Charge–Dipole Interactions in G-Quadruplex Thrombin-Binding Aptamer
SCIE
SCOPUS
- Title
- Charge–Dipole Interactions in G-Quadruplex Thrombin-Binding Aptamer
- Authors
- KIM, HYUN WOO; RHEE, YOUNG MIN; SHIN, SEUNG KOO
- Date Issued
- 2018-08
- Publisher
- ROYAL SOC CHEMISTRY
- Abstract
- DNAs form various structures through hydrogen-bonding, base-stacking and electrostatic interactions. Although these noncovalent interactions are known to be cooperative in stabilizing a G-quadruplex (G4) structure of DNA, we find from all-atom molecular dynamics simulations that the electrostatic charge-dipole interaction is competitive with both hydrogen-bonding and base-stacking interactions. For the thrombin-binding aptamer (TBA) forming a chair-type antiparallel G4 structure, we have examined effects of an intercalating metal ion [K+, Sr2+, Mn+: an ion having a charge of n(+) (n = 1-4) with the ionic radius of K+] on structural properties and noncovalent interactions. When K+ in the TBA center dot K+ complex is replaced with Sr2+, guanine dipoles in the two G-tetrads are realigned toward the central metal ion, thereby distorting the planar G4 geometry. Replacing K+ with Sr2+ significantly enhances the charge-dipole interaction but substantially reduces the number of hydrogen bonds in the G-tetrads. In the case of TBA center dot Mn+ complexes, as the charge n increases, the charge-dipole interaction increases but both of the hydrogen-bonding and base-stacking interactions decrease. These results suggest that the charge-dipole interaction realigning guanine dipoles in the G-tetrads is not cooperative but competitive with both hydrogen-bonding and base-stacking interactions favoring the planar G-tetrad geometry. Obviously, the charge state of an intercalating metal ion is as important as the ionic radius in forming a stable G4 structure. Thus, a delicate balance between these competing noncovalent interactions makes the chair-type antiparallel G4 structure of TBA selective for intercalating metal ions.
- URI
- https://oasis.postech.ac.kr/handle/2014.oak/94121
- DOI
- 10.1039/c8cp03050b
- ISSN
- 1463-9076
- Article Type
- Article
- Citation
- PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 20, no. 32, page. 21068 - 21074, 2018-08
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