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

IF 2.4 4区生物学 Q3 BIOPHYSICS

European Biophysics Journal Pub Date : 2025-06-12 DOI:10.1007/s00249-025-01766-8

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

{"title":"Studying SARS-CoV-2 ssRNA key sequence combining Fourier transform infrared spectroscopy and theoretical folding model.","authors":"Tiziana Mancini, Federica Bertelà, Marta Di Fabrizio, Salvatore Macis, Rosanna Mosetti, Stefano Lupi, Annalisa D'Arco","doi":"10.1007/s00249-025-01766-8","DOIUrl":null,"url":null,"abstract":"<p><p>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.</p>","PeriodicalId":548,"journal":{"name":"European Biophysics Journal","volume":" ","pages":""},"PeriodicalIF":2.4000,"publicationDate":"2025-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"European Biophysics Journal","FirstCategoryId":"2","ListUrlMain":"https://doi.org/10.1007/s00249-025-01766-8","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"BIOPHYSICS","Score":null,"Total":0}

引用次数: 0

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.

查看原文本刊更多论文

结合傅里叶变换红外光谱和理论折叠模型研究SARS-CoV-2 ssRNA关键序列。

傅里叶变换红外（FTIR）振动光谱法广泛应用于蛋白质和脱氧核糖核酸（DNA）二级结构的分析，是对分子结构变化最敏感的振动方法之一。尽管如此，对核糖核酸（rna）的FTIR研究很少。本研究通过FTIR光谱和计算方法研究了野生型SARS-CoV-2病毒体外稳定转录合成单链RNA （ssRNA）。我们进行了RNA FTIR光谱分析，确定了与糖和磷酸盐主链、碱基糖和碱基的振动相关的四个主要光谱区域。从核苷酸序列开始，我们对ssRNA片段进行了两次折叠预测，获得了RNA片段最可能的二级和三级结构。这些预测最终与实验数据进行了比较，从而进行了全面的结构研究。我们的研究结果在理解SARS-CoV-2 ssRNA片段的结构方面迈出了一步，并为传感应用提供了一个有希望的潜在起点。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

来源期刊

European Biophysics Journal 生物-生物物理

CiteScore

4.30

自引率

0.00%

发文量

审稿时长

6-12 weeks

期刊介绍： The journal publishes papers in the field of biophysics, which is defined as the study of biological phenomena by using physical methods and concepts. Original papers, reviews and Biophysics letters are published. The primary goal of this journal is to advance the understanding of biological structure and function by application of the principles of physical science, and by presenting the work in a biophysical context. Papers employing a distinctively biophysical approach at all levels of biological organisation will be considered, as will both experimental and theoretical studies. The criteria for acceptance are scientific content, originality and relevance to biological systems of current interest and importance. Principal areas of interest include: - Structure and dynamics of biological macromolecules - Membrane biophysics and ion channels - Cell biophysics and organisation - Macromolecular assemblies - Biophysical methods and instrumentation - Advanced microscopics - System dynamics.