Chemical RNA Cross-Linking: Mechanisms, Computational Analysis, and Biological Applications

Abstract

In recent years, RNA has emerged as a multifaceted biomolecule that is involved in virtually every function of the cell and is critical for human health. This has led to a substantial increase in research efforts to uncover the many chemical and biological aspects of RNA and target RNA for therapeutic purposes. In particular, analysis of RNA structures and interactions in cells has been critical for understanding their diverse functions and druggability. In the last 5 years, several chemical methods have been developed to achieve this goal, using chemical cross-linking combined with high-throughput sequencing and computational analysis. Applications of these methods resulted in important new insights into RNA functions in a variety of biological contexts. Given the rapid development of new chemical technologies, a thorough perspective on the past and future of this field is provided. In particular, the various RNA cross-linkers and their mechanisms, the computational analysis and challenges, and illustrative examples from recent literature are discussed.

Exploring antibiotic resistance with chemical tools

“…One potential new target for antibiotics are riboswitches. These structured RNA motifs 90 are usually found 5′ of coding transcripts and can bind small molecule metabolites with high affinity. 91,92 Upon binding, the RNA structure can change and alter the expression of the coding transcript.…”

G-Clamp Heterocycle Modification Containing Interstrand Photo-Cross-Linker to Capture Intracellular MicroRNA Targets

“…19 However, the uridine-specific reactivity of the psoralen moiety has a limited capacity for comprehensive identification of target mRNAs, especially those lacking uridine-paired sequence. 20 Therefore, the development of unbiased, cross-linking-based methods remains a long-standing goal for research of miRNA−mRNA interactions.…”

“…Psoralen has a characteristically planar tricyclic structure that can be intercalated at AT or AU sites in double-stranded DNAs or RNAs and can be activated upon 365 nm UV irradiation resulting in the formation of a cyclobutane adduct . However, the uridine-specific reactivity of the psoralen moiety has a limited capacity for comprehensive identification of target mRNAs, especially those lacking uridine-paired sequence . Therefore, the development of unbiased, cross-linking-based methods remains a long-standing goal for research of miRNA–mRNA interactions.…”

Unleashing the potential of catalytic RNAs to combat mis-spliced transcripts

“…Four decades ago, when IR is discovered, it revealed new insights of its role in regulation of gene expression, pathogenesis, and treatment approaches (Kumari et al, 2022). Researchers have been captivated in carrying out pre-clinical and clinical trials on new drug molecules to either interfere, inhibit, or alter the spliceosome itself or the splicing reactions to treat various spliceopathies (Rupaimoole and Slack, 2017;Bonnal et al, 2020;Desterro et al, 2020;Steensma et al, 2021;Childs-Disney et al, 2022;Murphy et al, 2022;Qin et al, 2022;Suresh et al, 2022;Zhu et al, 2022;Velema and Lu, 2023). It is worth noting that IR can be used as a diagnostic biomarker for the intronic expansion disorders in addition to its applications for therapeutic purposes (Sznajder et al, 2018).…”