The three-dimensional structure of RNA (ribonucleic acid) molecules is of fundamentally important for cellular processes. Many biological functions, including ribosome formation (the cell’s protein factory), depend on the correct folding of RNA. However, RNA molecules do not have a fixed structure; instead, they are dynamic and can adopt multiple conformations (spatial arrangements). This flexibility makes RNA folding process both biologically critical and challenging to study. Most current methods provide only snapshots of RNA structure and lack the ability to generate real-time and functional information.
Gor and his research team from the European Molecular Biology Laboratory (EMBL) aimed to monitor the folding behavior of synthesized RNA molecules in real-time at the single-molecule level and to characterize this process along with its functional consequences. Previous studies have typically examined either RNA structure or protein binding separately, making it difficult to observe both processes simultaneously within the same molecule. This study was designed to address this limitation.
In this study, multicolor single-molecule fluorescence microscopy (a high-precision optical imaging method in which each molecule is monitored) was used. The 3’ region of 16S ribosomal RNA from Escherichia coli bacteria was selected as the experimental system. This region is involved in ribosome formation and has been well characterized in previous biophysical studies. Using five different fluorescent dyes in a single experiment, transcription elongation (synthesis of RNA from a DNA template), accessibility of specific RNA regions, and ribosomal protein binding were monitored simultaneously. This approach enabled the identification of up to eight distinct RNA folding classes. Furthermore, the effects of antisense oligonucleotides (ASOs; short DNA sequences that bind to specific RNA regions), RNA modification enzymes, and ribosomal proteins on this process were also investigated.
The study revealed that multiple RNA folding states can coexist within the same RNA population and that these states can be selectively modulated by specific molecular factors. In an unexpected finding, regions with increased local RNA accessibility were found to correlate with the chaperonery activity of ribosomal proteins, suggesting that structural dynamics may enhance folding efficiency. It was also determined that RNA modification enzymes such as RsmB and RsmD are effective only on specific misfolded RNA subpopulations, an effect that may be overlooked in large-scale experiments. The data provide a detailed framework covering both co-transcriptional (occurring during RNA synthesis ) and posttranscriptional (occurring after synthesis) phases of RNA folding. These findings highlight the importance of identifying structural ensembles for future antisense therapeutic strategies and RNA-targeted drug development.
Translated by: Ayşenur Güneş
Editor: Elinsu Ak
Reference: Gor, K., Geissen, E. M., & Duss, O. (2026). Functional characterization of dynamic nascent RNA folding ensembles in real time. Science Advances, 12(12), Article eaec4037.
https://doi.org/10.1126/sciadv.aec4037
-Bioinfocodes Scientific News Service-
News articles prepared by our team members, reviewing and compiling scientific research
published in journals with and impact factor greater than 20 (click here for the list)