Excited States in Single-Stranded and i-Motif DNA with Silver Ions

We have studied the excited states and structural properties for the complexes of cytosine (dC)10 chains with silver ions (Ag+) in a wide range of the Ag+ to DNA ratio (r) and pH conditions using circular dichroism, steady-state absorption, and fluorescence spectroscopy along with the ultrafast fluorescence upconversion technique. We also calculated vertical electronic transition energies and determined the nature of the corresponding excited states in some models of the cytosine-Ag+ complexes. We show that (dC)10 chains in the presence of silver ions form a duplex stabilized by C-Ag+-C bonds. It is also shown that the i-motif structure formed by (dC)10 chains is destabilized in the presence of Ag+ ions. The excited-state properties in the studied complexes depend on the amount of binding ions and the binding sites, which is supported by the calculations. In particular, new low-lying excited states appear when the second Ag+ ion interacts with the O atom of cytosine in the C-Ag+-C pairs. A similar picture is observed in the case when one Ag+ ion interacts with one cytosine via the N7 atom.

Analytes Triggered Conformational Switch of i-Motif DNA inside Gold-Decorated Solid-State Nanopores

The nanopore-based technique is a useful tool for single-molecule sensing and characterization. In this work, we have developed a new DNA-functionalized gold-modified nanopore, and analytes can induce the conformational switch of i-motif DNA formed on the inner surface of the nanopore. i-Motif DNA structure can be formed in the presence of silver ions (Ag⁺), which will result in the change in surface charge and structure of the nanopore tip and ion current rectification (ICR) ratio. The i-motif DNA structure on nanopore surface will be destroyed after the addition of glutathione (GSH) due to the strong interaction of Ag-S bond, which results in the recovery of surface charge, steric hindrance, and ICR ratio. This analyte-triggered conformational switch of i-motif DNA can help us deeply understand the DNA technology inside single nanopore and will benefit the possible applications in an ultrasensitive detection and biological/chemical analysis.

Room temperature hysteretic spin crossover in a new cyanoheterometallic framework

A new iron(ii)-based spin-crossover compound with thermal hysteresis operating under ambient conditions is reported.

pH-Driven Actuation of DNA Origami via Parallel I-Motif Sequences in Solution and on Surfaces

As bottom up DNA nanofabrication creates increasingly complex and dynamic mechanisms, the implementation of actuators within the DNA nanotechnology toolkit has grown increasingly important. One such actuator, the I-motif, is fairly simple in that it consists solely of standard DNA sequences and does not require any modification chemistry or special purification beyond that typical for DNA oligomer synthesis. This study presents a new implementation of parallel I-motif actuators, emphasizing their future potential as drivers of complex internal motion between substructures. Here we characterize internal motion between DNA origami substructures via AFM and image analysis. Such parallel I-motif design and quantification of actuation provide a useful step toward more complex and effective molecular machines.

Temporal control of i-motif switch lifetimes for autonomous operation of transient DNA nanostructures

System integration of the DNA i-motif switch with a tunable pH environment allows programmable lifetimes of DNA duplex hybridization and higher level self-assemblies in closed and autonomous systems.

Functional DNA nanotechnology creates increasingly complex behaviors useful for sensing, actuation or computation, as enabled via the integration of dynamic and responsive structural DNA motifs. However, temporally controlled and dynamic DNA structures with programmable lifetimes, that are able to operate autonomously and self-revert to the starting state are challenging to achieve due to tedious and very system-specific sequence design. Here, we present a straightforward concept to program transient lifetimes into DNA duplexes based on the pH-sensitive DNA i-motif switch. We integrate the i-motif switch with an internal, non-linear pH-resetting function using a rationally designed chemical reaction framework, by which the switch autonomously undergoes a complete “off–on–off”-cycle without the use of additional external triggers. The lifetime of the activated “on”-state (i.e. the hybridized state) can be systematically programmed over several hours. The system can be readily implemented into hybrid DNA structures on larger length scales. Focusing on autonomous materials, we demonstrate temporal control of transient fluorescence signals and temporary aggregation of gold nanoparticles.

Nanomechanics of surface DNA switches probed by captive contact angle

Self-assembled monolayers of Thrombin Binding Aptamers (TBA) were prepared on gold surfaces with typical surface densities of close-packed ssDNA (4×10(12) and 8×10(12)molecules/cm(2)). CONtact Angle MOlecular REcognition (CONAMORE) in captive bubble geometry was then assessed to scan the surface work triggered by TBAs when switching from the elongated to the G-quadruplex conformation upon binding with Na(+) or K(+) cations. We found Na(+) and K(+) could induce comparable linear to G-quadruplex strokes, and resulted in values for surface work of ~-70 pN nm/molecule (~18 kBT). The strokes change the in-plane van der Waals and weak electrostatic interactions and accumulate to result in macroscopic surface work. Micro- to macroscopic translation strongly depends on the nature of the cation and TBA surface density. In particular, the K(+) stimulus triggers a macroscopic surface work of -2.2±0.2 and -5.3±0.2 mN/m for low and high packed monolayers, respectively, while Na(+) triggers up to -6.7±1.0 mN/m in the highly packed monolayer, but creates negligible work for the low packed monolayer. These results show that CONAMORE can contribute important information for the development of devices based on DNA switches, and ultimately help address some of the open challenges for DNA-based nanomachinery.

Scanning electrochemical microscopy monitoring in microcantilever platforms

The deflection of cantilever systems may be performed by an indirect electrochemical method that consists of measuring the local cantilever activity and deflection in a feedback generation-collection configuration of the SECM. This is illustrated during the electrochemically assisted adsorption of Br onto a gold-coated cantilever, either in its pristine state or previously coated with a thin organic barrier. It is further extended to the adsorption of an antibody in a heterogeneous immunoassay at an allergen-coated microcantilever platform. In both reactions, the cantilever deflection is qualitatively detected from the SECM tip current measurement and a quantitative estimate is obtained through modeling. This electroanalytical strategy provides an alternative approach to standard optical detection. It can overcome some limitations of the optical method by allowing electrochemical characterization of nonconductive cantilevers and appropriate use for closed systems.

Challenges for nanomechanical sensors in biological detection

Nanomechanical biosensing relies on changes in the movement and deformation of micro- and nanoscale objects when they interact with biomolecules and other biological targets. This field of research has provided ever-increasing records in the sensitivity of label-free detection but it has not yet been established as a practical alternative for biological detection. We analyze here the latest advancements in the field, along with the challenges remaining for nanomechanical biosensors to become a commonly used tool in biology and biochemistry laboratories.