Expert Writing (1997): Studying the Secondary Structure of Ribosomal RNA Using Atomic Force Microscopy

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Abstract: Ribosomal RNA (rRNA) was isolated using a repeated freeze-thaw method, which effectively disrupted ribosomes at low temperatures without the need for chemical extraction or denaturation. The rRNA was directly imaged on mica surfaces, allowing for a clear and undistorted observation. Atomic force microscopy (AFM) was employed to study the morphology of the rRNA molecules. The results revealed that the rRNA exhibits a multi-branched rod-like structure with a high degree of regularity. Based on their size and shape, the rRNA molecules were classified into three distinct categories. These groups corresponded to 28S, 18S, and 5S rRNAs, as predicted by computational models. All three types showed similar secondary structures, supporting the thermodynamically stable configurations commonly proposed for rRNA. The structural data obtained from 28S, 18S, 5.8S, and 5S rRNAs further validate the existing models of rRNA secondary structure, reinforcing the importance of thermal stability in maintaining these complex molecular architectures. This study provides valuable insights into the natural conformation of rRNA under native conditions, highlighting the potential of AFM as a powerful tool for studying RNA structure at the nanoscale.

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