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Title: Nucleotide-Specific Contrast for DNA Sequencing by Electron Spectroscopy

DNA sequencing by imaging in an electron microscope is an approach that holds promise to deliver long reads with low error rates and without the need for amplification. Earlier work using transmission electron microscopes, which use high electron energies on the order of 100 keV, has shown that low contrast and radiation damage necessitates the use of heavy atom labeling of individual nucleotides, which increases the read error rates. Other prior work using scattering electrons with much lower energy has shown to suppress beam damage on DNA. Here we explore possibilities to increase contrast by employing two methods, X-ray photoelectron and Auger electron spectroscopy. Using bulk DNA samples with monomers of each base, both methods are shown to provide contrast mechanisms that can distinguish individual nucleotides without labels. In conclusion, both spectroscopic techniques can be readily implemented in a low energy electron microscope, which may enable label-free DNA sequencing by direct imaging.
Authors:
 [1] ;  [2] ;  [3] ;  [1] ;  [3] ;  [2] ;  [4]
  1. Electron Optica Inc., Palo Alto, CA (United States)
  2. Stanford Univ. School of Medicine, Palo Alto, CA (United States)
  3. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  4. SPECS Surface Nano Analysis GmbH (Germany)
Publication Date:
Grant/Contract Number:
AC02-05CH11231
Type:
Published Article
Journal Name:
PLoS ONE
Additional Journal Information:
Journal Volume: 11; Journal Issue: 5; Journal ID: ISSN 1932-6203
Publisher:
Public Library of Science
Research Org:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
Country of Publication:
United States
Language:
English
Subject:
60 APPLIED LIFE SCIENCES; 59 BASIC BIOLOGICAL SCIENCES; X-ray photoelectron spectroscopy; Nitrogen; Oxygen; DNA sequencing; Nucleotide sequencing; Purines; Chemical elements; Electron microscopes
OSTI Identifier:
1337763
Alternate Identifier(s):
OSTI ID: 1378725

Mankos, Marian, Persson, Henrik H. J., N’Diaye, Alpha T., Shadman, Khashayar, Schmid, Andreas K., Davis, Ronald W., and Dedkov, Yuriy. Nucleotide-Specific Contrast for DNA Sequencing by Electron Spectroscopy. United States: N. p., Web. doi:10.1371/journal.pone.0154707.
Mankos, Marian, Persson, Henrik H. J., N’Diaye, Alpha T., Shadman, Khashayar, Schmid, Andreas K., Davis, Ronald W., & Dedkov, Yuriy. Nucleotide-Specific Contrast for DNA Sequencing by Electron Spectroscopy. United States. doi:10.1371/journal.pone.0154707.
Mankos, Marian, Persson, Henrik H. J., N’Diaye, Alpha T., Shadman, Khashayar, Schmid, Andreas K., Davis, Ronald W., and Dedkov, Yuriy. 2016. "Nucleotide-Specific Contrast for DNA Sequencing by Electron Spectroscopy". United States. doi:10.1371/journal.pone.0154707.
@article{osti_1337763,
title = {Nucleotide-Specific Contrast for DNA Sequencing by Electron Spectroscopy},
author = {Mankos, Marian and Persson, Henrik H. J. and N’Diaye, Alpha T. and Shadman, Khashayar and Schmid, Andreas K. and Davis, Ronald W. and Dedkov, Yuriy},
abstractNote = {DNA sequencing by imaging in an electron microscope is an approach that holds promise to deliver long reads with low error rates and without the need for amplification. Earlier work using transmission electron microscopes, which use high electron energies on the order of 100 keV, has shown that low contrast and radiation damage necessitates the use of heavy atom labeling of individual nucleotides, which increases the read error rates. Other prior work using scattering electrons with much lower energy has shown to suppress beam damage on DNA. Here we explore possibilities to increase contrast by employing two methods, X-ray photoelectron and Auger electron spectroscopy. Using bulk DNA samples with monomers of each base, both methods are shown to provide contrast mechanisms that can distinguish individual nucleotides without labels. In conclusion, both spectroscopic techniques can be readily implemented in a low energy electron microscope, which may enable label-free DNA sequencing by direct imaging.},
doi = {10.1371/journal.pone.0154707},
journal = {PLoS ONE},
number = 5,
volume = 11,
place = {United States},
year = {2016},
month = {5}
}