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Role of Alkali Metal Ions in G-Quadruplex Nucleic Acid Structure and Stability

  • Chapter
The Alkali Metal Ions: Their Role for Life

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

Abstract

G-quadruplexes are guanine-rich nucleic acids that fold by forming successive quartets of guanines (the G-tetrads), stabilized by intra-quartet hydrogen bonds, inter-quartet stacking, and cation coordination. This specific although highly polymorphic type of secondary structure deviates significantly from the classical B-DNA duplex. G-quadruplexes are detectable in human cells and are strongly suspected to be involved in a number of biological processes at the DNA and RNA levels. The vast structural polymorphism exhibited by G-quadruplexes, together with their putative biological relevance, makes them attractive therapeutic targets compared to canonical duplex DNA. This chapter focuses on the essential and specific coordination of alkali metal cations by G-quadruplex nucleic acids, and most notably on studies highlighting cation-dependent dissimilarities in their stability, structure, formation, and interconversion. Section 1 surveys G-quadruplex structures and their interactions with alkali metal ions while Section 2 presents analytical methods used to study G-quadruplexes. The influence of alkali cations on the stability, structure, and kinetics of formation of G-quadruplex structures of quadruplexes will be discussed in Sections 3 and 4. Section 5 focuses on the cation-induced interconversion of G-quadruplex structures. In Sections 3 to 5, we will particularly emphasize the comparisons between cations, most often K+ and Na+ because of their prevalence in the literature and in cells.

Please cite as: Met. Ions Life Sci. 16 (2016) 203–258

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Abbreviations

AUC:

analytical ultracentrifugation

CD:

circular dichroism

DFT-D:

dispersion-corrected density functional theory

DOSY:

diffusion ordered spectroscopy

DSC:

differential scanning calorimetry

EPR:

electron paramagnetic resonance

ESI-MS:

electrospray ionization mass spectrometry

FRET:

Förster resonance energy transfer

G4:

quadruplex nucleic acid

GMP:

guanosine 5′-monophosphate

HSQC:

heteronuclear single-quantum correlation spectroscopy

IDS:

isothermal difference spectra

IMS-MS:

ion-mobility spectrometry mass spectrometry

ITC:

isothermal titration calorimetry

LNA:

locked nucleic acid

MALDI-TOF:

matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

MAS:

magic-angle spinning

MD:

molecular dynamics

MS:

mass spectrometry

NMR:

nuclear magnetic resonance

NOE:

nuclear Overhauser effect

nt:

nucleotide

PAGE:

polyacrylamide gel electrophoresis

PBFI:

benzofuran-isophthalate crown ether indicator

PDB:

protein data bank

PNA:

peptide nucleic acid

QM:

quantum mechanics

RMSD:

root-mean-square deviation

SE-HPLC:

size-exclusion high-performance liquid chromatography

STM:

scanning tunneling microscope

TBA:

thrombin binding aptamer

TDS:

thermal difference spectra

TERRA:

telomeric repeat-containing RNA

TMAA:

trimethyl ammonium acetate

UTR:

untranslated region

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Acknowledgment

Pictures of G-quadruplexes from the PBD entries were generated with UCSF Chimera (alpha version 1.11) [325]. Funding was provided by Agence Nationale de la Recherche (OligoSwitch [ANR-12-IS07–0001], ‘Quarpdiem’ [ANR-12-BSV8–0008–01], and ‘VIBBnano’ [ANR-10-NANO-04–03]).

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Authors and Affiliations

  1. ARNA Laboratory, Université Bordeaux, IECB, 2, rue Robert Escarpit, F-33600, Pessac, France

    Eric Largy, Jean-Louis Mergny & Valérie Gabelica

  2. ARNA Laboratory, INSERM, U869, F-33000, Bordeaux, France

    Eric Largy, Jean-Louis Mergny & Valérie Gabelica

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  1. Eric Largy
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  2. Jean-Louis Mergny
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  3. Valérie Gabelica
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Correspondence to Jean-Louis Mergny or Valérie Gabelica .

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  1. Department of Chemistry Inorganic Chemistry, University of Basel, Basel, Basel Stadt, Switzerland

    Astrid Sigel

  2. Department of Chemistry Inorganic Chemistry, University of Basel, Basel, Switzerland

    Helmut Sigel

  3. Department of Chemistry, University of Zürich, Zürich, Switzerland

    Roland K. O. Sigel

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Largy, E., Mergny, JL., Gabelica, V. (2016). Role of Alkali Metal Ions in G-Quadruplex Nucleic Acid Structure and Stability. 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_7

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