Raman spectroscopic study of uridine nucleotides: structural information and conformational features

Carmona, Pedro; Rodrı́guez-Casado, Arantxa; Molina, Marina; Escobar, R.

doi:10.1002/(sici)1097-4555(199908)30:8<631::aid-jrs404>3.0.co;2-n

Cited by 9 publications

(3 citation statements)

References 26 publications

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“…Although the chemical structures for these two metabolites are extremely similar, the Raman spectra of the crystalline powders are surprisingly different ( Figure 4 and Figure 5 ), presumably due to a combination of intra- and inter-molecular forces. For the former, rotation about N1 and C1’, and puckering of the ribose moiety can influence vibrations, and for the latter, hydrogen bonding and the local crystal environment can influence vibrations [ 46 ].…”

Section: Resultsmentioning

confidence: 99%

Surface-enhanced Raman Spectral Measurements of 5-Fluorouracil in Saliva

et al. 2008

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The ability of surface-enhanced Raman spectroscopy (SERS) to measure 5-fluorouracil (5-FU) in saliva is presented. The approach is based on the capacity of Raman spectroscopy to provide a unique spectral signature for virtually every chemical, and the ability of SERS to provide μg/mL sensitivity. A simple sampling method, that employed 1-mm glass capillaries filled with silver-doped sol-gels, was developed to isolate 5-FU from potential interfering chemical components of saliva and simultaneously provide SERS-activity. The method involved treating a 1 mL saliva sample with 1 mL of acetic acid, drawing 10 μL of sample into a SERS-active capillary by syringe, and then measuring the SER spectrum. Quality SER spectra were obtained for samples containing as little as 2 μg of 5-FU in 1 mL saliva. The entire process, the acid pretreatment, extraction and spectral measurement, took less than 5 minutes. The SERS of 5-fluorouridine and 5-fluoro-2’-deoxyuridine, two major metabolites of 5-FU, were also measured and shown to have unique spectral peaks. These measurements suggest that disposable SERS-active capillaries could be used to measure 5-FU and metabolite concentrations in chemotherapy patient saliva, thereby providing metabolic data that would allow regulating dosage. Tentative vibrational mode assignments for 5-FU and its metabolites are also given.

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Section: Resultsmentioning

confidence: 99%

Surface-enhanced Raman Spectral Measurements of 5-Fluorouracil in Saliva

et al. 2008

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“…This band has been noted to increase in intensity when hydrogen bonding breaks down 22 1234 U A U. [9][10][11][20][21][22] C. 11 Uracil ring stretching 13,32 Large decrease in intensity in measured RNA spectra. Hypochromic.…”

Section: Ribosephosphatementioning

confidence: 99%

Deconstructing RNA: optical measurement of composition and structure

Hobro

Standley²,

Ahmad

et al. 2013

Phys. Chem. Chem. Phys.

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RNA molecules are involved in many pathways within the cell and their sequence composition, structure, conformational transitions and interactions with other molecules are all important factors in determining RNA function. Here we present a method for systematically and quantitatively determining characteristics of RNA using Raman spectroscopy. This method can be used to assess the composition and structure of a given RNA molecule, including ribose-phosphate sugar-pucker conformation, face-to-face base stacking and hydrogen bonding interactions. Three RNA molecules with different sequence and structural features (the exon splicing silencer 3 from HIV-1, an RNA aptamer against Runt-related transcription factor, and the SARS coronaviral stem loop 2) are presented as examples where the structure is crucial to the function of the RNA. We carry out piecewise analysis of the RNA spectra and show that using a nucleotide spectra library helps to unlock the entire ensemble of vibrational information. This analysis demonstrates the extent to which RNA characteristics can be elucidated, using purely optical methods.

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“…rU) and altered local conformation in duplexes. Interpretation of the difference spectra is possible due to the extensive study of NA complexes including polynucleotides [13,15,16], oligonucleotides [17][18][19][20] and mononucleotides [21,22]. Nucleotide substitution in the mismatch duplex is reflected by negative bands of adenosine at 1299, 1338, 1478, 1509 and 1572 cm À1 and positive bands of uridine at 782, 1228 and 1695 cm À1 .…”

Section: Conformational Changes Due To a Mismatch Basepairmentioning

confidence: 99%