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Title: DNA Methylation Detection Using Resonance and Nanobowtie-Antenna-Enhanced Raman Spectroscopy

Abstract

In this paper, we show that DNA carrying 5-methylcytosine modifications or methylated DNA (m-DNA) can be distinguished from DNA with unmodified cytosine by Raman spectroscopy enhanced by both a bowtie nanoantenna and excitation resonance. In particular, m-DNA can be identified by a peak near 1000 cm-1 and changes in the Raman peaks in the 1200–1700 cm-1 band that are enhanced by the ring-absorption resonance. The identification is robust to the use of resonance Raman and nanoantenna excitation used to obtain significant signal improvement. The primary differences are three additional Raman peaks with methylation at 1014, 1239, and 1639 cm-1 and spectral intensity inversion at 1324 (C5=C6) and 1473 cm-1 (C4=N3) in m-DNA compared to that of DNA with unmodified cytosine. We attribute this to the proximity of the methyl group to the antenna, which brings the (C5=C6) mode closer to experiencing a stronger near-field enhancement. We also show distinct Raman spectral features attributed to the transition of DNA from a hydrated state, when dissolved, to a dried/denatured state. We observe a general broadening of the larger lines and a transfer of spectral weight from the ~1470 cm-1 vibration to the two higher-energy lines of the dried m-DNA solution. We attributemore » the new spectral characteristics to DNA softening under high salt conditions and find that the m-DNA is still distinguishable via the ~1000 cm-1 peak and distribution of the signal in the 1200–1700 cm-1 band. The nanoantenna gain exceeds 20,000, whereas the real signal ratio is much less because of a low average enhanced region occupancy even with these relatively high DNA concentrations. It is improved when fixed DNA in a salt crystal lies near the nanoantenna. Finally, the Raman resonance gain profile is consistent with A-term expectations, and the resonance is found at ~259 nm excitation wavelength.« less

Authors:
 [1];  [1];  [2];  [1];  [1]
  1. North Carolina State Univ., Raleigh, NC (United States). Dept. of Physics
  2. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States). Center for Nanophase Materials Sciences
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); North Carolina State Univ., Raleigh, NC (United States)
Sponsoring Org.:
USDOE Office of Science (SC); National Inst. of Health (NIH) (United States); National Science Foundation (NSF)
OSTI Identifier:
1468193
Grant/Contract Number:  
AC05-00OR22725; R21CA13207; CBET 1067508
Resource Type:
Accepted Manuscript
Journal Name:
Biophysical Journal
Additional Journal Information:
Journal Volume: 114; Journal Issue: 11; Journal ID: ISSN 0006-3495
Publisher:
Elsevier
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

Li, Ling, Lim, Shuang Fang, Puretzky, Alexander, Riehn, Robert, and Hallen, Hans D. DNA Methylation Detection Using Resonance and Nanobowtie-Antenna-Enhanced Raman Spectroscopy. United States: N. p., 2018. Web. https://doi.org/10.1016/j.bpj.2018.04.021.
Li, Ling, Lim, Shuang Fang, Puretzky, Alexander, Riehn, Robert, & Hallen, Hans D. DNA Methylation Detection Using Resonance and Nanobowtie-Antenna-Enhanced Raman Spectroscopy. United States. https://doi.org/10.1016/j.bpj.2018.04.021
Li, Ling, Lim, Shuang Fang, Puretzky, Alexander, Riehn, Robert, and Hallen, Hans D. Thu . "DNA Methylation Detection Using Resonance and Nanobowtie-Antenna-Enhanced Raman Spectroscopy". United States. https://doi.org/10.1016/j.bpj.2018.04.021. https://www.osti.gov/servlets/purl/1468193.
@article{osti_1468193,
title = {DNA Methylation Detection Using Resonance and Nanobowtie-Antenna-Enhanced Raman Spectroscopy},
author = {Li, Ling and Lim, Shuang Fang and Puretzky, Alexander and Riehn, Robert and Hallen, Hans D.},
abstractNote = {In this paper, we show that DNA carrying 5-methylcytosine modifications or methylated DNA (m-DNA) can be distinguished from DNA with unmodified cytosine by Raman spectroscopy enhanced by both a bowtie nanoantenna and excitation resonance. In particular, m-DNA can be identified by a peak near 1000 cm-1 and changes in the Raman peaks in the 1200–1700 cm-1 band that are enhanced by the ring-absorption resonance. The identification is robust to the use of resonance Raman and nanoantenna excitation used to obtain significant signal improvement. The primary differences are three additional Raman peaks with methylation at 1014, 1239, and 1639 cm-1 and spectral intensity inversion at 1324 (C5=C6) and 1473 cm-1 (C4=N3) in m-DNA compared to that of DNA with unmodified cytosine. We attribute this to the proximity of the methyl group to the antenna, which brings the (C5=C6) mode closer to experiencing a stronger near-field enhancement. We also show distinct Raman spectral features attributed to the transition of DNA from a hydrated state, when dissolved, to a dried/denatured state. We observe a general broadening of the larger lines and a transfer of spectral weight from the ~1470 cm-1 vibration to the two higher-energy lines of the dried m-DNA solution. We attribute the new spectral characteristics to DNA softening under high salt conditions and find that the m-DNA is still distinguishable via the ~1000 cm-1 peak and distribution of the signal in the 1200–1700 cm-1 band. The nanoantenna gain exceeds 20,000, whereas the real signal ratio is much less because of a low average enhanced region occupancy even with these relatively high DNA concentrations. It is improved when fixed DNA in a salt crystal lies near the nanoantenna. Finally, the Raman resonance gain profile is consistent with A-term expectations, and the resonance is found at ~259 nm excitation wavelength.},
doi = {10.1016/j.bpj.2018.04.021},
journal = {Biophysical Journal},
number = 11,
volume = 114,
place = {United States},
year = {2018},
month = {6}
}

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Cited by: 4 works
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Figures / Tables:

Figure 1 Figure 1: Background spectrum used in the spectra analysis routine. It was collected by averaging and normalizing spectra of buffer solution on top of aluminum bowtie antenna coverslip.

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Works referenced in this record:

Cellular differentiation, cytidine analogs and DNA methylation
journal, May 1980


Tet Proteins Can Convert 5-Methylcytosine to 5-Formylcytosine and 5-Carboxylcytosine
journal, July 2011


Hypomethylation distinguishes genes of some human cancers from their normal counterparts
journal, January 1983

  • Feinberg, Andrew P.; Vogelstein, Bert
  • Nature, Vol. 301, Issue 5895
  • DOI: 10.1038/301089a0

The 5-methylcytosine content of DNA from human tumors
journal, January 1983

  • Gama-Sosa, Miguel A.; Slagel, Valerie A.; Trewyn, Ronald W.
  • Nucleic Acids Research, Vol. 11, Issue 19
  • DOI: 10.1093/nar/11.19.6883

Conventional and Nanotechniques for DNA Methylation Profiling
journal, January 2013

  • Shanmuganathan, Rajasree; Basheer, Nazeema B.; Amirthalingam, Laxmi
  • The Journal of Molecular Diagnostics, Vol. 15, Issue 1
  • DOI: 10.1016/j.jmoldx.2012.06.007

A decade of exploring the cancer epigenome — biological and translational implications
journal, September 2011

  • Baylin, Stephen B.; Jones, Peter A.
  • Nature Reviews Cancer, Vol. 11, Issue 10
  • DOI: 10.1038/nrc3130

Cancer as a dysregulated epigenome allowing cellular growth advantage at the expense of the host
journal, June 2013

  • Timp, Winston; Feinberg, Andrew P.
  • Nature Reviews Cancer, Vol. 13, Issue 7
  • DOI: 10.1038/nrc3486

Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity
journal, July 2014

  • Smallwood, Sébastien A.; Lee, Heather J.; Angermueller, Christof
  • Nature Methods, Vol. 11, Issue 8
  • DOI: 10.1038/nmeth.3035

A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands.
journal, March 1992

  • Frommer, M.; McDonald, L. E.; Millar, D. S.
  • Proceedings of the National Academy of Sciences, Vol. 89, Issue 5
  • DOI: 10.1073/pnas.89.5.1827

Development of techniques for DNA-methylation analysis
journal, October 2015


DNA Methylation: A Profile of Methods and Applications
journal, September 2002

  • Fraga, Mario F.; Esteller, Manel
  • BioTechniques, Vol. 33, Issue 3
  • DOI: 10.2144/02333rv01

Identification of 5-methylcytosine in DNA fragments immobilized on nitrocellulose paper.
journal, June 1980

  • Sano, H.; Royer, H. D.; Sager, R.
  • Proceedings of the National Academy of Sciences, Vol. 77, Issue 6
  • DOI: 10.1073/pnas.77.6.3581

Purification of CpG islands using a methylated DNA binding column
journal, March 1994

  • Cross, Sally H.; Charlton, Jillian A.; Nan, Xinsheng
  • Nature Genetics, Vol. 6, Issue 3
  • DOI: 10.1038/ng0394-236

Chromatin modification mapping in nanochannels
journal, November 2013

  • Lim, Shuang Fang; Karpusenko, Alena; Blumers, Ansel L.
  • Biomicrofluidics, Vol. 7, Issue 6
  • DOI: 10.1063/1.4833257

Use of restriction enzymes to study eukaryotic DNA methylation
journal, January 1978


A Nanocarbon Film Electrode as a Platform for Exploring DNA Methylation
journal, March 2008

  • Kato, Dai; Sekioka, Naoyuki; Ueda, Akio
  • Journal of the American Chemical Society, Vol. 130, Issue 12
  • DOI: 10.1021/ja710536p

Identification of epigenetic DNA modifications with a protein nanopore
journal, January 2009

  • Wallace, Emma V. B.; Stoddart, David; Heron, Andrew J.
  • Chemical Communications, Vol. 46, Issue 43
  • DOI: 10.1039/c0cc02864a

Detection and mapping of 5-methylcytosine and 5-hydroxymethylcytosine with nanopore MspA
journal, October 2013

  • Laszlo, A. H.; Derrington, I. M.; Brinkerhoff, H.
  • Proceedings of the National Academy of Sciences, Vol. 110, Issue 47
  • DOI: 10.1073/pnas.1310240110

Probing DNA Methylation in Breast Cancer Cell Lines Using Solid-State Nanopores
journal, January 2014


Direct Detection and Mapping of DNA Methylation in Single Molecules using Nanopore MspA
journal, January 2014

  • Laszlo, Andrew H.; Derrington, Ian M.; Brinkerhoff, Henry
  • Biophysical Journal, Vol. 106, Issue 2
  • DOI: 10.1016/j.bpj.2013.11.1255

Single-Site Resolution Detection of Methylation in DNA with Graphene Nanopores
journal, February 2016


Detection of DNA Methylation with Aerolysin Nanopore
journal, February 2017


Nanoelectromechanics of Methylated DNA in a Synthetic Nanopore
journal, February 2009


Surface-Enhanced Raman Spectroscopy of Nucleic Acid Compounds and Their Mixtures
journal, November 1991


SERS of cytosine and its methylated derivatives on metal colloids
journal, January 1992

  • Śanchez-Cortés, S.; Garcia-Ramos, J. V.
  • Journal of Raman Spectroscopy, Vol. 23, Issue 1
  • DOI: 10.1002/jrs.1250230108

SERS of cytosine and its methylated derivatives on gold sols
journal, February 1995

  • Camafeita, L. E.; Sánchez-Cortés, S.; García-Ramos, J. V.
  • Journal of Raman Spectroscopy, Vol. 26, Issue 2
  • DOI: 10.1002/jrs.1250260207

Surface-Enhanced Raman Scattering Based Ligase Detection Reaction
journal, January 2009

  • Huh, Yun Suk; Lowe, Adam J.; Strickland, Aaron D.
  • Journal of the American Chemical Society, Vol. 131, Issue 6
  • DOI: 10.1021/ja807526v

Detecting Chemically Modified DNA Bases Using Surface-Enhanced Raman Spectroscopy
journal, November 2011

  • Barhoumi, Aoune; Halas, Naomi J.
  • The Journal of Physical Chemistry Letters, Vol. 2, Issue 24
  • DOI: 10.1021/jz201423b

Single base extension reaction-based surface enhanced Raman spectroscopy for DNA methylation assay
journal, January 2012


Direct Surface-Enhanced Raman Scattering Analysis of DNA Duplexes
journal, November 2014

  • Guerrini, Luca; Krpetić, Željka; van Lierop, Danny
  • Angewandte Chemie International Edition, Vol. 54, Issue 4
  • DOI: 10.1002/anie.201408558

Highly sensitive DNA methylation analysis at CpG resolution by surface-enhanced Raman scattering via ligase chain reaction
journal, January 2015

  • Wang, Yuling; Wee, Eugene J. H.; Trau, Matt
  • Chemical Communications, Vol. 51, Issue 54
  • DOI: 10.1039/C5CC03921E

Resonance enhanced Raman scatter in liquid benzene at vapor-phase absorption peaks
journal, January 2013

  • Willitsford, Adam; Chadwick, C. Todd; Hallen, Hans
  • Optics Express, Vol. 21, Issue 22
  • DOI: 10.1364/OE.21.026150

Deep ultraviolet Raman spectroscopy: A resonance-absorption trade-off illustrated by diluted liquid benzene
journal, December 2015

  • Chadwick, C. T.; Willitsford, A. H.; Philbrick, C. R.
  • Journal of Applied Physics, Vol. 118, Issue 24
  • DOI: 10.1063/1.4938531

Resonance-Enhanced Raman Scattering of Ring-Involved Vibrational Modes in the 1 B 2u Absorption Band of Benzene, Including the Kekule Vibrational Modes ν 9 and ν 10
journal, January 2016

  • Willitsford, Adam H.; Chadwick, C. Todd; Kurtz, Stewart
  • The Journal of Physical Chemistry A, Vol. 120, Issue 4
  • DOI: 10.1021/acs.jpca.5b08159

Near-field enhanced ultraviolet resonance Raman spectroscopy using aluminum bow-tie nano-antenna
journal, September 2012

  • Li, Ling; Fang Lim, Shuang; Puretzky, Alexander A.
  • Applied Physics Letters, Vol. 101, Issue 11
  • DOI: 10.1063/1.4746747

Method for automated background subtraction from Raman spectra containing known contaminants
journal, January 2009

  • Beier, Brooke D.; Berger, Andrew J.
  • The Analyst, Vol. 134, Issue 6
  • DOI: 10.1039/b821856k

Vibrational spectra of nucleic acid constituents—II
journal, April 1973

  • Susi, H.; Ard, J. S.; Purcell, J. M.
  • Spectrochimica Acta Part A: Molecular Spectroscopy, Vol. 29, Issue 4
  • DOI: 10.1016/0584-8539(73)80102-3

F.T.-I.R. and laser-raman spectra of cytosine and cytidine
journal, January 1986


Surface-enhanced Raman spectroscopy of DNA bases
journal, June 1986

  • Otto, C.; van den Tweel, T. J. J.; de Mul, F. F. M.
  • Journal of Raman Spectroscopy, Vol. 17, Issue 3
  • DOI: 10.1002/jrs.1250170311

Raman spectral study of metal–cytosine complexes: A density functional theoretical (DFT) approach
journal, September 2011

  • Liu, Shuanjiang; Zheng, Guimei; Li, Jianxin
  • Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, Vol. 79, Issue 5
  • DOI: 10.1016/j.saa.2011.05.049

Characterisation of DNA methylation status using spectroscopy (mid-IR versus Raman) with multivariate analysis
journal, October 2010

  • Kelly, Jemma G.; Najand, Ghazal M.; Martin, Francis L.
  • Journal of Biophotonics, Vol. 4, Issue 5
  • DOI: 10.1002/jbio.201000085

pH-Dependent UV Resonance Raman Spectra of Cytosine and Uracil
journal, April 2009

  • Billinghurst, Brant E.; Oladepo, Sulayman A.; Loppnow, Glen R.
  • The Journal of Physical Chemistry B, Vol. 113, Issue 20
  • DOI: 10.1021/jp811327w

Excited-State Structural Dynamics of Cytosine from Resonance Raman Spectroscopy
journal, February 2006

  • Billinghurst, Brant E.; Loppnow, Glen R.
  • The Journal of Physical Chemistry A, Vol. 110, Issue 7
  • DOI: 10.1021/jp0561571

UV-Resonance-Raman Studies of Protonated Nucleic Acid Bases
journal, July 1991

  • Gfrörer, A.; Schnetter, M. E.; Wolfrum, J.
  • Berichte der Bunsengesellschaft für physikalische Chemie, Vol. 95, Issue 7
  • DOI: 10.1002/bbpc.19910950711

Direct Quantification of DNA Base Composition by Surface-Enhanced Raman Scattering Spectroscopy
journal, July 2016

  • Morla-Folch, Judit; Alvarez-Puebla, Ramon A.; Guerrini, Luca
  • The Journal of Physical Chemistry Letters, Vol. 7, Issue 15
  • DOI: 10.1021/acs.jpclett.6b01424

A reusable laser wrapped graphene-Ag array based SERS sensor for trace detection of genomic DNA methylation
journal, June 2017


Dependence of the melting temperature of DNA on salt concentration
journal, April 1965


The denaturation of DNA
journal, December 1993


Differential stability of DNA based on salt concentration
journal, May 2016


    Works referencing / citing this record:

    Deep‐Ultraviolet Biomolecular Imaging and Analysis
    journal, December 2018

    • Kumamoto, Yasuaki; Taguchi, Atsushi; Kawata, Satoshi
    • Advanced Optical Materials, Vol. 7, Issue 5
    • DOI: 10.1002/adom.201801099

    Resonance Raman imagery of semi-fossilized soft tissues
    conference, September 2018

    • Hallen, Hans D.; Long, Brandon; Zheng, Wenxia
    • Ultrafast Nonlinear Imaging and Spectroscopy VI
    • DOI: 10.1117/12.2321298

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