Vibrational analysis of nucleic acids. IV. normal modes of the DNA phosphodiester structure modeled by diethyl phosphate

Guan, Yifu; Thomas, George J.

doi:10.1002/(sici)1097-0282(199612)39:6<813::aid-bip7>3.0.co;2-y

Cited by 33 publications

(12 citation statements)

References 38 publications

(10 reference statements)

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“…Vibrations of the PO4 -phosphate group of phosphorylated tyrosine are observed at 1070 cm −1 and corresponds to the O-P-O symmetric stretching mode [28][29][30][32][33][34]. The weak band at 1092 cm −1 band is due to the antisymmetric O-P-O stretching vibration [30,33,34]. To summarize, most of the spectral shifts observed upon tyrosine phosphorylation are very similar to those observed in previously reported Raman studies [27,31,35,36].…”

Section: Resultssupporting

confidence: 84%

“…The band positions of aromatic amino acids are sensitive to the microenvironment and may shift by up to 5 cm −1 in the Raman spectra of proteins [31]. Vibrations of the PO 4 − phosphate group of phosphorylated tyrosine are observed at 1070 cm −1 and corresponds to the O-P-O symmetric stretching mode [28][29][30][32][33][34]. The weak band at 1092 cm −1 band is due to the antisymmetric O-P-O stretching vibration [30,33,34].…”

Section: Resultsmentioning

confidence: 99%

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Aberrant Protein Phosphorylation in Cancer by Using Raman Biomarkers

Abramczyk

Imiela

Brożek-Płuska

et al. 2019

Cancers

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1) Background: Novel methods are required for analysing post-translational modifications of protein phosphorylation by visualizing biochemical landscapes of proteins in human normal and cancerous tissues and cells. (2) Methods: A label-free Raman method is presented for detecting spectral changes that arise in proteins due to phosphorylation in the tissue of human breasts, small intestines, and brain tumours, as well as in the normal human astrocytes and primary glioblastoma U-87 MG cell lines. Raman spectroscopy and Raman imaging are effective tools for monitoring and analysing the vibrations of functional groups involved in aberrant phosphorylation in cancer without any phosphorecognition of tag molecules. (3) Results: Our results based on 35 fresh human cancer and normal tissues prove that the aberrant tyrosine phosphorylation monitored by the unique spectral signatures of Raman vibrations is a universal characteristic in the metabolic regulation in different types of cancers. Overexpressed tyrosine phosphorylation in the human breast, small intestine and brain tissues and in the human primary glioblastoma U-87 MG cell line was monitored by using Raman biomarkers. (4) We showed that the bands at 1586 cm −1 and 829 cm −1 , corresponding to phosphorylated tyrosine, play a pivotal role as a Raman biomarker of the phosphorylation status in aggressive cancers. We found that the best Raman biomarker of phosphorylation is the 1586/829 ratio showing the statistical significance at p Values of ≤ 0.05. (5) Conclusions: Raman spectroscopy and imaging have the potential to be used as screening functional assays to detect phosphorylated target proteins and will help researchers to understand the role of phosphorylation in cellular processes and cancer progression. The abnormal and excessive high level of tyrosine phosphorylation in cancer samples compared with normal samples was found in the cancerous human tissue of breasts, small intestines and brain tumours, as well as in the mitochondria and lipid droplets of the glioblastoma U-87 MG cell line. Detailed insights are presented into the intracellular oncogenic metabolic pathways mediated by phosphorylated tyrosine.2 of 25 the abnormalities of many types of cancer, for example, finding over 30,000 mutations in breast cancer cells. Thus, the available evidence appears to suggest that scientific research based solely on cancer genomics cannot continue.Presently, a growing number of reports have led to increased interest in the benefits of metabolic regulation in cancers. While the transformation of oncogenic genes can be directly connected to cancer cell metabolism, mutated metabolic enzymes may also trigger malignant transformations [1][2][3].Understanding the mechanism of the altered energy metabolism that replaces the more efficient oxidative phosphorylation to yield adenosine triphosphate (ATP) by the less efficient process of glycolysis represents the pivotal problem that must be solved to advance the study of cancer. During the past decade, many studies have suggested...

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Section: Resultssupporting

confidence: 84%

Section: Resultsmentioning

confidence: 99%

Aberrant Protein Phosphorylation in Cancer by Using Raman Biomarkers

Abramczyk

Imiela

Brożek-Płuska

et al. 2019

Cancers

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“…Ref. 27 includes an ab-initio normalized potential energy distribution (PED) which suggests contributions from dierent local coordinates to the overall normal mode elongations. As listed in Table 1, such elongations include the phosphate group (ν P 2 ), the phosphodiester linkage (ν L1 , ν L2 , ν L3 ) and the furanose main chain and rings (ν R1 , ν R2 ).…”

Section: Linear Vibrational Spectramentioning

confidence: 99%

“…Stationary infrared (IR) and Raman spectra have been analyzed by normal mode calculations in the harmonic limit only 27,28 and frequency positions of particular bands have been used as -rather indirect -indicators of a particular helix geometry. 29,30 Both (diagonal) anharmonicities of backbone modes and anharmonic couplings between them have remained unknown and not been addressed by theory.…”

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confidence: 99%

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Anharmonic Backbone Vibrations in Ultrafast Processes at the DNA–Water Interface

et al. 2015

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The vibrational modes of the deoxyribose-phosphodiester backbone moiety of DNA and their interactions with the interfacial aqueous environment are addressed with two-dimensional (2D) infrared spectroscopy on a femto- to picosecond time scale. Beyond the current understanding in the harmonic approximation, the anharmonic character and delocalization of the backbone modes in the frequency range from 900 to 1300 cm(-1) are determined with both diagonal anharmonicities and intermode couplings on the order of 10 cm(-1). Mediated by the intermode couplings, energy transfer between the backbone modes takes place on a picosecond time scale, parallel to vibrational relaxation and energy dissipation into the environment. Probing structural dynamics noninvasively via the time evolution of the 2D lineshapes, limited structural fluctuations are observed on a 300 fs time scale of low-frequency motions of the helix, counterions, and water shell. Structural disorder of the DNA-water interface and DNA-water hydrogen bonds are, however, preserved for times beyond 10 ps. The different interactions of limited strength ensure ultrafast vibrational relaxation and dissipation of excess energy in the backbone structure, processes that are important for the structural integrity of hydrated DNA.

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Temperature dependence of the raman spectrum of DNA. II. Raman signatures of premelting and melting transitions of poly(dA)·poly(dT) and comparison with poly(dA‐dT)·poly(dA‐dT)*

Movileanu¹,

Benevides²,

Thomas³

2002

Biopolymers

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113

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The temperature dependence of the Raman spectrum of poly(dA).poly(dT) (dA: deoxyadenosine; dT: thymidine), a model for DNA containing consecutive adenine.thymine (A.T) pairs, has been analyzed using a spectrometer of high spectral precision and sensitivity. Three temperature intervals are distinguished: (a) premelting (10 < t < 70 degrees C), in which the native double helix is structurally altered but not dissociated into single strands; (b) melting (70 < t < 80 degrees C), in which the duplex is dissociated into single strands; and (c) postmelting (80 < t degrees C), in which no significant structural change can be detected. The distinctive Raman difference signatures observed between 10 and 70 degrees C and between 70 and 80 degrees C are interpreted in terms of the structural changes specific to premelting and melting transitions, respectively. Premelting alters the low-temperature conformation of the deoxyribose-phosphate backbone and eliminates base hydrogen bonding that is distinct from canonical Watson-Crick hydrogen bonding; these premelting perturbations occur without disruption of base stacking. Conversely, melting eliminates canonical Watson-Crick pairing and base stacking. The results are compared with those reported previously on poly(dA-dT).poly(dA-dT), the DNA structure consisting of alternating A.T and T.A pairs (L. Movileanu, J. M. Benevides, and G. J. Thomas, Jr. Journal of Raman Spectroscopy, 1999, Vol. 30, pp. 637-649). Poly(dA).poly(dT) and poly(dA-dT).poly(dA-dT) exhibit strikingly dissimilar temperature-dependent Raman profiles prior to the onset of melting. However, the two duplexes exhibit very similar melting transitions, including the same Raman indicators of ruptured Watson-Crick pairing, base unstacking and collapse of backbone order. A detailed analysis of the data provides a comprehensive Raman assignment scheme for adenosine and thymidine residues of B-DNA, delineates Raman markers diagnostic of consecutive A.T and alternating A.T/T.A tracts of DNA, and identifies the distinct Raman difference signatures for premelting and melting transitions in the two types of sequences.

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Vibrational analysis of nucleic acids. IV. normal modes of the DNA phosphodiester structure modeled by diethyl phosphate

Cited by 33 publications

References 38 publications

Aberrant Protein Phosphorylation in Cancer by Using Raman Biomarkers

Aberrant Protein Phosphorylation in Cancer by Using Raman Biomarkers

Anharmonic Backbone Vibrations in Ultrafast Processes at the DNA–Water Interface

Temperature dependence of the raman spectrum of DNA. II. Raman signatures of premelting and melting transitions of poly(dA)·poly(dT) and comparison with poly(dA‐dT)·poly(dA‐dT)*

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