Structural insights into cation binding and polymorphism in Oxytricha nova

telomeric G-quadruplex through enhanced sampling simulations

Sangeetha Balasubramanian1), Sanjib Senapati1)*

1)
Department of Biotechnology and BJM School of Biosciences, Indian institute of Technology Madras,
Chennai, India.

* Corresponding Author: sanjibs@iitm.ac.in

G-quadruplexes (GQs) are higher order structures of DNA or RNA and are regulatory in nature.
These structures are majorly found in the telomeric regions and help in protecting the telomeres
from cellular damage, thereby maintaining the genome stability in eukaryotes 1. Structural
diversity in GQs arise due to variation in the sequence, topology of the folds and the bound
cations like Na+, K+, etc. G-quadruplexes are often considered as therapeutic targets since they
are located at important regulatory regions in the genome. Synthetic G-quadruplexes are also
designed to behave as aptamers, biomarkers, and in nanotechnology for the generation of
nanowires2. However, the polymorphism of GQs expressed with respect to their physiological
environment poses a challenge in utilizing GQ structures for therapeutic or industrial purposes.
Also, the structural features responsible for defining the ion specificity with respect to GQ
folding topology and for regulating the ion exchange with bulk have been overlooked till date. In
this regard, the present study aims to understand the structure of the non-polymorphic O.nova
GQ3,4 and elucidate the role of diagonal loops in regulating the uptake of Na+ and K+ cations.
All-atom molecular dynamics simulations were used to study the uptake of cations from bulk
solvent and to elucidate the structural features responsible for the non-specific ion uptake. This
study highlights the importance of ion hydration shell and a plausible gating mechanism of T-
loops towards the non-polymorphic nature (Fig1). The free energy landscape for the cation
movement through the central core of GQ, obtained by Umbrella sampling and Thermodynamic
integration, has revealed the in-plane position of Na+ as energetically favorable than sandwich
position (shown in Fig2) which is an interesting observation when compared to previous studies
on related GQs. The dynamic nature of GQ stem allows the coordination of different cations,
while the loops regulate the ion exchange. A better understanding of these regulating features
will be helpful while designing non-polymorphic GQs as biomarkers, aptamers and for other
biological functions.

References
[1] S. Neidle et al., Quadruplex Nucleic Acids, The Royal Society of Chemistry: Cambridge, 2006.
[2] K. Chakraborty et al., Annu.al Reviews Biochemistry, 85 (2016), 349-373
[3] P. Schultze et al., Nucleic Acids Research, 27 (1999), 3018–3028.
[4] J. Y. Lee et al., Biochemistry, 47 (2008), 3389–3396.

Fig.1 Pore formed by the diagonal T-loop facilitating the dehydration Fig.2 (a) The free energy landscape for the movement of Na+ (red)
and entry of Na+ (a) and K+ (b) ions. The solvent accessible surface of and K+ (green) through the central core of Oxy-GQ extracted by
GQ is shown. Ion-Thymine bridging waters are displayed in licorice, Umbrella sampling
the Na+ and K+ ions as purple and green spheres, respectively