Structural organisation of nucleic acids from tumour cells

Repnytska, O. P.; Довбешко, Г. И.; Tryndiak, V. P.; Todor, I N; Kosenkov, D. V.

doi:10.1039/b304904c

Cited by 21 publications

(12 citation statements)

References 19 publications

(24 reference statements)

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“…The second principal component was the ratio of intensities at 1712 cm 1 and at 1700 cm 1 , marker bands for DNA conformations in A, B or Z-form. Earlier, we estimated the contribution of the above mentioned components and found that they show a preferential contribution [20].…”

Section: Seira Spectroscopy and Spectral Evaluationmentioning

confidence: 95%

Gold and colloidal gold surface influence on dna conformational change

Dovbeshko¹,

Lashkaryov²

2004

Semicond. Phys. Quantum Electron. Optoelectron.

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DNA conformational changes caused by gold and colloidal gold surface have been studied by surface enhanced infrared spectroscopy (SEIRA), spectroscopy of plasmon resonance (SPR), atomic force microscopy (AFM) and principal component analysis. Experimental data have shown that DNA conformation is slightly influenced by gold surface, while it is strongly altered by colloidal gold. Spectroscopic features of DNA-colloidal gold system have shown that the intensity of the asymmetric PO 2 band at 1240 cm 1 decreases by two times, and that of symmetric band at 1090 cm 1 decreases by 2.4 times whereas the halfwidth of phosphate bands increases by 3540 cm 1 ; a frequency shift of asymmetric band position from 1240 to 1246 cm 1 and a symmetric band from 1090 to 1106 cm 1 has been observed. It was shown that intensity variation and shift of DNA base vibrations together with the broadening of OH, NH, and CH stretching vibrations occur due to DNA conformational changes and the redistribution of the H-bonding network. A supposition about DNA condensation by colloidal gold was made. SEIRA and AFM data have showed major DNA structural changes occurred on gold colloidal particles. It was found that all the spectral features are more prominent for DNAcolloidal gold system deposited on gold substrate than on CaF 2 substrate.

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Section: Seira Spectroscopy and Spectral Evaluationmentioning

confidence: 95%

Gold and colloidal gold surface influence on dna conformational change

Dovbeshko¹,

Lashkaryov²

2004

Semicond. Phys. Quantum Electron. Optoelectron.

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“…Loading plots for LDF1-2 are shown in Figure 9, with band assignments given in Table 7A-B [52][53][54][55][56][57][58]. Key Features from LDF1 (Table 7A) -Because urethral cells have negative scores, negative moieties corresponding to negative peaks are prominent in these cells (refer back to Figure 8(b)).…”

Section: Loading Plot Analysismentioning

confidence: 99%

Classification of fixed urological cells using Raman tweezers

Harvey

Hughes

Ward

et al. 2009

Journal of Biophotonics

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In this paper we report on preliminary investigations into using Raman tweezers to classify urological cell lines. This builds on earlier work within the group, whereby Raman tweezer methodologies were developed, and the application of this technique to differentiate between live prostate cancer (CaP) and bladder cells lines (PC-3 and MGH-U1 respectively) was demonstrated.In this present study we analysed chemically fixed cells using two different fixative methods; SurePath (a commercial available liquid based cytology media) and 4% v/v formalin/PBS fixatives. The study has been expanded from our previous live cell study to include the androgen sensitive CaP cell line LNCaP, primary benign prostate hyperplasia (BPH) cells as well as primary urethral cells. Raman light from the cells was collected using a 514.5 nm Ar-ion laser excitation source in back-scattering configuration mode.Principal component-linear discriminate analysis (PC-LDA) models of resulting cell spectra were generated and these were validated using a blind comparison. Sensitivities and specificities of > 72% and 90% respectively, for SurePath fixed cells, and > 93% and 98% respectively for 4% v/v formalin/PBS fixed cells was achieved. The higher prediction results for the formalin fixed cells can be attributed to a better signal-to-noise ratio for spectra obtained from these cells.Following on from this work, urological cell lines were exposed to urine for up to 12 hours to determine the effect of urine on the ability to classify these cells. Results indicate that urine has no detrimental effect on prediction results.

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“…It is reported to be reliable in determining distribution of basic biomolecular tissue components, as well as information on molecular secondary protein structure and fatty acyl chain peroxidation level (14). Its ability to function as a biomolecular probe for individual cells in vitro without causing toxic or detectable biochemical changes in them allows it to be used as an effective probe at the submicroscopic level (26). This gives credibility to the use of FTIR IR spectroscopy as a new molecular histopathology tool.…”

Section: Discussionmentioning

confidence: 94%

Biomolecular diagnosis of human glioblastoma multiforme using Synchrotron mid-infrared spectromicroscopy

Ali

Lu²,

Das³

et al. 2010

Int J Mol Med

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Abstract. Glioblastoma multiforme (GBM) is one of the most malignant human tumors, with a uniformly poor outcome. One obstacle in curing malignant brain tumors is the limitation of conventional light microscopy in detecting microscopic residual tumor in biopsy samples from the perimeter of the surgically resected tumor. We further refined the identification of GBM tumor tissue at the sub-cellular level, utilising the technique of Synchrotron, sourced mid-infrared (mid-IR) spectromicroscopy. Paired, thin (5 μm) cryosections of snap-frozen human GBM tumor samples removed at elective surgery were mounted on glass slides (hematoxylin and eosin-stained tissue section) and calcium fluoride (CaF 2 ) windows (unstained tissue section for transmission spectromicroscopy), respectively. Concordance of tumor bearing areas identified in the stained section with the unstained IR tissue section was confirmed by the pathologist of the study. Compared with molecular signatures obtained from normal control brain tissue, unique spectroscopic patterns were detected in GBM tumor samples from 6 patients. The identifying features of GBM were: i) high protein-to-lipid ratios (amide I+II/CH 2 symmetric stretch; amide I+II/CH 2 +CH 3 symmetric and asymmetric stretch), and ii) considerable enhancement of the intensities of characteristic peaks at 2,957 and 2,871 cm -1 representing CH 3 asymmetric and symmetric stretch, respectively. Spectral data sets were subjected to Ward's algorithm for assignment to similar groups, and then subjected to hierarchical cluster analysis (HCA) by means of false color digital maps. False color images of 5 clusters obtained by HCA identified dominant clusters corresponding to tumor tissue. Corroboration of these findings in a larger number of GBM may allow for more precise identification of these and other types of brain tumors.

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Structural organisation of nucleic acids from tumour cells

Cited by 21 publications

References 19 publications

Gold and colloidal gold surface influence on dna conformational change

Gold and colloidal gold surface influence on dna conformational change

Classification of fixed urological cells using Raman tweezers

Biomolecular diagnosis of human glioblastoma multiforme using Synchrotron mid-infrared spectromicroscopy

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