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Discrimination of base differences in oligonucleotides using mid-infrared spectroscopy and multivariate analysis.

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Discrimination of base differences in oligonucleotides using mid-infrared spectroscopy and multivariate analysis. / Kerns, Jemma; Martin-Hirsch, Pierre L.; Martin, Frank L.

In: Analytical Chemistry, Vol. 81, No. 13, 01.07.2009, p. 5314-5319.

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@article{c404213abdc8401480d9010719abf944,
title = "Discrimination of base differences in oligonucleotides using mid-infrared spectroscopy and multivariate analysis.",
abstract = "Attenuated total reflection Fourier transform-infrared (ATR-FTIR) spectroscopy was employed to interrogate a panel of simple oligonucleotides designed to contain various base differences; combined with subsequent multivariate analysis, we set out to determine whether the specificity of this approach would point to a novel means for mutation detection. Oligonucleotides were designed that were 15 bases in length and contained various combinations of purines (adenine, guanine) or pyrimidines (cytosine, thymine). These were applied to 1 cm × 1 cm low-E reflective glass slides, and triplicate samples were interrogated using ATR-FTIR spectroscopy. Per oligonucleotide sample, 10 independent spectral acquisitions were obtained. Prior to multivariate analysis, infrared spectra were baseline-corrected and vector normalized over the 1750−760 cm−1 region specific to the chemical bonds of organic molecules. Spectral categories were then analyzed using principal component analysis (PCA) followed by linear discriminant analysis (LDA). Scores plots revealed that PCA-LDA clearly segregated different oligonucleotide sequences, even in the presence of a single base difference. Loadings plots confirmed the chemical entities associated with distinguishing base differences. These results suggest that mid-IR spectroscopy might have future roles in interrogating polymorphic forms of a DNA template.",
author = "Jemma Kerns and Martin-Hirsch, {Pierre L.} and Martin, {Frank L.}",
year = "2009",
month = jul
day = "1",
doi = "10.1021/ac900546m",
language = "English",
volume = "81",
pages = "5314--5319",
journal = "Analytical Chemistry",
issn = "0003-2700",
publisher = "American Chemical Society",
number = "13",

}

RIS

TY - JOUR

T1 - Discrimination of base differences in oligonucleotides using mid-infrared spectroscopy and multivariate analysis.

AU - Kerns, Jemma

AU - Martin-Hirsch, Pierre L.

AU - Martin, Frank L.

PY - 2009/7/1

Y1 - 2009/7/1

N2 - Attenuated total reflection Fourier transform-infrared (ATR-FTIR) spectroscopy was employed to interrogate a panel of simple oligonucleotides designed to contain various base differences; combined with subsequent multivariate analysis, we set out to determine whether the specificity of this approach would point to a novel means for mutation detection. Oligonucleotides were designed that were 15 bases in length and contained various combinations of purines (adenine, guanine) or pyrimidines (cytosine, thymine). These were applied to 1 cm × 1 cm low-E reflective glass slides, and triplicate samples were interrogated using ATR-FTIR spectroscopy. Per oligonucleotide sample, 10 independent spectral acquisitions were obtained. Prior to multivariate analysis, infrared spectra were baseline-corrected and vector normalized over the 1750−760 cm−1 region specific to the chemical bonds of organic molecules. Spectral categories were then analyzed using principal component analysis (PCA) followed by linear discriminant analysis (LDA). Scores plots revealed that PCA-LDA clearly segregated different oligonucleotide sequences, even in the presence of a single base difference. Loadings plots confirmed the chemical entities associated with distinguishing base differences. These results suggest that mid-IR spectroscopy might have future roles in interrogating polymorphic forms of a DNA template.

AB - Attenuated total reflection Fourier transform-infrared (ATR-FTIR) spectroscopy was employed to interrogate a panel of simple oligonucleotides designed to contain various base differences; combined with subsequent multivariate analysis, we set out to determine whether the specificity of this approach would point to a novel means for mutation detection. Oligonucleotides were designed that were 15 bases in length and contained various combinations of purines (adenine, guanine) or pyrimidines (cytosine, thymine). These were applied to 1 cm × 1 cm low-E reflective glass slides, and triplicate samples were interrogated using ATR-FTIR spectroscopy. Per oligonucleotide sample, 10 independent spectral acquisitions were obtained. Prior to multivariate analysis, infrared spectra were baseline-corrected and vector normalized over the 1750−760 cm−1 region specific to the chemical bonds of organic molecules. Spectral categories were then analyzed using principal component analysis (PCA) followed by linear discriminant analysis (LDA). Scores plots revealed that PCA-LDA clearly segregated different oligonucleotide sequences, even in the presence of a single base difference. Loadings plots confirmed the chemical entities associated with distinguishing base differences. These results suggest that mid-IR spectroscopy might have future roles in interrogating polymorphic forms of a DNA template.

UR - http://www.scopus.com/inward/record.url?scp=67649921085&partnerID=8YFLogxK

U2 - 10.1021/ac900546m

DO - 10.1021/ac900546m

M3 - Journal article

VL - 81

SP - 5314

EP - 5319

JO - Analytical Chemistry

JF - Analytical Chemistry

SN - 0003-2700

IS - 13

ER -