Infrared and Raman Spectroscopy

Tsuboi, Masamichi

doi:10.1016/b978-0-12-701901-7.50010-0

Cited by 44 publications

(19 citation statements)

References 93 publications

(100 reference statements)

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“…A similar downward shift of this band is characteristic for DNA denaturation or strand separation. 58,81 A slight peak intensity increase of the 1682 cm Ϫ1 band can be noted at 3 [Cr]/[P] (Figures 4 and 6). A major intensity increase of this band occurs during DNA denaturation due to increased hyperchromicity.…”

Section: Vcd and Afm Of Dna With Crmentioning

confidence: 92%

“…A major intensity increase of this band occurs during DNA denaturation due to increased hyperchromicity. 58,70 These two features may indicate the possibility of DNA denaturation. However, the other features of absorption spectra that are characteristic for DNA denaturation are not present.…”

Section: Vcd and Afm Of Dna With Crmentioning

confidence: 96%

“…54,55,68 In the sugar-phosphate region the prominent absorption at 1086 cm Ϫ1 with its corresponding strong positive VCD couplet at 1089(Ϫ)/1068(ϩ) cm Ϫ1 has been assigned to symmetric POO stretching of the phosphate groups. [57][58][59] The absorption at 1053 cm Ϫ1 is due to a COO sugar ring vibration. The low wavenumber component of the broad positive VCD lobe between 1070 and 1060 cm Ϫ1 may arise partly from this mode.…”

Section: CMmentioning

confidence: 99%

“…For example, ir can be used to determine unambiguously nucleic acid conformations. [57][58][59] One of the aims of the present study was to determine whether VCD can detect DNA condensation analogously to ECD by the appearance of anomalous VCD spectra. If successful, VCD could emerge as a tool able to monitor DNA condensation while determining simultaneously the secondary structure, thereby resolving the problem of different experimental conditions.…”

Section: Introductionmentioning

confidence: 99%

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Vibrational CD (VCD) and atomic force microscopy (AFM) study of DNA interaction with Cr³⁺ ions: VCD and AFM evidence of DNA condensation

et al. 2002

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The interaction of natural calf thymus DNA with Cr(3+) ions was studied at room temperature by means of vibrational CD (VCD) and infrared absorption (ir) spectroscopy, and atomic force microscopy (AFM). Cr(3+) ion binding mainly to N(7) (G) and to phosphate groups was demonstrated. Psi-type VCD spectra resembling electronic CD (ECD) spectra, which appear during psi-type DNA condensation, were observed. These spectra are characterized mainly by an anomalous, severalfold increase of VCD intensity. Such anomalous VCD spectra were assigned to DNA condensation with formation of large and dense particles of a size comparable to the wavelength of the probing ir beam and possessing large-scale helicity. Atomic force microscopy confirmed DNA condensation by Cr(3+) ions and the formation of tight DNA particles responsible for the psi-type VCD spectra. Upon increasing the Cr(3+) ion concentration the shape of the condensates changed from loose flower-like structures to highly packed dense spheres. No DNA denaturation was seen even at the highest concentration of Cr(3+) ions studied. The secondary structure of DNA remained in a B-form before and after the condensation. VCD and ir as well as AFM proved to be an effective combination for investigating DNA condensation. In addition to the ability of VCD to determine DNA condensation, VCD and ir can in the same experiment provide unambiguous information about the secondary structure of DNA contained in the condensed particles.

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Section: Vcd and Afm Of Dna With Crmentioning

confidence: 92%

Section: Vcd and Afm Of Dna With Crmentioning

confidence: 96%

Section: CMmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Vibrational CD (VCD) and atomic force microscopy (AFM) study of DNA interaction with Cr³⁺ ions: VCD and AFM evidence of DNA condensation

et al. 2002

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“…The computations are thus in agreement with the experimental assignments of the main guanine vibrations. [56][57][58][59] The binding of cis-Pt to the N7 site of guanine makes the carbonyl bond slightly stronger and shifts it up to 1694 cm -1 . The ring mode signal at 1591 cm -1 shifts up to 1604 cm -1 and significantly increases in intensity at the expense of the 1573 cm -1 vibration, the intensity of which decays and shifts to lower wavenumbers at 1564 cm -1 .…”

Section: Resultsmentioning

confidence: 99%

DNA Oligonucleotide−cis-Platin Binding: Ab Initio Interpretation of the Vibrational Spectra

2007

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The cis-platin binding to the d(CCTGGTCC)*d(GGACCAGG) model DNA octamer was monitored with infrared absorption (IR) and vibrational circular dichroism (VCD) spectroscopies. The spectra were modeled with the aid of density functional computations and a Cartesian coordinate-based transfer of molecular property tensors from smaller DNA fragments. Because of the fragmentation, the tensors could be calculated with a higher precision. Environmental effects, such as the presence of the solvent or the cis-platin ligand, could be included in the modeling. The solvent was modeled by an explicit inclusion of hydrogen-bound water molecules, positions of which were estimated from a molecular dynamics simulation, or by the polarized continuum COSMO model. The B3LYP and BPW91 functionals used for the calculations of the spectral parameters were combined with the relativistic LANL2DZ platinum pseudo-potentials. The simulations reproduced the main IR and VCD DNA spectral features and explained most of the changes observed experimentally upon metal binding. The results confirmed that the influence of the ligand on DNA vibrational properties is quite complex; it originates in the geometry deformation and normal mode coupling pattern changes of the platinated octamer, as well as in local perturbations of the electronic structure and force field of the GC base pairs to which the platinum is bound. Many of the local effects could be accounted for by a point charge used in place of the metal in the GC complex.

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The etiology and prediction of breast cancer. Fourier transform-infrared spectroscopy reveals progressive alterations in breast DNA leading to a cancer-like phenotype in a high proportion of normal women

Malins

Polissar

Nishikida

et al. 1995

Cancer

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Background. The authors previously have shown by gas chromatography‐mass spectrometry that the hydroxyl radical (.OH) induces alterations in the DNA base structure of the female breast, which are premalignant markers of breast cancer. Fourier transform‐infrared (FT‐IR) spectroscopy also has a high potential for revealing a broad array of structural changes in DNA that may provide important new insight into breast cancer etiology and prediction. Methods. DNA from normal reduction mammoplasty tissue, invasive ductal carcinoma, and nearby microscopically normal tissue was analyzed by FT‐IR spectroscopy. Statistical models based on DNA spectral properties were developed and compared with a statistical model previously used with base modifications. Results. Substantial differences were found in the spectral properties of DNA from women with normal and cancerous breast tissue, indicating an ability to discriminate cancerous tissue from noncancerous tissue with a sensitivity and specificity of 83%. Most importantly, the normal population was divided into subgroups in which a nonrandom progression was identified and a cancer‐like DNA phenotype that was highly correlated (r ⩾ 0.90) with that of the patients with cancer was exhibited in 59% of the women. The spectral data, which also were highly correlated with the base‐model data, were used to establish a model for predicting the probability of breast cancer. Consistent with the high cancer reoccurrence rate in the ipsilateral breast, 8 of 10 of the microscopically normal tissue specimens remaining after tumor excision were classified as cancerous using this model. Conclusions. Progressive structural changes in the DNA of the normal female breast, leading to a premalignant cancer‐like phenotype in a high proportion of women, are the basis for a new paradigm for understanding the etiology of breast cancer and predicting its occurrence at early stages of oncogenesis. The results also suggest therapeutic strategies for potentially reversing the extent of DNA damage, which may be useful in disease prevention and treatment. Cancer 1995;75:503‐17.

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Infrared and Raman Spectroscopy

Cited by 44 publications

References 93 publications

Vibrational CD (VCD) and atomic force microscopy (AFM) study of DNA interaction with Cr³⁺ ions: VCD and AFM evidence of DNA condensation

Vibrational CD (VCD) and atomic force microscopy (AFM) study of DNA interaction with Cr³⁺ ions: VCD and AFM evidence of DNA condensation

DNA Oligonucleotide−cis-Platin Binding: Ab Initio Interpretation of the Vibrational Spectra

The etiology and prediction of breast cancer. Fourier transform-infrared spectroscopy reveals progressive alterations in breast DNA leading to a cancer-like phenotype in a high proportion of normal women

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Infrared and Raman Spectroscopy

Cited by 44 publications

References 93 publications

Vibrational CD (VCD) and atomic force microscopy (AFM) study of DNA interaction with Cr3+ ions: VCD and AFM evidence of DNA condensation

Vibrational CD (VCD) and atomic force microscopy (AFM) study of DNA interaction with Cr3+ ions: VCD and AFM evidence of DNA condensation

DNA Oligonucleotide−cis-Platin Binding: Ab Initio Interpretation of the Vibrational Spectra

The etiology and prediction of breast cancer. Fourier transform-infrared spectroscopy reveals progressive alterations in breast DNA leading to a cancer-like phenotype in a high proportion of normal women

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Vibrational CD (VCD) and atomic force microscopy (AFM) study of DNA interaction with Cr³⁺ ions: VCD and AFM evidence of DNA condensation

Vibrational CD (VCD) and atomic force microscopy (AFM) study of DNA interaction with Cr³⁺ ions: VCD and AFM evidence of DNA condensation