B-CePs as cross-linking probes for the investigation of RNA higher-order structure. Issue 12 (14th June 2021)

• Record Type: Journal Article
• Authors: Sosic, Alice; Göttlich, Richard; Fabris, Dan; Gatto, Barbara
• Is Part Of: Nucleic acids research. Volume 49:Issue 12(2021)
• Page Start: 6660
• Page End: 6672
• Publication Date: 2021-06-14
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gkab468
• Languages: English
• ISSNs: 0305-1048

Abstract

Abstract: Elucidating the structure of RNA and RNA ensembles is essential to understand biological functions. In this work, we explored the previously uncharted reactivity of bis-chloropiperidines (B-CePs) towards RNA. We characterized at the molecular level the different adducts induced by the fast reacting compound B-CeP 1 with RNA. Following an approach based on solution thermal melting coupled with ESI mass spectrometry (STHEM-ESI), we proved the ability of B-CePs to induce inter-molecular cross-links between guanines in double stranded RNA. These results open the possibility of using B-CePs as structural probes for investigating higher-order structures, such as the kissing loop complex established by the dimerization initiation site (DIS) of the HIV-1 genome. We confirmed the potential of B-CePs to reveal the identity of RNA structures involved in long-range interactions, expecting to benefit the characterization of samples that are not readily amenable to traditional high-resolution techniques, and thus promoting the elucidation of pertinent RNA systems associated with old and new diseases. Graphical Abstract: