High-Throughput Block Optical DNA Sequence Identification.
Identifieur interne : 000A59 ( PubMed/Corpus ); précédent : 000A58; suivant : 000A60High-Throughput Block Optical DNA Sequence Identification.
Auteurs : Dodderi Manjunatha Sagar ; Lee Erik Korshoj ; Katrina Bethany Hanson ; Partha Pratim Chowdhury ; Peter Britton Otoupal ; Anushree Chatterjee ; Prashant NagpalSource :
- Small (Weinheim an der Bergstrasse, Germany) [ 1613-6829 ] ; 2018.
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 to Exploration step
pubmed:29205813Le document en format XML
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<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>
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<ArticleTitle>High-Throughput Block Optical DNA Sequence Identification.</ArticleTitle>
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<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>
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<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Sagar</LastName>
<ForeName>Dodderi Manjunatha</ForeName>
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<AffiliationInfo><Affiliation>Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, SEEC 27 UCB Suite N321, Boulder, CO, 80303, USA.</Affiliation>
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<Author ValidYN="Y"><LastName>Korshoj</LastName>
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<AffiliationInfo><Affiliation>Materials Science and Engineering, University of Colorado Boulder, 596 UCB, Boulder, CO, 80303, USA.</Affiliation>
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