Studying SARS-CoV-2 ssRNA key sequence combining Fourier transform infrared spectroscopy and theoretical folding model.

Tiziana Mancini, Federica Bertelà, Marta Di Fabrizio, Salvatore Macis, Rosanna Mosetti, Stefano Lupi, Annalisa D'Arco

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Article in European biophysics journal : EBJ, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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7 authors.

Tiziana ManciniDepartment of Physics, Sapienza University of Rome, P.Le A. Moro 2, 00185, Rome, Italy. tiziana.mancini@uniroma1.it.ORCID http://orcid.org/0000-0003-4399-3869

Federica BertelàDepartment of Physics, Sapienza University of Rome, P.Le A. Moro 2, 00185, Rome, Italy. federica.bertela@uniroma1.it.

Marta Di FabrizioLaboratory of Biological Electron Microscopy, School of Basic Sciences, Institute of Physics, EPFL and Department of Fundamental Microbiology, Faculty of Biology and Medicine, UNIL, 1015, Lausanne, Switzerland.

Salvatore MacisDepartment of Physics, Sapienza University of Rome, P.Le A. Moro 2, 00185, Rome, Italy.

Rosanna MosettiDepartment of Physics, Sapienza University of Rome, P.Le A. Moro 2, 00185, Rome, Italy.

Stefano LupiDepartment of Physics, Sapienza University of Rome, P.Le A. Moro 2, 00185, Rome, Italy.

Annalisa D'ArcoDepartment of Physics, Sapienza University of Rome, P.Le A. Moro 2, 00185, Rome, Italy.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Fourier transform infrared (FTIR) vibrational spectroscopy is widely used for the analysis of both protein and deoxyribonucleic acid (DNA) secondary structures, being one of the most sensitive vibrational methods to changes in molecular structure. Despite this, only few FTIR studies on ribonucleic acids (RNAs) are available. Here, we investigated a stabilized in vitro transcribed synthetic single-stranded RNA (ssRNA) from wild-type SARS-CoV-2 virus through FTIR spectroscopy and computational methods. We carried out RNA FTIR spectroscopic analysis identifying four main spectral regions of interest associated with the vibrations of sugar and phosphate backbone, base-sugar and bases. Starting from the nucleotides' sequence, we applied two folding predictions to the ssRNA fragment, obtaining the most likely secondary and tertiary structures of the RNA fragment. These predictions have finally been compared to experimental data leading to a comprehensive structural investigation. Our results represent a step forward in understanding the structure of the SARS-CoV-2 ssRNA fragment and a promising potential starting point for sensing applications.

Indexed as

RNA, ViralSARS-CoV-2COVID-19Models, MolecularNucleic Acid ConformationSpectroscopy, Fourier Transform InfraredRNA, ViralFolding predictionFourier transform infrared spectroscopyRNASecondary structure

Identifiers

PMID40504245

DOI10.1007/s00249-025-01766-8

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