Aptamer-Based K⁺ Sensor: Process of Aptamer Transforming into G-Quadruplex

Abstract

G-rich aptamers have been widely applied to develop various sensors for detecting proteins, small molecules, and cations, which is based on the target-induced conformational transfer from single strand to G-quadruplex. However, the transforming process is unclear. Here, with PW17 as an aptamer example, the forming process of G-quadruplex induced by K(+) is investigated by circular dichroism spectroscopy, electrospray ionization mass spectroscopy, and native gel electrophoresis. The results demonstrate that PW17 undergoes a conformational transforming process from loose and unstable to compact and stable G-quadruplex, which is strictly K(+) concentration-dependent. The process contains three stages: (1) K(+) (<0.5 mM) could induce PW17 forming a loose and unstable G-quadruplex; (2) the compact and stable K(+)-stabilized G-quadruplex is almost formed when K(+) is equal to or larger than 7 mM; and (3) when K(+) ranges from 0.5 mM to 7 mM, the transformation of K(+)-stabilized PW17 from loose and unstable to compact and stable occurs. Interestingly, dimeric G-quadruplex through 5'-5' stacking is involved in the forming process until completely formed at 40 mM K(+). Moreover, the total process is thermodynamically controlled. With PW17 as a sensing probe and PPIX as a fluorescent probe for detection of K(+), three linear fluorescent ranges are observed, which corresponds to the three forming stages of G-quadruplex. Clarifying the forming process provides a representative example to deeply understand and further design aptamer-based biosensers and logic devices.

Thermal conductivities of graphyne nanotubes from atomistic simulations

“…The scaling exponent of 1.0 before the crossover is consistent with the prediction of the ballistic phonon transport [32]. The scaling exponent of 0.48 after the crossover is larger than the reported values of 0.21 [32], 0.40 [25] and less than 0.54 [35] due to different force fields used.…”

“…where J is the heat flux, @T=@z the temperature gradient and A the cross-section area of the GNT-n. We follow the standard practice to treat the GNT as a hollow tube of diameter d and a wall thickness of 0.142 nm, just as the same as the length of sp 2 C-C bond in graphene [24,25]. The factor 2 in the denominator accounts for the periodicity of the system.…”

Thermal Conductivity of Amorphous Materials

“…Thermal transport in low‐dimensional nanostructures, which can be very different from their bulk counterparts, has continuously attracted intensive interest from both academia and industry. A significant size dependence has been observed in the thermal conductivity of 1D materials, including carbon nanotubes and semiconductor nanowires, and of 2D nanomaterials, such as graphene, attributed to the superdiffusion heat spread . Compared with bulk counterparts, the thermal conductivity of nanostructures is remarkably reduced because of the quantum confinement effect and surface phonon scattering.…”

Tuning the Coupling in Single‐Molecule Heterostructures: DNA‐Programmed and Reconfigurable Carbon Nanotube‐Based Nanohybrids

“…In addition, reversibly reconfigurable heterostructures were assembled where a Guanidine(G)‐rich sequence was used as a linker. The QD's position relative to the end of the SWCNT could then be controlled by the addition and removal of K + , which induces the folding of the sequence into a G‐quadruplex (G4) and shortens the distance between the two components15 (cryptand 222 allowed us to revert the linker back to its extended conformation restoring the original distance between the two nanostructures). We demonstrate how this stimuli‐responsive strategy allows real‐time control over the coupling between the SWCNT and QD and can be further exploited for the sensing of K + from mM to pM concentrations.…”