MersV1, Main, Exploration, bibRecord, 000955

High-Throughput Block Optical DNA Sequence Identification.

Identifieur interne : 000955 ( Main/Exploration ); précédent : 000954; suivant : 000956

High-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.

RBID : pubmed:29205813

Descripteurs français

English descriptors

KwdEn :
- DNA (chemistry), Sequence Analysis, DNA (methods), Spectrophotometry, Infrared, Spectroscopy, Fourier Transform Infrared, Spectrum Analysis, Raman.
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

Affiliations:

États-Unis

Le 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>
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High-Throughput Block Optical DNA Sequence Identification.

High-Throughput Block Optical DNA Sequence Identification.

Source :

Descripteurs français

English descriptors

Abstract

Links toward previous steps (curation, corpus...)

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