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Characterisation of DNA methylation status using spectroscopy (mid‐IR versus Raman) with multivariate analysis
Author(s) -
Kelly Jemma G.,
Najand Ghazal M.,
Martin Francis L.
Publication year - 2011
Publication title -
journal of biophotonics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.877
H-Index - 66
eISSN - 1864-0648
pISSN - 1864-063X
DOI - 10.1002/jbio.201000085
Subject(s) - attenuated total reflection , methylation , raman spectroscopy , dna methylation , principal component analysis , oligonucleotide , fourier transform infrared spectroscopy , spectroscopy , cytosine , analytical chemistry (journal) , chemistry , microbiology and biotechnology , dna , biology , gene , gene expression , biochemistry , optics , chromatography , physics , computer science , artificial intelligence , quantum mechanics
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. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)