Structural characterization of the 5′ untranslated RNA of hepatitis C virus by vibrational spectroscopy

Rodrı́guez-Casado, Arantxa; Bartolomé, Javier; Carréño, Vicente; Molina, Marina; Carmona, Pedro

doi:10.1016/j.bpc.2006.06.010

Cited by 11 publications

(10 citation statements)

References 30 publications

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“…The nonhelical regions of HDV (bulge, loop, etc.) are likely candidates for generating these conformational perturbations , . A semiquantitative analysis on the basis of band intensity decrease of −O−P−O− indicates that the deviation is ∼3% the intensity of the peak in the parent spectrum, suggesting that the conformational change is small.…”

Section: Resultsmentioning

confidence: 99%

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Competition between Co(NH₃)₆³⁺ and Inner Sphere Mg²⁺ Ions in the HDV Ribozyme

et al. 2009

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Divalent cations play critical structural and functional roles in many RNAs. While the hepatitis delta virus (HDV) ribozyme can undergo self-cleavage in the presence of molar concentrations of monovalent cations, divalent cations such as Mg 2+ are required for efficient catalysis under physiological conditions. Moreover, the cleavage reaction can be inhibited with Co(NH 3 ) 6 3+ , an analog of Mg(H 2 O) 6 2+ . Here, the binding of Mg 2+ and Co(NH 3 ) 6 3+ to the HDV ribozyme are studied by Raman microscopic analysis of crystals. Raman difference spectra acquired at different metal ion conditions reveal changes in the ribozyme. When Mg 2+ alone is introduced to the ribozyme, inner sphere coordination of Mg(H 2 O) x 2+ (x≤5) to non-bridging PO 2 − oxygen, and changes in base stretches and phosphodiester group conformation are observed. In addition, binding of Mg 2+ induces deprotonation of a cytosine assigned to the general acid C75, consistent with solution studies. When Co(NH 3 ) 6 3+ alone is introduced, deprotonation of C75 is again observed, as are distinctive changes in base vibrational ring modes and phosphodiester backbone conformation. In contrast to Mg 2+ binding, Co(NH 3 ) 6 3+ binding does not perturb PO 2 − group vibrations, consistent with its ability to make only outer sphere contacts. Surprisingly, competitive binding studies reveal that Co(NH 3 ) 6 3+ ions displace some inner sphere-coordinated magnesium species, including ions coordinated to PO 2 − groups or the N7 of a guanine, likely G1 at the active site. These observations contrast with the tenet that Co(NH 3 ) 6 3+ ions displace only outer sphere magnesium ions. Overall, our data support two classes of inner sphere Mg 2+ -PO 2 − binding sites: sites that Co(NH 3 ) 6 3+ can displace, and others it cannot.Metal ions play essential roles in the structure and function of ribozymes. Effects of metal ions on the small nucleolytic HDV ribozyme (Figure 1) have been studied for a number of years (1-9). Self-cleavage of the HDV ribozyme has only a weak dependence on divalent ion identity. For instance, self-cleavage is efficient in the presence millimolar amounts of Mg 2+ , Ca 2+ , *To whom correspondence should be addressed: Paul Carey, Tel. (216) Fax. (216) prc5@cwru.edu; and Barbara Golden, Tel. (765) Fax. (765) barbgolden@purdue.edu; and Philip Bevilacqua: Tel. (814) Fax. (814) 863-8403; pcb@chem.psu.edu. † This project was supported by NSF Grant MCB-0527102 (P.C.B.), the Purdue University Department of Biochemistry and Cancer Center (B.L.G), and NIH Grant GM-54072 (P.R.C.). SUPPORTING INFORMATION AVAILABLEDerivations of equation 1, 2 and 3, and analysis of competitive binding of Co(NH 3 ) 6 3+ and Mg 2+ in the HDV ribozyme when Hill coefficient is held to 2 ( Figure S1). This material is available free of charge via the internet at http://pubs.acs.org. NIH Public Access Author ManuscriptBiochemistry. Author manuscript; available in PMC 2010 December 22. Published in final edited form as:Biochemistry. (1,5). In addition...

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Section: Resultsmentioning

confidence: 99%

“…The data suggest that 2−3% of the linkages undergo a change in the ribose moiety when Mg 2+ binds. In addition, the changes are in opposite directions for the two ions, with Mg 2+ binding slightly increasing the C2′-endo and cobalt hexamine increasing the C3′-endo conformations ,, .…”

Section: Discussionmentioning

confidence: 98%

Competition between Co(NH₃)₆³⁺ and Inner Sphere Mg²⁺ Ions in the HDV Ribozyme

et al. 2009

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“…The 1095 cm À1 band is relatively broad due to heterogeneity in the local environments of phosphate groups, which is consistent with the characteristic structural variety along the ribose-phosphate backbone of the viral RNA. 17 Of particular interest is the present finding that the binding of HCVc-120 has a negligible effect on the A-form secondary structure of duplex stems in 5 0 UTR, 17 as reflected in the 850-800 cm À1 region of the difference spectrum (Fig. 1).…”

Section: Resultsmentioning

confidence: 76%

Core Protein—Nucleic Acid Interactions in Hepatitis C Virus as Revealed by Raman and Circular Dichroism Spectroscopy

2007

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Molecular interactions required for hepatitis C virus (HCV) assembly are not well known and are poorly understood. The 5' untranslated region (5'UTR) of the RNA genome is highly conserved and has extensive secondary structure, and the highly basic core protein is rich in arginine residues. Using Raman and circular dichroism (CD) spectroscopies, specific interactions have been demonstrated here between the 5'UTR sequence and the core protein that may be important for the specific encapsidation of the viral genome during HCV replication. These interactions can be described as follows: (1) hydrogen bonding of arginine with unpaired guanine and/or with wobble GU base pairs, and arginine-phosphate electrostatic contacts; (2) although the percentage of base pairs in the A-form is maintained in 5'UTR, the HCVc-120 protein is beta-sheet and beta-helix enriched upon formation of protein-5'UTR macromolecular assemblies; (3) protein-5'UTR interactions resulting in protein alpha-helix formation involve guanine bases in duplex segments. The mentioned interactions may represent novel targets for antiviral strategies against this important virus.

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“…Raman spectroscopy has already been used in virological studies as a structural characterization of 5 0 untranslated RNA from hepatitis C virus [28], investigation of a single tobacco mosaic virus [29], study of chicken embryo cells infected with ALVAC virus [30], characterization of different virus strains [31] and identification of new emerging influenza viruses [32]. All these studies proved that Raman spectroscopy is a powerful technique in virus studies, as well as being non-destructive, fast and having a simple procedure.…”

Section: Raman Spectroscopymentioning

confidence: 99%

Spectroscopy with computational analysis in virological studies: A decade (2006–2016)

Santos

Morais

Nascimento

et al. 2017

TrAC Trends in Analytical Chemistry

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a b s t r a c tThis review presents a retrospective of the studies carried out in the last 10 years (2006e2016) using spectroscopic methods as a research tool in the field of virology. Spectroscopic analyses are sensitive to variations in the biochemical composition of the sample, are non-destructive, fast and require the least sample preparation, making spectroscopic techniques tools of great interest in biological studies. Herein important chemometric algorithms that have been used in virological studies are also evidenced as a good alternative for analyzing the spectra, discrimination and classification of samples. Techniques that have not yet been used in the field of virology are also suggested. This methodology emerges as a new and promising field of research, and may be used in the near future as diagnosis tools for detecting diseases caused by viruses.

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Structural characterization of the 5′ untranslated RNA of hepatitis C virus by vibrational spectroscopy

Cited by 11 publications

References 30 publications

Competition between Co(NH₃)₆³⁺ and Inner Sphere Mg²⁺ Ions in the HDV Ribozyme

Competition between Co(NH₃)₆³⁺ and Inner Sphere Mg²⁺ Ions in the HDV Ribozyme

Core Protein—Nucleic Acid Interactions in Hepatitis C Virus as Revealed by Raman and Circular Dichroism Spectroscopy

Spectroscopy with computational analysis in virological studies: A decade (2006–2016)

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Structural characterization of the 5′ untranslated RNA of hepatitis C virus by vibrational spectroscopy

Cited by 11 publications

References 30 publications

Competition between Co(NH3)63+ and Inner Sphere Mg2+ Ions in the HDV Ribozyme

Competition between Co(NH3)63+ and Inner Sphere Mg2+ Ions in the HDV Ribozyme

Core Protein—Nucleic Acid Interactions in Hepatitis C Virus as Revealed by Raman and Circular Dichroism Spectroscopy

Spectroscopy with computational analysis in virological studies: A decade (2006–2016)

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Competition between Co(NH₃)₆³⁺ and Inner Sphere Mg²⁺ Ions in the HDV Ribozyme

Competition between Co(NH₃)₆³⁺ and Inner Sphere Mg²⁺ Ions in the HDV Ribozyme