In situ Surface Charge Density Visualization of Self-assembled DNA Nanostructures after Ion Exchange

Ion-mediated control of structural integrity and reconfigurability of DNA nanostructures

Nucleic acid-based biomolecular self-assembly enables the creation of versatile functional architectures. Electrostatic screening of the negative charges of nucleic acids is essential for their folding and stability; thus, ions play a critical role in nucleic acid self-assembly in both biology and nanotechnology. However, the ion-DNA interplay and the resulting ion-specific structural integrity and responsiveness of DNA constructs are underexploited. Here, we harness a wide range of mono- and divalent ions to control the structural features of DNA origami constructs. Using atomic force microscopy and Förster resonance energy transfer (FRET) spectroscopy down to the single-molecule level, we report on the global and local structural performance and responsiveness of DNA origami constructs following self-assembly, upon post-assembly ion exchange and post-assembly ion-mediated reconfiguration. We determined the conditions for highly efficient DNA origami folding in the presence of several mono- (Li⁺, Na⁺, K⁺, Cs⁺) and divalent (Ca²⁺, Sr²⁺, Ba²⁺) ions, expanding the range where DNA origami structures can be exploited for custom-specific applications. We then manipulated fully folded constructs by exposing them to unfavorable ionic conditions that led to the emergence of substantial disintegrity but not to unfolding. Moreover, we found that poorly assembled nanostructures at low ion concentrations undergo substantial self-repair upon ion addition in the absence of free staple strands. This reconfigurability occurs in an ion type- and concentration-specific manner. Our findings provide a fundamental understanding of the ion-mediated structural responsiveness of DNA origami at the nanoscale enabling applications under a wide range of ionic conditions.

Self-snapping hydrogel-based electroactive microchannels as nerve guidance conduits

Peripheral nerve regeneration with large defects needs innovative design of nerve guidance conduits (NGCs) which possess anisotropic guidance, electrical induction and right mechanical properties in one. Herein, we present, for the first time, facile fabrication and efficient neural differentiation guidance of anisotropic, conductive, self-snapping, hydrogel-based NGCs. The hydrogels were fabricated via crosslinking of graphitic carbon nitride (g-C₃N₄) upon exposure with blue light, incorporated with graphene oxide (GO). Incorporation of GO and in situ reduction greatly enhanced surface charges, while decayed light penetration endowed the hydrogel with an intriguing self-snapping feature by the virtue of a crosslinking gradient. The hydrogels were in the optimal mechanical stiffness range for peripheral nerve regeneration and supported normal viability and proliferation of neural cells. The PC12 ​cells differentiated on the electroactive g-C₃N₄ H/rGO3 (3 ​mg/mL GO loading) hydrogel presented 47% longer neurite length than that of the pristine g-C₃N₄ H hydrogel. Furthermore, the NGC with aligned microchannels was successfully fabricated using sacrificial melt electrowriting (MEW) moulding, the anisotropic microchannels of the 10 ​μm width showed optimal neurite guidance. Such anisotropic, electroactive, self-snapping NGCs may possess great potential for repairing peripheral nerve injuries.

Probing and Visualizing Interfacial Charge at Surfaces in Aqueous Solution

Surface charge density and distribution play an important role in almost all interfacial processes, influencing, for example, adsorption, colloidal stability, functional material activity, electrochemical processes, corrosion, nanoparticle toxicity, and cellular processes such as signaling, absorption, and adhesion. Understanding the heterogeneity in, and distribution of, surface and interfacial charge is key to elucidating the mechanisms underlying reactivity, the stability of materials, and biophysical processes. Atomic force microscopy (AFM) and scanning ion conductance microscopy (SICM) are highly suitable for probing the material/electrolyte interface at the nanoscale through recent advances in probe design, significant instrumental (hardware and software) developments, and the evolution of multifunctional imaging protocols. Here, we assess the capability of AFM and SICM for surface charge mapping, covering the basic underpinning principles alongside experimental considerations. We illustrate and compare the use of AFM and SICM for visualizing surface and interfacial charge with examples from materials science, geochemistry, and the life sciences.

Scanning Ion Conductance Microscopy

Scanning ion conductance microscopy (SICM) has emerged as a versatile tool for studies of interfaces in biology and materials science with notable utility in biophysical and electrochemical measurements. The heart of the SICM is a nanometer-scale electrolyte filled glass pipette that serves as a scanning probe. In the initial conception, manipulations of ion currents through the tip of the pipette and appropriate positioning hardware provided a route to recording micro- and nanoscopic mapping of the topography of surfaces. Subsequent advances in instrumentation, probe design, and methods significantly increased opportunities for SICM beyond recording topography. Hybridization of SICM with coincident characterization techniques such as optical microscopy and faradaic electrodes have brought SICM to the forefront as a tool for nanoscale chemical measurement for a wide range of applications. Modern approaches to SICM realize an important tool in analytical, bioanalytical, biophysical, and materials measurements, where significant opportunities remain for further exploration. In this review, we chronicle the development of SICM from the perspective of both the development of instrumentation and methods and the breadth of measurements performed.

Surface Charge Measurements with Scanning Ion Conductance Microscopy Provide Insights into Nitrous Acid Speciation at the Kaolin Mineral-Air Interface

Unique surface properties of aluminosilicate clay minerals arise from anisotropic distribution of surface charge across their layered structures. Yet, a molecular-level understanding of clay mineral surfaces has been hampered by the lack of analytical techniques capable of measuring surface charges at the nanoscale. This is important for understanding the reactivity, colloidal stability, and ion-exchange capacity properties of clay minerals, which constitute a major fraction of global soils. In this work, scanning ion conductance microscopy (SICM) is used for the first time to visualize the surface charge and topography of dickite, a well-ordered member of the kaolin subgroup of clay minerals. Dickite displayed a pH-independent negative charge on basal surfaces whereas the positive charge on edges increased from pH 6 to 3. Surface charges responded to malonate addition, which promoted dissolution/precipitation reactions. Results from SICM were used to interpret heterogeneous reactivity studies showing that gas-phase nitrous acid (HONO) is released from the protonation of nitrite at Al-OH₂⁺ groups on dickite edges at pH well above the aqueous pK_a of HONO. This study provides nanoscale insights into mineral surface processes that affect environmental processes on the local and global scale.

Reversible Supra-Folding of User-Programmed Functional DNA Nanostructures on Fuzzy Cationic Substrates

We report that user-defined DNA nanostructures, such as two-dimensional (2D) origamis and nanogrids, undergo a rapid higher-order folding transition, referred to as supra-folding, into three-dimensional (3D) compact structures (origamis) or well-defined μm-long ribbons (nanogrids), when they adsorb on a soft cationic substrate prepared by layer-by-layer deposition of polyelectrolytes. Once supra-folded, origamis can be switched back on the surface into their 2D original shape through addition of heparin, a highly charged anionic polyelectrolyte known as an efficient competitor of DNA-polyelectrolyte complexation. Orthogonal to DNA base-pairing principles, this reversible structural reconfiguration is also versatile; we show in particular that 1) it is compatible with various origami shapes, 2) it perfectly preserves fine structural details as well as site-specific functionality, and 3) it can be applied to dynamically address the spatial distribution of origami-tethered proteins.