AZ conformational transition in poly(rArU) and structure marker bands in UV resonance Raman spectroscopy

Tomkova, A.; Chinsky, L.; Miškovský, Pavol; Turpin, Pierre‐Yves

doi:10.1016/0022-2860(93)07895-4

Cited by 9 publications

(5 citation statements)

References 15 publications

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“…For a detailed analysis of the spectra, we can rely on the published calculations of the vibrational modes that have been at least partially confirmed by the experiments monitoring the influence of the environmental conditions on these modes in simple molecules, mostly methylated bases, nucleosides, or nucleotides (see Table S1, Supplementary Information). [ 4,21,24,35–56 ] Despite some differences in the published data, the basic characteristics of the Raman bands in the measured area are clear and can be assigned to fundamental transitions of vibrational modes localized at least in large part on the nucleobases. Most of the detected Raman bands belong to vibrations of purine bases, i.e.…”

Section: Resultsmentioning

confidence: 96%

Full UV resonance Raman analysis of temperature effects on the structural arrangement of DNA segments

Klener

Štěpánek

2020

J Raman Spectroscopy

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Temperature dependence of vibrational spectra provides important information about the geometry and stability of nucleic acid segments. Even in cases of simple structural transitions between the folded and unfolded states, three types of spectral changes may occur – the actual structural transition, the influence of temperature change on the oligonucleotide in the folded state, and that in the unfolded state. In this work, the temperature dependences of UV resonance Raman spectroscopy (RRS) spectra excited at 244 and 257 nm were measured on two dodecadeoxynucleotides, duplex and hairpin. In both cases, the total base composition was the same, containing (in the folded state) a double‐strand section of guanine‐cytosine (GC) pairs and a central section of adenine‐thymine (AT) pairs forming a flexible part of the double helix in the duplex or the loop in the hairpin. Principal component analysis (PCA) showed that UV RRS spectrum, unlike non‐resonance RS, can reliably distinguish between the three types of temperature changes. Spectral images of the changes confirmed the B‐form double helix of GC sections in both the duplex and hairpin and different base positions in AT base sections. Additionally, minimal stacking interactions between the bases in the loop and other types of interactions of adenine with the bases of the stem in the hairpin were shown, and the main effects of heating in the folded state on the GC sections manifested weakening of stacking interactions. The results demonstrate UV RRS potential for studies of non‐canonical nucleic acid structures, providing properly analyzed and executed measurements of temperature dependence.

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Section: Resultsmentioning

confidence: 96%

Full UV resonance Raman analysis of temperature effects on the structural arrangement of DNA segments

Klener

Štěpánek

2020

J Raman Spectroscopy

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“…One indication of the increasing use of the UVRR method in structural biology is the large number of recent reports describing UV laser Raman instrumentation for biological applications. In the majority of cases, a pulsed laser has been employed as the Raman excitation source (Su et al, 1990;Teraoka et al, 1990; Kaminaka and Kitagawa, 1992;Asher, 1993;Hashimoto et al, 1993;Manoharan et al, 1993;Toyama et al, 1993;Leonard et al, 1994;Tomkova et al, 1994). However, use of the pulsed laser is plagued with the fundamental problem of Raman saturation, i.e., the depopulation of the ground electronic state and overpopulation of an excited electronic state (Johnson et al, 1986).…”

Section: Introductionmentioning

confidence: 99%

Design and performance of an ultraviolet resonance Raman spectrometer for proteins and nucleic acids

Russell

Vohník

Thomas

1995

Biophysical Journal

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We describe an ultraviolet resonance Raman (UVRR) spectrometer appropriate for structural studies of biological macromolecules and their assemblies. Instrument design includes the following features: a continuous wave, intracavity doubled, ultraviolet laser source for excitation of the Raman spectrum; a rotating cell (or jet source) for presentation of the sample to the laser beam; a Cassegrain optic with f/1.0 aperture for collection of the Raman scattering; a quartz prism dispersing element for rejection of stray light and Rayleigh scattering; a 0.75-m single grating monochromator for dispersion of the Raman scattering; and a liquid-nitrogen-cooled, charge-coupled device for detection of the Raman photons. The performance of this instrument, assessed on the basis of the observed signal-to-noise ratios, the apparent resolution of closely spaced spectral bands, and the wide spectrometer bandpass of 2200 cm-1, is believed superior to previously described UVRR spectrometers of similar design. Performance characteristics of the instrument are demonstrated in UVRR spectra obtained from standard solvents, p-ethylphenol, which serves as a model for the tyrosine side chain, the DNA nucleotide deoxyguanosine-5'-monophosphate, and the human tumor necrosis factor binding protein, which is considered representative of soluble globular proteins.

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“…[14,20] On A → Z conformational transition in poly(rA-rU), a wavenumber downshifting from 788 to 780 cm −1 was observed in the ring-breathing mode of uracil appearing near these wavenumbers. [27] This wavenumber shifting is also predicted on the basis of theoretical calculations for uridine residue having the C3 -endo/anti and C2 -endo/anti nucleoside structures which are present in the A and Z nucleic acid forms, respectively. [25] In addition, in some mononucleotide crystals having the uridine nucleoside C3 -endo/anti structure, the above uracil mode appears near 790 cm −1 whereas it is located near 780 cm −1 for crystals having the uridine C2 -endo/anti conformation.…”

Section: Nucleoside Conformation Marker Bandsmentioning

confidence: 97%

“…Resonance Raman spectra of poly(rA-rU) and poly(rA)·poly(rU) in aqueous solutions show wavenumber upshifting for a ring vibration of adenine from 718 to 724 cm −1 on an anti/syn riboadenosine nucleoside reorientation [A (C3 -endo/anti)→ Z (C3 -endo/syn) conformational transition]. [27] Therefore, the presence of two riboadenosine bands at 724 and 719 cm −1 in the Raman spectra of this HCV RNA sequence could be ascribed to two different nucleoside conformations. However, the lack of nonresonance Raman marker bands that are unambiguously related to the C3 -endo/syn structure in riboadenosine does not permit exact detection of this nucleoside conformation in the loop.…”

Section: Nucleoside Conformation Marker Bandsmentioning

confidence: 99%

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Raman spectra and structure of a 25mer HCV RNA

Carmona

Molina

Rodrı́guez-Casado

2009

J Raman Spectroscopy

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We have employed Raman spectroscopy to investigate the conformation of an (Hepatitis C virus) HCV RNA 25mer (1-25 nucleotides) in solution. The principal findings of this study are (1) the A-form secondary structure involving C3 -endo/anti ribofuranose pucker is predominant; (2) some uridine and guanosine nucleoside residues adopt the C2 -endo/anti and C3 -endo/syn conformations, respectively, which appear in looped nucleotide sequences; and (3) six out of nine guanine residues are base-paired probably forming a stem. These results are interpreted as formation of a hairpin whose secondary structure is consistent with that proposed on the basis of phylogenetic comparisons with other viral RNAs.

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AZ conformational transition in poly(rArU) and structure marker bands in UV resonance Raman spectroscopy

Cited by 9 publications

References 15 publications

Full UV resonance Raman analysis of temperature effects on the structural arrangement of DNA segments

Full UV resonance Raman analysis of temperature effects on the structural arrangement of DNA segments

Design and performance of an ultraviolet resonance Raman spectrometer for proteins and nucleic acids

Raman spectra and structure of a 25mer HCV RNA

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