Laser Raman spectroscopy of biomolecules. X‐frequency and intensity of the phosphodiester stretching vibrations of cyclic nucleotides

Forrest, Gary T.; Lord, R. C.

doi:10.1002/jrs.1250060108

Cited by 18 publications

(14 citation statements)

References 17 publications

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“…The peak corresponding to wavenumber 1117.8 cm –1 indicates the two phosphate stretching vibrations in the ATP biomolecule. 34 The adenine vibrations are the most prominent in the ATP molecule and form the backbone of vibrations ranging from 1000 to 1750 cm –1 . The peak at 1275.1 cm –1 constitutes the stretching modes of C 8 N 7 , C 8 N 9 , and N 1 C 2 bonds and bending modes of N 1 C 2 and C 2 H bonds.…”

Section: Resultsmentioning

confidence: 99%

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Probing the Interaction at the Nano–Bio Interface Using Raman Spectroscopy: ZnO Nanoparticles and Adenosine Triphosphate Biomolecules

et al. 2014

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With the advent of nanobiotechnology, there will be an increase in the interaction between engineered nanomaterials and biomolecules. Nanoconjugates with cells, organelles, and intracellular structures containing DNA, RNA, and proteins establish sequences of nano–bio boundaries that depend on several intricate complex biophysicochemical reactions. Given the complexity of these interactions, and their import in governing life at the molecular level, it is extremely important to begin to understand such nanoparticle–biomaterial association. Here we report a unique method of probing the kinematics between an energy biomolecule, adenosine triphosphate (ATP), and hydrothermally synthesized ZnO nanostructures using micro Raman spectroscopy, X-ray diffraction, and electron microscopy experiments. For the first time we have shown by Raman spectroscopy analysis that the ZnO nanostructures interact strongly with the nitrogen (N7) atom in the adenine ring of the ATP biomolecule. Raman spectroscopy also confirms the importance of nucleotide base NH2 group hydrogen bonding with water molecules and phosphate group ionization and their pH dependence. Calculation of molecular bond force constants from Raman spectroscopy reinforces our experimental data. These data present convincing evidence of pH-dependent interactions between ATP and zinc oxide nanomaterials. Significantly, Raman spectroscopy is able to probe such difficult to study and subtle nano–bio interactions and may be applied to elegantly elucidate the nano–bio interface more generally.

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Section: Resultsmentioning

confidence: 99%

“…The peak at 1395.8 cm –1 is assigned to vibrations due to C 5 N 7 and C 8 N 9 bonds. 34 The 1493.6 cm –1 peak is due to vibrations pertaining to stretching of the C 4 N 9 bond and bending of the C 8 H bond. The peak at 1548.5 cm –1 is a characteristic feature of vibrations of N 3 C 4 and C 4 C 5 bonds in the adenine entity.…”

Section: Resultsmentioning

confidence: 99%

Probing the Interaction at the Nano–Bio Interface Using Raman Spectroscopy: ZnO Nanoparticles and Adenosine Triphosphate Biomolecules

et al. 2014

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“…1b and 2b. This band corresponds to the symmetric O-P-0 stretching frequency (14)(15)(16)(22)(23)(24). A similar band has previously been assigned to A-form DNA or RNA (14)(15)(16)(22)(23)(24).…”

Section: Backbone Conformationmentioning

confidence: 86%

“…Since deuterium exchange did not shift the position of the band significantly, it is probable that the 863 cm-1 band is comprised of vibrations sensitive to the sugar-phosphate backbone. These vibrations in turn reflect the conformation of the sugar moiety of the polynucleotide chain (14)(15)(16)(22)(23)(24).…”

Section: Backbone Conformationmentioning

confidence: 99%

The Structure of Triple Helical Poly(U)·Poly(A)·Poly(U) Studied by Raman Spectroscopy

O’Connor

Bina²

1984

Journal of Biomolecular Structure and Dynamics

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Using Raman spectroscopy, we examined the ribose-phosphate backbone conformation, the hydrogen bonding interactions, and the stacking of the bases of the poly(U).poly(A).poly(U) triple helix. We compared the Raman spectra of poly(U).poly(A).poly(U) in H2O and D2O with those obtained for single-stranded poly(A) and poly(U) and for double-stranded poly(A).poly(U). The presence of a Raman band at 863 cm-1 indicated that the backbone conformations of the two poly(U) chains are different in the triple helix. The sugar conformation of the poly(U) chain held to the poly(A) by Watson-Crick base pairing is C3' endo; that of the second poly(U) chain may be C2' endo. Raman hypochromism of the bands associated with base vibrations demonstrated that uracil residues stack to the same extent in double helical poly(A).poly(U) and in the triple-stranded structure. An increase in the Raman hypochromism of the bands associated with adenine bases indicated that the stacking of adenine residues is greater in the triple helix than in the double helical form. Our data further suggest that the environment of the carbonyls of the uracil residues is different for the different strands.

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“…The structural asymmetry between the 02-P and 03-P bonds in crystalline nucleotides implies an asymmetry of the corresponding force constants. There is significant experimental evidence that the dioxy vibrations are not localized (19). As a consequence, even small contributions to the dipole moment perpendicular to the directions of either the 02-03 direction or to the bisector of the 02-P-03 angle can significantly change the direction of the observed dipole moment without significantly altering its magnitude.…”

Section: Calculation Of the Effective Partial Charge Distributionmentioning

confidence: 99%

A reinterpretation of the infrared linear dichroism of oriented nucleic acid films and a calculation of some effective partial changes on the ribose phosphate backbone

Beetz¹,

Ascarelli²,

Arnott³

1979

Biophysical Journal

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In this paper we show, based on symmetry considerations, that structural information cannot be obtained from the linear infrared dichroism of the dioxy vibrations of the phosphate group of nucleic acids. Consequently, the discrepancies between the results of x-ray structure measurements and linear dichroism measurements are not meaningful. The linear dichroism measurements are instead important for a calculation of transition dipole moments that involve both the vibrations of all the atoms of the nucleotide and their charges. Independent information on either the atomic displacements contributing to a given vibration or the atomic charges permits a refinement of the unknown quantities. Based on the molecular dynamics calculations of Prohofsky et al., atomic charges of DNA are calculated to reproduce the observed linear dichroism results. Some of the resulting charges are unexpected and may reflect the inadequacy of the molecular dynamic calculation.

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Laser Raman spectroscopy of biomolecules. X‐frequency and intensity of the phosphodiester stretching vibrations of cyclic nucleotides

Cited by 18 publications

References 17 publications

Probing the Interaction at the Nano–Bio Interface Using Raman Spectroscopy: ZnO Nanoparticles and Adenosine Triphosphate Biomolecules

Probing the Interaction at the Nano–Bio Interface Using Raman Spectroscopy: ZnO Nanoparticles and Adenosine Triphosphate Biomolecules

The Structure of Triple Helical Poly(U)·Poly(A)·Poly(U) Studied by Raman Spectroscopy

A reinterpretation of the infrared linear dichroism of oriented nucleic acid films and a calculation of some effective partial changes on the ribose phosphate backbone

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