Detecting DNA Methylation Using Surface-Enhanced Raman Spectroscopy

Abid Hasan, Syed Mohammad; He, Yuyang; Chang, Te-Wei; Wang, Jianwei; Gartia, Manas Ranjan

doi:10.1021/acs.jpcc.8b10178

Title: Detecting DNA Methylation Using Surface-Enhanced Raman Spectroscopy

Full Record
Other Related Research

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 »« less

Authors:

^[1];

^[2]; Chang, Te-Wei ^[3];

^[2];

^[1]

Louisiana State Univ., Baton Rouge, LA (United States). Dept. of Mechanical and Industrial Engineering
Louisiana State Univ., Baton Rouge, LA (United States). Dept. of Geology and Geophysics and Center for Computation and Technology
Intel Corporation,Hillsboro, OR (United States)

Publication Date:: Fri Dec 14 00:00:00 EST 2018

Research Org.:: Lawrence Berkeley National Lab. (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.

Copy to clipboard


                    Abid Hasan, Syed Mohammad, He, Yuyang, Chang, Te-Wei, Wang, Jianwei, & Gartia, Manas Ranjan. Detecting DNA Methylation Using Surface-Enhanced Raman Spectroscopy.  United States.  https://doi.org/10.1021/acs.jpcc.8b10178

Copy to clipboard


                    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.  https://doi.org/10.1021/acs.jpcc.8b10178.  https://www.osti.gov/servlets/purl/1543660.

Copy to clipboard


                    
@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         = {Fri Dec 14 00:00:00 EST 2018},

  month        = {Fri Dec 14 00:00:00 EST 2018}

}

Copy to clipboard

Journal Article:

Free Publicly Available Full Text

Accepted Manuscript (DOE)

Publisher's Version of Record

https://doi.org/10.1021/acs.jpcc.8b10178

Other availability

Search WorldCat to find libraries that may hold this journal

Citation Metrics:

Cited by: 7 works

Citation information provided by
Web of Science

Save / Share:

Export Metadata

Save to My Library

Similar Records in DOE PAGES and OSTI.GOV collections:

Combined high-performance liquid chromatography/ sup 32 P-postlabeling assay of N7-methyldeoxyguanosine

Journal Article Shields, P G ; Povey, A C ; Wilson, V L ; ... - Cancer Research; (USA)

A highly sensitive and specific assay for the detection of N7-methyl-2{prime}-deoxyguanosine (N7methyldG) has been developed by combining high-performance liquid chromatography, {sup 32}P-postlabeling, and nucleotide chromatography. Separation of normal nucleotides and adducts by high-performance liquid chromatography and then combining a portion of 2{prime}-deoxyguanosine to the N7methyldG allows for quantitation using an internal standard. The directly determined molar ratio is not subject to errors in digestion, variable ATP-specific activity, or assumptions in relative adduct-labeling efficiency. The detection limit was one N7methyldG adduct in 10(7) unmodified 2{prime}-deoxyguanosine bases. N7methyldG adducts have been detected in 5 human lung samples in which O6-methyl-2{prime}-deoxyguanosine adducts hadmore »« less
Induction of Gter dot C to Ater dot T transitions by the acridine half-mustard ICR-191 supports a mispairing mechanism for mutagenesis by some bulky mutagens

Journal Article Sahasrabudhe, S R ; Luo, Xun ; Humayun, M Z - Biochemistry; (USA)

As the most nucleophilic atom in DNA, the guanine N7 atom is a major site of attack for a large number of chemical mutagens as well as chemotherapeutic agents. Paradoxically, while methylation of guanine N7 is believed to be largely nonmutagenic, aflatoxin B{sub 1}, among the most potent mutagens, appears to exert its mutagenic activity through adduction at this site. On the basis of an analysis of the specificity of mutations induced by various adduct forms of aflatoxin B{sub 1}, the authors have previously proposed mechanisms that can both resolve the paradox and account for the specificity of mutagenesis bymore »« less
https://doi.org/10.1021/bi00501a006
Crystal and solution structures of d(CGC[e{sup 6}G]AATTCGCG)-drug complexes reveal conformational polymorphism of O{sup 6}-ethyl-guanine:cytosine base pair

Conference Sriram, M ; Yang, D ; Gao, Y G

O6-ethyl-guanine (e{sup 6}G) is a relatively persistent alkylation lesion caused by the exposure of DNA to carcinogen N-ethyl-N-nitrosurea. We have studied the structural consequences of the e{sup 6}G incorporation in DNA by X-ray crystallography and NMR. We have obtained crystals of the modified DNA dodecamer d(CGC[e{sup 6}G]AATTCGCG) complexed to several minor groove binding drugs including Hoechst 33258, Hoechst 33342, netropsin, and SN6999. The space froup of the crystals from those complexes is P2{sub 1}2{sub 1}2{sub 1}. However, the crystal structure of the SN6999 complex is nor isomorphous to that from the other three complexes. In all four refined crystal structures,more »« less
Bypass of Aflatoxin B[subscript 1] Adducts by the Sulfolobus solfataricus DNA Polymerase IV

Journal Article Banerjee, Surajit ; Brown, Kyle L ; Egli, Martin ; ... - J. Am. Chem. Soc.

Aflatoxin B{sub 1} (AFB{sub 1}) is oxidized to an epoxide in vivo, which forms an N7-dG DNA adduct (AFB{sub 1}-N7-dG). The AFB{sub 1}-N7-dG can rearrange to a formamidopyrimidine (AFB{sub 1}-FAPY) derivative. Both AFB{sub 1}-N7-dG and the {beta}-anomer of the AFB{sub 1}-FAPY adduct yield G {yields} T transversions in Escherichia coli, but the latter is more mutagenic. We show that the Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) bypasses AFB{sub 1}-N7-dG in an error-free manner but conducts error-prone replication past the AFB{sub 1}-FAPY adduct, including misinsertion of dATP, consistent with the G {yields} T mutations observed in E. coli. Three ternarymore »« less
https://doi.org/10.1021/ja2015668
Synthesis and characterization of trans-(Pt(NH3)2Cl2) adducts of d(CCTCGAGTCTCC). d(GGAGACTCGAGG)

Journal Article Lepre, C A ; Chassot, L ; Costello, C E ; ... - Biochemistry; (USA)

The reaction of trans-diamminedichloroplatinum(II) (trans-DDP), the inactive isomer of the anticancer drug cisplatin, with the single-stranded deoxydodecanucleotide d(CCTCGAGTCTCC) in aqueous solution at 37 degrees C was monitored by reversed-phase HPLC. Consumption of the dodecamer follows pseudo-first-order reaction kinetics with a rate constant of 1.25 (4) x 10(-4) s-1. Two intermediates, shown to be monofunctional adducts in which Pt is coordinated to the guanine N7 positions, were trapped with NH4(HCO3) and identified by enzymatic degradation analysis. These monofunctional adducts and a third, less abundant, one are rapidly removed from the DNA by thiourea under mild conditions. When allowed to react further,more »« less
https://doi.org/10.1021/bi00455a031

Similar Records