month>01</Month></PubDate></JournalIssue><Title>Small (Weinheim an der Bergstrasse, Germany)</Title><ISOAbbreviation>Small</ISOAbbreviation></Journal><ArticleTitle>High-Throughput Block Optical DNA Sequence Identification.</ArticleTitle><ELocationID EIdType="doi" ValidYN="Y">10.1002/smll.201703165</ELocationID><Abstract><AbstractText>Optical techniques for molecular diagnostics or DNA sequencing generally rely on small molecule fluorescent labels, which utilize light with a wavelength of several hundred nanometers for detection. Developing a label-free optical DNA sequencing technique will require nanoscale focusing of light, a high-throughput and multiplexed identification method, and a data compression technique to rapidly identify sequences and analyze genomic heterogeneity for big datasets. Such a method should identify characteristic molecular vibrations using optical spectroscopy, especially in the "fingerprinting region" from ≈400-1400 cm<sup>-1</sup> . Here, surface-enhanced Raman spectroscopy is used to demonstrate label-free identification of DNA nucleobases with multiplexed 3D plasmonic nanofocusing. While nanometer-scale mode volumes prevent identification of single nucleobases within a DNA sequence, the block optical technique can identify A, T, G, and C content in DNA k-mers. The content of each nucleotide in a DNA block can be a unique and high-throughput method for identifying sequences, genes, and other biomarkers as an alternative to single-letter sequencing. Additionally, coupling two complementary vibrational spectroscopy techniques (infrared and Raman) can improve block characterization. These results pave the way for developing a novel, high-throughput block optical sequencing method with lossy genomic data compression using k-mer identification from multiplexed optical data acquisition.</AbstractText><CopyrightInformation>© 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Sagar</LastName><ForeName>Dodderi Manjunatha</ForeName><Initials>DM</Initials><AffiliationInfo><Affiliation>Department of Chemical and Biological Engineering, University of Colorado Boulder, 596 UCB, Boulder, CO, 80303, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, SEEC 27 UCB Suite N321, Boulder, CO, 80303, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Korshoj</LastName><ForeName>Lee Erik</ForeName><Initials>LE</Initials><AffiliationInfo><Affiliation>Department of Chemical and Biological Engineering, University of Colorado Boulder, 596 UCB, Boulder, CO, 80303, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, SEEC 27 UCB Suite N321, Boulder, CO, 80303, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hanson</LastName><ForeName>Katrina Bethany</ForeName><Initials>KB</Initials><AffiliationInfo><Affiliation>Department of Chemical and Biological Engineering, University of Colorado Boulder, 596 UCB, Boulder, CO, 80303, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, SEEC 27 UCB Suite N321, Boulder, CO, 80303, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chowdhury</LastName><ForeName>Partha Pratim</ForeName><Initials>PP</Initials><AffiliationInfo><Affiliation>Department of Chemical and Biological Engineering, University of Colorado Boulder, 596 UCB, Boulder, CO, 80303, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, SEEC 27 UCB Suite N321, Boulder, CO, 80303, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Otoupal</LastName><ForeName>Peter Britton</ForeName><Initials>PB</Initials><AffiliationInfo><Affiliation>Department of Chemical and Biological Engineering, University of Colorado Boulder, 596 UCB, Boulder, CO, 80303, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Chatterjee</LastName><ForeName>Anushree</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Chemical and Biological Engineering, University of Colorado Boulder, 596 UCB, Boulder, CO, 80303, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Nagpal</LastName><ForeName>Prashant</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Department of Chemical and Biological Engineering, University of Colorado Boulder, 596 UCB, Boulder, CO, 80303, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, SEEC 27 UCB Suite N321, Boulder, CO, 80303, USA.</Affiliation></AffiliationInfo><AffiliationInfo><Affiliation>Materials Science and Engineering, University of Colorado Boulder, 596 UCB, Boulder, CO, 80303, USA.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2017</Year><Month>12</Month><Day>04</Day></ArticleDate></Article><MedlineJournalInfo><Country>Germany</Country><MedlineTA>Small</MedlineTA><NlmUniqueID>101235338</NlmUniqueID><ISSNLinking>1613-6810</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>9007-49-2</RegistryNumber><NameOfSubstance UI="D004247">DNA</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D004247" MajorTopicYN="N">DNA</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D013055" MajorTopicYN="N">Spectrophotometry, Infrared</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017550" MajorTopicYN="N">Spectroscopy, Fourier Transform Infrared</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013059" MajorTopicYN="N">Spectrum Analysis, Raman</DescriptorName></MeshHeading></MeshHeadingList><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="Y">FTIR spectroscopy</Keyword><Keyword MajorTopicYN="Y">Raman spectroscopy</Keyword><Keyword MajorTopicYN="Y">block nucleotide identification</Keyword><Keyword MajorTopicYN="Y">optical DNA sequencing</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2017</Year><Month>09</Month><Day>12</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2017</Year><Month>10</Month><Day>22</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2017</Year><Month>12</Month><Day>6</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2019</Year><Month>9</Month><Day>24</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2017</Year><Month>12</Month><Day>6</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">29205813</ArticleId><ArticleId IdType="doi">10.1002/smll.201703165</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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