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Title: Detecting DNA Methylation Using Surface-Enhanced Raman Spectroscopy

Abstract

Among all of the epigenetic events that are responsible for various diseases such as cancer, lupus, and several birth defects, DNA methylation is one of the crucial ones. It occurs because of the alkylation of various bases. These modifications of genes carried through altered creations of proteins ultimately lead to various diseases. For example, a vital cause behind canine lymphoma is found to be DNA methylation in the guanine base. In this work, we analyzed the methylated and nonmethylated guanine structure with the assistance of surface-enhanced Raman spectroscopy and density functional theory (DFT). Because of their vulnerability for causing DNA methylation, the N7 and O6 positions of the guanine structure were the positions of interest with the addition of various adducts such as methyl, hydroxyethyl, and deuterated methyl groups. To distinguish the methylated samples from the nonmethylated ones, principal component analysis was performed, and the same analysis was used to distinguish their methylated positions and added adducts. The experimental results were then explained by structure optimization and frequency calculation of the molecules based on DFT calculations. To understand the charge distribution and detect the possible locations of alkylation of DNA bases, electrostatic potential, highest occupied molecular orbital, and lowest unoccupiedmore » molecular orbital for each of the molecules were analyzed, and the reactivity was discussed in the light of electronic structure calculations. The results presented in this study demonstrate a potential label-free technique to examine epigenetic modification of DNA.« less

Authors:
ORCiD logo [1]; ORCiD logo [2];  [3]; ORCiD logo [2]; ORCiD logo [1]
  1. Louisiana State Univ., Baton Rouge, LA (United States). Dept. of Mechanical and Industrial Engineering
  2. Louisiana State Univ., Baton Rouge, LA (United States). Dept. of Geology and Geophysics and Center for Computation and Technology
  3. Intel Corporation,Hillsboro, OR (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC); Univ. of California, Oakland, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1543660
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Physical Chemistry. C
Additional Journal Information:
Journal Volume: 123; Journal Issue: 1; Journal ID: ISSN 1932-7447
Publisher:
American Chemical Society
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; 59 BASIC BIOLOGICAL SCIENCES; Chemistry; Science & Technology - Other Topics; Materials Science

Citation Formats

Abid Hasan, Syed Mohammad, He, Yuyang, Chang, Te-Wei, Wang, Jianwei, and Gartia, Manas Ranjan. Detecting DNA Methylation Using Surface-Enhanced Raman Spectroscopy. United States: N. p., 2018. Web. doi:10.1021/acs.jpcc.8b10178.
Abid Hasan, Syed Mohammad, He, Yuyang, Chang, Te-Wei, Wang, Jianwei, & Gartia, Manas Ranjan. Detecting DNA Methylation Using Surface-Enhanced Raman Spectroscopy. United States. doi:10.1021/acs.jpcc.8b10178.
Abid Hasan, Syed Mohammad, He, Yuyang, Chang, Te-Wei, Wang, Jianwei, and Gartia, Manas Ranjan. Fri . "Detecting DNA Methylation Using Surface-Enhanced Raman Spectroscopy". United States. doi:10.1021/acs.jpcc.8b10178.
@article{osti_1543660,
title = {Detecting DNA Methylation Using Surface-Enhanced Raman Spectroscopy},
author = {Abid Hasan, Syed Mohammad and He, Yuyang and Chang, Te-Wei and Wang, Jianwei and Gartia, Manas Ranjan},
abstractNote = {Among all of the epigenetic events that are responsible for various diseases such as cancer, lupus, and several birth defects, DNA methylation is one of the crucial ones. It occurs because of the alkylation of various bases. These modifications of genes carried through altered creations of proteins ultimately lead to various diseases. For example, a vital cause behind canine lymphoma is found to be DNA methylation in the guanine base. In this work, we analyzed the methylated and nonmethylated guanine structure with the assistance of surface-enhanced Raman spectroscopy and density functional theory (DFT). Because of their vulnerability for causing DNA methylation, the N7 and O6 positions of the guanine structure were the positions of interest with the addition of various adducts such as methyl, hydroxyethyl, and deuterated methyl groups. To distinguish the methylated samples from the nonmethylated ones, principal component analysis was performed, and the same analysis was used to distinguish their methylated positions and added adducts. The experimental results were then explained by structure optimization and frequency calculation of the molecules based on DFT calculations. To understand the charge distribution and detect the possible locations of alkylation of DNA bases, electrostatic potential, highest occupied molecular orbital, and lowest unoccupied molecular orbital for each of the molecules were analyzed, and the reactivity was discussed in the light of electronic structure calculations. The results presented in this study demonstrate a potential label-free technique to examine epigenetic modification of DNA.},
doi = {10.1021/acs.jpcc.8b10178},
journal = {Journal of Physical Chemistry. C},
number = 1,
volume = 123,
place = {United States},
year = {2018},
month = {12}
}

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