The X-ray Structures of Six Octameric RNA Duplexes in the Presence of Different Di- and Trivalent Cations.

Michelle Schaffer,Meitian Wang,Guanya Peng,Roland Sigel,Joachim Schnabl,Vincent Olieric,Bernhard Spingler

doi:10.3390/ijms17070988

Michelle Schaffer, Meitian Wang + Show 5 more

Open Access

https://doi.org/10.3390/ijms17070988

Copy DOI

Abstract

Due to the polyanionic nature of RNA, the principles of charge neutralization and electrostatic condensation require that cations help to overcome the repulsive forces in order for RNA to adopt a three-dimensional structure. A precise structural knowledge of RNA-metal ion interactions is crucial to understand the mechanism of metal ions in the catalytic or regulatory activity of RNA. We solved the crystal structure of an octameric RNA duplex in the presence of the di- and trivalent metal ions Ca2+, Mn2+, Co2+, Cu2+, Sr2+, and Tb3+. The detailed investigation reveals a unique innersphere interaction to uracil and extends the knowledge of the influence of metal ions for conformational changes in RNA structure. Furthermore, we could demonstrate that an accurate localization of the metal ions in the X-ray structures require the consideration of several crystallographic and geometrical parameters as well as the anomalous difference map.

Highlights

Metal ions play a crucial role in the folding of RNA and its catalytic mechanism, which are central in RNA biology
The MINAS (Metal Ions in Nucleic AcidS) database [10] allows searching for any specific metal binding sites found in nucleic acids and it distinguishes between outer- and innersphere coordination
In order to investigate the influence of metal ions on RNA structure, six octameric RNA duplex structures were solved in the presence of different metal ions

Summary

Introduction

Metal ions play a crucial role in the folding of RNA and its catalytic mechanism, which are central in RNA biology. Cations influence the folding pathway by bringing together unfolded molecules, promoting the formation of secondary structures, stabilizing intermediate structures, and by maintaining the final native structure [3,5,6]. Nucleic acids, with their negative charge, are excellent targets for metal ions and metal-containing compounds. A second type of binding, called innersphere binding, occurs directly between a metal ion and atoms of the RNA [9]. The MINAS (Metal Ions in Nucleic AcidS) database [10] allows searching for any specific metal binding sites found in nucleic acids and it distinguishes between outer- and innersphere coordination

Methods

Results

Discussion

Conclusion