Three-input logic gate based on DNA strand displacement reaction

In this paper, three kinds of three-input logic gates are designed based on DNA strand displacement reaction, which are three-input OR logic gate, three-input AND logic gate, and three-input MAJORITY logic gate. The logic gates designed in this paper takes different DNA strands as input and fluorescence signals as output. The biochemical experimental results verify my designs. The results show that DNA strand displacement technology has important application value in DNA computing, especially in the construction of DNA molecular logic gates.

Lab-on-a-DNA origami: nanoengineered single-molecule platforms

DNA origami nanostructures are self-assembled into almost arbitrary two- and three-dimensional shapes from a long, single-stranded viral scaffold strand and a set of short artificial oligonucleotides. Each DNA strand can be functionalized individually using well-established DNA chemistry, representing addressable sites that allow for the nanometre precise placement of various chemical entities such as proteins, molecular chromophores, nanoparticles, or simply DNA motifs. By means of microscopic and spectroscopic techniques, these entities can be visualized or detected, and either their mutual interaction or their interaction with external stimuli such as radiation can be studied. This gives rise to the Lab-on-a-DNA origami approach, which is introduced in this Feature Article, and the state-of-the-art is summarized with a focus on light-harvesting nanoantennas and DNA platforms for single-molecule analysis either by optical spectroscopy or atomic force microscopy (AFM). Light-harvesting antennas can be generated by the precise arrangement of chromophores to channel and direct excitation energy. At the same time, plasmonic nanoparticles represent a complementary approach to focus light on the nanoscale. Plasmonic nanoantennas also allow for the observation of single molecules either by Raman scattering or fluorescence spectroscopy and DNA origami platforms provide unique opportunities to arrange nanoparticles and molecules to be studied. Finally, the analysis of single DNA motifs by AFM allows for an investigation of radiation-induced processes in DNA with unprecedented detail and accuracy.

Single molecule DNA origami nanoarrays with controlled protein orientation

The nanoscale organization of functional (bio)molecules on solid substrates with nanoscale spatial resolution and single-molecule control-in both position and orientation-is of great interest for the development of next-generation (bio)molecular devices and assays. Herein, we report the fabrication of nanoarrays of individual proteins (and dyes) via the selective organization of DNA origami on nanopatterned surfaces and with controlled protein orientation. Nanoapertures in metal-coated glass substrates were patterned using focused ion beam lithography; 88% of the nanoapertures allowed immobilization of functionalized DNA origami structures. Photobleaching experiments of dye-functionalized DNA nanostructures indicated that 85% of the nanoapertures contain a single origami unit, with only 3% exhibiting double occupancy. Using a reprogrammed genetic code to engineer into a protein new chemistry to allow residue-specific linkage to an addressable ssDNA unit, we assembled orientation-controlled proteins functionalized to DNA origami structures; these were then organized in the arrays and exhibited single molecule traces. This strategy is of general applicability for the investigation of biomolecular events with single-molecule resolution in defined nanoarrays configurations and with orientational control of the (bio)molecule of interest.

Challenges and Perspectives of DNA Nanostructures in Biomedicine

DNA nanotechnology holds substantial promise for future biomedical engineering and the development of novel therapies and diagnostic assays. The subnanometer-level addressability of DNA nanostructures allows for their precise and tailored modification with numerous chemical and biological entities, which makes them fit to serve as accurate diagnostic tools and multifunctional carriers for targeted drug delivery. The absolute control over shape, size, and function enables the fabrication of tailored and dynamic devices, such as DNA nanorobots that can execute programmed tasks and react to various external stimuli. Even though several studies have demonstrated the successful operation of various biomedical DNA nanostructures both in vitro and in vivo, major obstacles remain on the path to real-world applications of DNA-based nanomedicine. Here, we summarize the current status of the field and the main implementations of biomedical DNA nanostructures. In particular, we focus on open challenges and untackled issues and discuss possible solutions.

Quantitative Assessment of Tip Effects in Single-Molecule High-Speed Atomic Force Microscopy Using DNA Origami Substrates

High-speed atomic force microscopy (HS-AFM) is widely employed in the investigation of dynamic biomolecular processes at a single-molecule level. However, it remains an open and somewhat controversial question, how these processes are affected by the rapidly scanned AFM tip. While tip effects are commonly believed to be of minor importance in strongly binding systems, weaker interactions may significantly be disturbed. Herein, we quantitatively assess the role of tip effects in a strongly binding system using a DNA origami-based single-molecule assay. Despite its femtomolar dissociation constant, we find that HS-AFM imaging can disrupt monodentate binding of streptavidin (SAv) to biotin (Bt) even under gentle scanning conditions. To a lesser extent, this is also observed for the much stronger bidentate SAv-Bt complex. The presented DNA origami-based assay can be universally employed to quantify tip effects in strongly and weakly binding systems and to optimize the experimental settings for their reliable HS-AFM imaging.

On-Chip Neo-Glycopeptide Synthesis for Multivalent Glycan Presentation

Single glycan-protein interactions are often weak, such that glycan binding partners commonly utilize multiple, spatially defined binding sites to enhance binding avidity and specificity. Current array technologies usually neglect defined multivalent display. Laser-based array synthesis technology allows for flexible and rapid on-surface synthesis of different peptides. By combining this technique with click chemistry, neo-glycopeptides were produced directly on a functionalized glass slide in the microarray format. Density and spatial distribution of carbohydrates can be tuned, resulting in well-defined glycan structures for multivalent display. The two lectins concanavalin A and langerin were probed with different glycans on multivalent scaffolds, revealing strong spacing-, density-, and ligand-dependent binding. In addition, we could also measure the surface dissociation constant. This approach allows for a rapid generation, screening, and optimization of a multitude of multivalent scaffolds for glycan binding.

A dual signal amplification strategy combining thermally initiated SI-RAFT polymerization and DNA-templated silver nanoparticles for electrochemical determination of DNA

A highly sensitive method is described for determination of DNA. It is based on dual signal amplification, viz. (a)DNA-templated metal deposition, and (b) thermally initiated surface-initiated reversible addition-fragmentation chain transfer (SI-RAFT) polymerization. A peptide nucleic acid (PNA) with a terminal thiol group was grasped onto a gold electrode by self-assembly. The modified electrode serves as a probe to selectively capture target DNA (tDNA). In the next step, Zr(IV) ions are bound to the phosphate groups of the tDNA. A chain-transfer agent (CTA) for thermally initiated SI-RAFT polymerization, 4-cyano-4-(phenylcarbonothioylthio)pentanoic acid (CPAD), was immobilized on tDNA by conjugation of the carboxy group to Zr(IV) ions. Subsequently, numerous monomers of glycosyloxyethyl methacrylate (GEMA) were connected to the CPAD by thermally initiated SI-RAFT polymerization with azobisisobutyronitrile (AIBN) serving as the free-radical thermal initiator. Afterwards, hydroxyl groups of the GEMA were oxidized to aldehyde groups reacting with sodium periodate, and silver nanoparticles were further introduced on the surface of electrode via "silver mirror reaction". This results in a large electrochemical signal amplification. Under optimized conditions, the electrochemical signal (best measured at a working potential of 0 V vs. SCE (KCl; 3 M)) increases linearly with the logarithm of tDNA concentration in the 10 to 10⁶ aM concentration range. The detection limit is as low as 5.6 aM (~34 molecules in a 10 μL sample). This is lower by factors between 2 and 1800 times than detection limits of most other ultra-sensitive electrochemical DNA assays. Graphical abstractSchematic representation of a dual signal amplification strategy combining thermally initiated surface-initiated reversible addition-fragmentation chain transfer polymerization (SI-RAFT) and DNA-templated silver nanoparticles for electrochemical determination of DNA.