High-Throughput Block Optical DNA Sequence Identification.
Identifieur interne : 000958 ( Main/Merge ); précédent : 000957; suivant : 000959High-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
Links toward previous steps (curation, corpus...)
- to stream PubMed, to step Corpus: 000A59
- to stream PubMed, to step Curation: 000A59
- to stream PubMed, to step Checkpoint: 000899
- to stream Ncbi, to step Merge: 001C74
- to stream Ncbi, to step Curation: 001C74
- to stream Ncbi, to step Checkpoint: 001C74
Links to Exploration step
pubmed:29205813Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">High-Throughput Block Optical DNA Sequence Identification.</title>
<author><name sortKey="Sagar, Dodderi Manjunatha" sort="Sagar, Dodderi Manjunatha" uniqKey="Sagar D" first="Dodderi Manjunatha" last="Sagar">Dodderi Manjunatha Sagar</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>
<wicri:noRegion>80303</wicri:noRegion>
</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>
<wicri:noRegion>80303</wicri:noRegion>
</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>
<wicri:noRegion>80303</wicri:noRegion>
</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>
<wicri:noRegion>80303</wicri:noRegion>
</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>
<wicri:noRegion>80303</wicri:noRegion>
</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>
<wicri:noRegion>80303</wicri:noRegion>
</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>
<wicri:noRegion>80303</wicri:noRegion>
</affiliation>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PubMed</idno>
<date when="2018">2018</date>
<idno type="RBID">pubmed:29205813</idno>
<idno type="pmid">29205813</idno>
<idno type="doi">10.1002/smll.201703165</idno>
<idno type="wicri:Area/PubMed/Corpus">000A59</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000A59</idno>
<idno type="wicri:Area/PubMed/Curation">000A59</idno>
<idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000A59</idno>
<idno type="wicri:Area/PubMed/Checkpoint">000899</idno>
<idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">000899</idno>
<idno type="wicri:Area/Ncbi/Merge">001C74</idno>
<idno type="wicri:Area/Ncbi/Curation">001C74</idno>
<idno type="wicri:Area/Ncbi/Checkpoint">001C74</idno>
<idno type="wicri:Area/Main/Merge">000958</idno>
</publicationStmt>
<sourceDesc><biblStruct><analytic><title xml:lang="en">High-Throughput Block Optical DNA Sequence Identification.</title>
<author><name sortKey="Sagar, Dodderi Manjunatha" sort="Sagar, Dodderi Manjunatha" uniqKey="Sagar D" first="Dodderi Manjunatha" last="Sagar">Dodderi Manjunatha Sagar</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>
<wicri:noRegion>80303</wicri:noRegion>
</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>
<wicri:noRegion>80303</wicri:noRegion>
</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>
<wicri:noRegion>80303</wicri:noRegion>
</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>
<wicri:noRegion>80303</wicri:noRegion>
</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>
<wicri:noRegion>80303</wicri:noRegion>
</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>
<wicri:noRegion>80303</wicri:noRegion>
</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>
<wicri:noRegion>80303</wicri:noRegion>
</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>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/Main/Merge
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000958 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Merge/biblio.hfd -nk 000958 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Sante |area= MersV1 |flux= Main |étape= Merge |type= RBID |clé= pubmed:29205813 |texte= High-Throughput Block Optical DNA Sequence Identification. }}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Merge/RBID.i -Sk "pubmed:29205813" \ | HfdSelect -Kh $EXPLOR_AREA/Data/Main/Merge/biblio.hfd \ | NlmPubMed2Wicri -a MersV1
This area was generated with Dilib version V0.6.33. |