Seeding the Self-Assembly of DNA Origamis at Surfaces

Optimizing Binding among Bimolecular Tethered Complexes

Tethered motion is ubiquitous in nature, offering controlled movement and spatial constraints to otherwise chaotic systems. The enhanced functionality and practical utility of tethers has been exploited in biotechnology, catalyzing the design of novel biosensors and molecular assembly techniques. While notable technological advances incorporating tethered motifs have been made, a theoretical gap persists within the paradigm, hindering a comprehensive understanding of tethered-based technologies. In this work, we focus on the characterization of the binding kinetics of two tethered molecules functionalized to a hard surface. Using a mean-field approximation, the binding time of such bimolecular system is determined analytically. Furthermore, estimates of the grafting site separation and polymer lengths which expedite binding are provided. These estimates, along with the analytical theories and frameworks established here, have the potential to improve efficacy in self-assembly methods in DNA nanotechnology and can be extended to more biologically specific endeavors including targeted drug-delivery and molecular sensing.

Life at the interface: Engineering bio-nanomaterials through interfacial molecular self-assembly

Interfacial self-assembly describes the directed organization of molecules and colloids at phase boundaries. Believed to be fundamental to the inception of primordial life, interfacial assembly is exploited by a myriad of eukaryotic and prokaryotic organisms to execute physiologic activities and maintain homeostasis. Inspired by these natural systems, chemists, engineers, and materials scientists have sought to harness the thermodynamic equilibria at phase boundaries to create multi-dimensional, highly ordered, and functional nanomaterials. Recent advances in our understanding of the biophysical principles guiding molecular assembly at gas-solid, gas-liquid, solid-liquid, and liquid-liquid interphases have enhanced the rational design of functional bio-nanomaterials, particularly in the fields of biosensing, bioimaging and biotherapy. Continued development of non-canonical building blocks, paired with deeper mechanistic insights into interphase self-assembly, holds promise to yield next generation interfacial bio-nanomaterials with unique, and perhaps yet unrealized, properties. This article is categorized under: Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Therapeutic Approaches and Drug Discovery > Emerging Technologies.

Mechanism of DNA origami folding elucidated by mesoscopic simulations

Many experimental and computational efforts have sought to understand DNA origami folding, but the time and length scales of this process pose significant challenges. Here, we present a mesoscopic model that uses a switchable force field to capture the behavior of single- and double-stranded DNA motifs and transitions between them, allowing us to simulate the folding of DNA origami up to several kilobases in size. Brownian dynamics simulations of small structures reveal a hierarchical folding process involving zipping into a partially folded precursor followed by crystallization into the final structure. We elucidate the effects of various design choices on folding order and kinetics. Larger structures are found to exhibit heterogeneous staple incorporation kinetics and frequent trapping in metastable states, as opposed to more accessible structures which exhibit first-order kinetics and virtually defect-free folding. This model opens an avenue to better understand and design DNA nanostructures for improved yield and folding performance.

Site-directed placement of three-dimensional DNA origami

The combination of lithographic methods with two-dimensional DNA origami self-assembly has led, among others, to the development of photonic crystal cavity arrays and the exploration of sensing nanoarrays where molecular devices are patterned on the sub-micrometre scale. Here we extend this concept to the third dimension by mounting three-dimensional DNA origami onto nanopatterned substrates, followed by silicification to provide hybrid DNA-silica structures exhibiting mechanical and chemical stability and achieving feature sizes in the sub-10-nm regime. Our versatile and scalable method relying on self-assembly at ambient temperatures offers the potential to three-dimensionally position any inorganic and organic components compatible with DNA origami nanoarchitecture, demonstrated here with gold nanoparticles. This way of nanotexturing could provide a route for the low-cost production of complex and three-dimensionally patterned surfaces and integrated devices designed on the molecular level and reaching macroscopic dimensions.

Potential-Dependent Adhesion Forces between dsDNA and Electroactive Surfaces

A promising approach to regulating the interactions between polyelectrolytes and materials is the use of electroactive surfaces that can change their charge state. However, common electroactive groups are too unstable to be practical for this purpose. Here we have performed a single molecule force spectroscopy study of the interactions between dsDNA and an 1,1'-biferrocenylene (BFD = bis(fulvalene)diiron)-terminated self-assembled monolayer surface that allows us to reversibly change the charge state. We found that the interaction force between DNA and the surface is correlated to the oxidation state of the BFD groups, which is conveniently controlled by the electrochemical potentials. We discovered that the electroactive SAM produces much stronger interaction forces than its nonelectroactive counterpart. A model based on the Grahame equation was able to quantitatively reproduce the experimentally observed relation between the applied potentials and adhesion forces. Our electroactive surface provides a model system for quantitative studies of the interactions between polyelectrolyte and charged surfaces in liquid. These insights may enable new opportunities for actively manipulating the binding, orientations, and conformations of polyelectrolytes for biosensing, nanomotors, and other applications.

Probing Heterogeneous Folding Pathways of DNA Origami Self-Assembly at the Molecular Level with Atomic Force Microscopy

A myriad of DNA origami nanostructures have been demonstrated in various intriguing applications. In pursuit of facile yet high-yield synthesis, the mechanisms underlying DNA origami folding need to be resolved. Here, we visualize the folding processes of several multidomain DNA origami structures under ambient annealing conditions in solution using atomic force microscopy with submolecular resolution. We reveal the coexistence of diverse transitional structures that might result in the same prescribed products. Based on the experimental observations and the simulation of the energy landscapes, we propose the heterogeneity of the folding pathways of multidomain DNA origami structures. Our findings may contribute to understanding the high-yield folding mechanism of DNA origami.

Visual Construction of Logical AND and NAND Gates

DNA logic gates are an important branch of DNA computing and have a wide range of applications in DNA computing. In this study, logic circuits of AND gate and NAND gate are built on origami substrate. The realization of AND gate uses polymerase strand displacement (PSD) reaction and hybridization chain reaction (HCR). If there is a fluorescent band “1” displayed, the result is true. The realization of the NAND gate requires a cyclic reaction. If there is a fluorescent band “A” or “T” displayed, the result is true; if no fluorescent band is displayed, the result is false.

Multifunctional Hyphae Carbon Powering Lithium-Sulfur Batteries

Biotechnology can bring new breakthroughs on design and fabrication of energy materials and devices. In this work, a novel and facile biological self-assembly technology to fabricate multifunctional Rhizopus hyphae carbon fiber (RHCF) and its derivatives on a large scale for electrochemical energy storage is proposed. Crosslinked hollow carbon fibers are successfully prepared by conversion of Rhizopus hyphae, and macroscopic production of centimeter-level carbon balls consisting of hollow RHCFs is further realized. Moreover, the self-assembled RHCF balls show strong adsorption characteristics on metal ions and can be converted into a series of derivatives such as RHCF/metal oxides. Notably, the designed RHCF derivatives are demonstrated with powerful multifunctionability as cathode, anode, and separator for lithium-sulfur batteries (LSBs). The RHCF can act as the host material to combine with metal oxide (CoO) and S, Li metal, and a polypropylene (PP) separator to form a new RHCF/CoO-S cathode, an RHCF/Li anode, and an RHCF/PP separator, respectively. Consequently, the optimized LSB full cell presents excellent cycling performance and superior high-rate capacity (881.3 mA h g^-1 at 1 C). This work provides a new method for large-scale preparation of hollow carbon fibers and derivatives for advanced energy storage and conversion.

Toward a Quantitative Relationship between Nanoscale Spatial Organization and Hybridization Kinetics of Surface Immobilized Hairpin DNA Probes

Hybridization of DNA probes immobilized on a solid support is a key process for DNA biosensors and microarrays. Although the surface environment is known to influence the kinetics of DNA hybridization, so far it has not been possible to quantitatively predict how hybridization kinetics is influenced by the complex interactions of the surface environment. Using spatial statistical analysis of probes and hybridized target molecules on a few electrochemical DNA (E-DNA) sensors, functioning through hybridization-induced conformational change of redox-tagged hairpin probes, we developed a phenomenological model that describes how the hybridization rates for single probe molecules are determined by the local environment. The predicted single-molecule rate constants, upon incorporation into numerical simulation, reproduced the overall kinetics of E-DNA sensor surfaces at different probe densities and different degrees of probe clustering. Our study showed that the nanoscale spatial organization is a major factor behind the counterintuitive trends in hybridization kinetics. It also highlights the importance of models that can account for heterogeneity in surface hybridization. The molecular level understanding of hybridization at surfaces and accurate prediction of hybridization kinetics may lead to new opportunities in development of more sensitive and reproducible DNA biosensors and microarrays.

Stepwise Strategy for One-Pot Synthesis of Single-Stranded DNA Rings from Multiple Short Fragments

Cyclic rings of single-stranded (ss) DNA have various unique properties, but wider applications have been hampered by their poor availability. This paper reports a convenient one-pot method in which these rings are efficiently synthesized by using T4 DNA ligase through convergent cyclization of easily available short DNA fragments. The key to the present method is to separate all the splint oligonucleotides into several sets, and add each set sequentially at an appropriate interval to the solutions containing all the short DNA fragments. Compared with simple one-pot strategies involving simultaneous addition of all the splints at the beginning of the reaction, both the selectivity and the yields of target ssDNA rings are greatly improved. This convergent method is especially useful for preparing large-sized rings that are otherwise hard to obtain. By starting from six short DNA fragments (71-82 nt), prepared by a DNA synthesizer, a ssDNA ring of 452-nt size was synthesized in 35 mol % yield and in high selectivity. Satisfactorily pure DNA rings were obtainable simply by treating the crude products with exonuclease.

Highly Sensitive Polydiacetylene Ensembles for Biosensing and Bioimaging

Polydiacetylenes are prepared from amphiphilic diacetylenes first through self-assembly and then polymerization. Different from common supramolecular assemblies, polydiacetylenes have stable structure and very special optical properties such as absorption, fluorescence, and Raman. The hydrophilic head of PDAs is easy to be chemically modified with functional groups for detection and imaging applications. PDAs will undergo a specific color change from blue to red, fluorescence enhancement and Raman spectrum changes in the presence of receptor ligands. These properties allow PDA-based sensors to have high sensitivity and specificity during analysis. Therefore, the PDAs have been widely used for detection of viruses, bacteria, proteins, antibiotics, hormones, sialic acid, metal ions and as probes for bioimaging in recent years. In this review, the preparation, polymerization, and detection mechanisms of PDAs are discussed, and some representative research advances in the field of bio-detection and bioimaging are highlighted.