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Sodium and Potassium Interactions with Nucleic Acids

  • Chapter
The Alkali Metal Ions: Their Role for Life

Part of the book series: Metal Ions in Life Sciences ((MILS,volume 16))

Abstract

Metal ions are essential cofactors for the structure and functions of nucleic acids. Yet, the early discovery in the 70s of the crucial role of Mg2+ in stabilizing tRNA structures has occulted for a long time the importance of monovalent cations. Renewed interest in these ions was brought in the late 90s by the discovery of specific potassium metal ions in the core of a group I intron. Their importance in nucleic acid folding and catalytic activity is now well established. However, detection of K+ and Na+ ions is notoriously problematic and the question about their specificity is recurrent. Here we review the different methods that can be used to detect K+ and Na+ ions in nucleic acid structures such as X-ray crystallography, nuclear magnetic resonance or molecular dynamics simulations. We also discuss specific versus non-specific binding to different structures through various examples.

Please cite as: Met. Ions Life Sci. 16 (2016) 167–201

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Abbreviations

AMBER:

Assisted Model Building and Energy Refinement

BWYV:

beet western yellow virus

CSD:

Cambridge Structural Database

DIS:

dimerization initiation site

FMN:

flavin mononucleotide

GDP:

guanosine diphosphate

glms ribozyme:

glucosamine-6-phosphate activated ribozyme

GTPase:

guanosine triphosphate hydrolyzing enzymes

HDV:

hepatitis delta virus

MAD:

multi-wavelength anomalous dispersion

MD:

molecular dynamics

miRNA:

microRNA

NMR:

nuclear magnetic resonance

PDB:

Protein Data Bank

RNase:

ribonuclease

rRNA:

ribosomal RNA

SAM:

S-adenosyl methionine

SIMS:

secondary ion mass spectroscopy

SPC/E:

extended simple point charge water model

SRP:

signal recognition particle

THF:

tetrahydrofolate

tRNA:

transfer RNA

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Acknowledgments

P.A. wishes to thank Prof. Eric Westhof and E.E. wishes to thank Dr. Philippe Dumas for ongoing support. This work has been published under the framework of the LABEX: ANR-10-LABX0036_NETRNA and benefits from a funding from the state managed by the French National Research Agency as part of the program “Investments for the future”.

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    Pascal Auffinger, Luigi D’Ascenzo & Eric Ennifar

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Auffinger, P., D’Ascenzo, L., Ennifar, E. (2016). Sodium and Potassium Interactions with Nucleic Acids. In: Sigel, A., Sigel, H., Sigel, R. (eds) The Alkali Metal Ions: Their Role for Life. Metal Ions in Life Sciences, vol 16. Springer, Cham. https://doi.org/10.1007/978-3-319-21756-7_6

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