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

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https://doi.org/10.1002/jbio.201000085
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Keywords

Base Sequence, DNA Methylation, DNA, Single-Stranded, Discriminant Analysis, Multivariate Analysis, Principal Component Analysis, Spectroscopy, Fourier Transform Infrared, Spectrum Analysis, Raman

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Characterisation of DNA methylation status using spectroscopy (mid-IR versus Raman) with multivariate analysis. / Kelly, Jemma G.; Najand, Ghazal M.; Martin, Francis L.
In: Journal of Biophotonics, Vol. 4, No. 5, 05.2011, p. 345-354.

Research output: Contribution to Journal/Magazine › Journal article › peer-review

Bibtex

@article{621720d9a5f8442bb4ef61705993299e,

title = "Characterisation of DNA methylation status using spectroscopy (mid-IR versus Raman) with multivariate analysis",

abstract = "Methylation status plays important roles in the regulation of gene expression and significantly influences the dynamics, bending and flexibility of DNA. The aim of this study was to determine whether attenuated total reflection Fourier-transform infrared (ATR-FTIR) or Raman spectroscopy with subsequent multivariate analysis could determine methylation patterning in oligonucleotides variously containing 5-methylcytosine, cytosine and guanine bases. Applied to Low-E reflective glass slides, 10 independent spectral acquisitions were acquired per oligonucleotide sample. Resultant spectra were baseline-corrected and vector normalised over the 1750 cm(-1) -760 cm(-1) (for ATR-FTIR spectroscopy) or the 1750 cm(-1) -600 cm(-1) (for Raman spectroscopy) regions. Data were then analysed using principal component analysis (PCA) coupled with linear discriminant analysis (LDA). Exploiting this approach, biomolecular signatures enabling sensitive and specific discrimination of methylation patterning were derived. For DNA sequence and methylation analysis, this approach has the potential to be an important tool, especially when material is scarce.",

keywords = "Base Sequence, DNA Methylation, DNA, Single-Stranded, Discriminant Analysis, Multivariate Analysis, Principal Component Analysis, Spectroscopy, Fourier Transform Infrared, Spectrum Analysis, Raman",

author = "Kelly, {Jemma G.} and Najand, {Ghazal M.} and Martin, {Francis L.}",

note = "Copyright {\textcopyright} 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.",

year = "2011",

month = may,

doi = "10.1002/jbio.201000085",

language = "English",

volume = "4",

pages = "345--354",

journal = "Journal of Biophotonics",

issn = "1864-063X",

publisher = "Wiley-VCH Verlag",

number = "5",

}

RIS

TY - JOUR

T1 - Characterisation of DNA methylation status using spectroscopy (mid-IR versus Raman) with multivariate analysis

AU - Kelly, Jemma G.

AU - Najand, Ghazal M.

AU - Martin, Francis L.

PY - 2011/5

Y1 - 2011/5

N2 - Methylation status plays important roles in the regulation of gene expression and significantly influences the dynamics, bending and flexibility of DNA. The aim of this study was to determine whether attenuated total reflection Fourier-transform infrared (ATR-FTIR) or Raman spectroscopy with subsequent multivariate analysis could determine methylation patterning in oligonucleotides variously containing 5-methylcytosine, cytosine and guanine bases. Applied to Low-E reflective glass slides, 10 independent spectral acquisitions were acquired per oligonucleotide sample. Resultant spectra were baseline-corrected and vector normalised over the 1750 cm(-1) -760 cm(-1) (for ATR-FTIR spectroscopy) or the 1750 cm(-1) -600 cm(-1) (for Raman spectroscopy) regions. Data were then analysed using principal component analysis (PCA) coupled with linear discriminant analysis (LDA). Exploiting this approach, biomolecular signatures enabling sensitive and specific discrimination of methylation patterning were derived. For DNA sequence and methylation analysis, this approach has the potential to be an important tool, especially when material is scarce.

AB - Methylation status plays important roles in the regulation of gene expression and significantly influences the dynamics, bending and flexibility of DNA. The aim of this study was to determine whether attenuated total reflection Fourier-transform infrared (ATR-FTIR) or Raman spectroscopy with subsequent multivariate analysis could determine methylation patterning in oligonucleotides variously containing 5-methylcytosine, cytosine and guanine bases. Applied to Low-E reflective glass slides, 10 independent spectral acquisitions were acquired per oligonucleotide sample. Resultant spectra were baseline-corrected and vector normalised over the 1750 cm(-1) -760 cm(-1) (for ATR-FTIR spectroscopy) or the 1750 cm(-1) -600 cm(-1) (for Raman spectroscopy) regions. Data were then analysed using principal component analysis (PCA) coupled with linear discriminant analysis (LDA). Exploiting this approach, biomolecular signatures enabling sensitive and specific discrimination of methylation patterning were derived. For DNA sequence and methylation analysis, this approach has the potential to be an important tool, especially when material is scarce.

KW - Base Sequence

KW - DNA Methylation

KW - DNA, Single-Stranded

KW - Discriminant Analysis

KW - Multivariate Analysis

KW - Principal Component Analysis

KW - Spectroscopy, Fourier Transform Infrared

KW - Spectrum Analysis, Raman

U2 - 10.1002/jbio.201000085

DO - 10.1002/jbio.201000085

M3 - Journal article

C2 - 21520428

VL - 4

SP - 345

EP - 354

JO - Journal of Biophotonics

JF - Journal of Biophotonics

SN - 1864-063X

IS - 5

ER -

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