DNA Lattice Research Articles

Synthetic molecular switches driven by DNA-modifying enzymes

Taking inspiration from natural systems, in which molecular switches are ubiquitous in the biochemistry regulatory network, we aim to design and construct synthetic molecular switches driven by DNA-modifying enzymes, such as DNA polymerase and nicking endonuclease. The enzymatic treatments on our synthetic DNA constructs controllably switch ON or OFF the sticky end cohesion and in turn cascade to the structural association or disassociation. Here we showcase the concept in multiple DNA nanostructure systems with robust assembly/disassembly performance. The switch mechanisms are first illustrated in minimalist systems with a few DNA strands. Then the ON/OFF switches are realized in complex DNA lattice and origami systems with designated morphological changes responsive to the specific enzymatic treatments.

Lateral Energy Absorption Analysis of a New Bioinspired DNA Lattice Structure

Lateral Energy Absorption Analysis of a New Bioinspired DNA Lattice Structure

M-State and N-Color (M-N = 1-1, 2-1, and 1-2) Turing Algorithms Demonstrated via DNA Self-Assembly.

The fast and extensive generation of patterns using specific algorithms is a major challenge in the field of DNA algorithmic self-assembly. Turing machines (TMs) are simple computable machines that execute certain algorithms using carefully designed logic gates. We investigate Turing algorithms for the generation of patterns on algorithmic lattices using specific logic gates. Logic gates can be implemented into Turing building blocks. We discuss comprehensive methods for designing Turing building blocks to demonstrate an M-state and N-color Turing machine (M-N TM). The M-state and N-color (M-N = 1-1, 2-1, and 1-2) TMs generate Turing patterns that can be fabricated via DNA algorithmic self-assembly. The M-N TMs require two-input and three-output logic gates. We designed the head, tape, and transition rule tiles to demonstrate TMs for the 1-1, 2-1, and 1-2 Turing algorithms. By analyzing the characteristics of the Turing patterns, we classified them into two classes (DL and DR for states grown diagonally to the left and right, respectively) for the 1-1 TM, three for the 2-1 TM, and nine for the 1-2 TM. Among these, six representative Turing patterns generated using rules R11-0 and R11-1 for 1-1 TM, R21-01 and R21-09 for 2-1 TM, and R12-02 and R12-08 for 1-2 TM were constructed with DNA building blocks. Turing patterns on the DNA lattices were visualized by atomic force microscopy. The Turing patterns on the DNA lattices were similar to those simulated patterns. Implementing the Turing algorithms into DNA building blocks, as demonstrated via DNA algorithmic self-assembly, can be extended to a higher order of state and color to generate more complicated patterns, compute arithmetic operations, and solve mathematical functions.

DNA lattice growth with single, double, and triple double-crossover boundaries by stepwise self-assembly

Construction of various nanostructures with nanometre-scale precision through various DNA building blocks depends upon self-assembly, base-pair complementarity and sequence programmability. During annealing, unit tiles are formed by the complementarity of base pairs in each strand. Enhancement of growth of target lattices is expected if seed lattices (i.e. boundaries for growth of target lattices) are initially present in a test tube during annealing. Although most processes for annealing DNA nanostructures adopt a one-step high temperature method, multi-step annealing provides certain advantages such as reusability of unit tiles and tuneability of lattice formation. We can construct target lattices effectively (through multi-step annealing) and efficiently (via boundaries) by multi-step annealing and combining boundaries. Here, we construct efficient boundaries made of single, double, and triple double-crossover DNA tiles for growth of DNA lattices. Two unit double-crossover DNA tile-based lattices and copy-logic implemented algorithmic lattices were introduced to test the growth of target lattices on boundaries. We used multi-step annealing to tune the formation of DNA crystals during fabrication of DNA crystals comprised of boundaries and target lattices. The formation of target DNA lattices was visualized using atomic force microscopy (AFM). The borders between boundaries and lattices in a single crystal were clearly differentiable from AFM images. Our method provides way to construct various types of lattices in a single crystal, which might generate various patterns and enhance the information capacity in a given crystal.

Protein Diffusion Along Protein and DNA Lattices: Role of Electrostatics and Disordered Regions.

Diffusion is a pervasive process present in a broad spectrum of cellular reactions. Its mathematical description has existed for nearly two centuries and permits the construction of simple rules for evaluating the characteristic timescales of diffusive processes and some of their determinants. Although the term diffusion originally referred to random motions in three-dimensional (3D) media, several biological diffusion processes in lower dimensions have been reported. One-dimensional (1D) diffusions have been reported, for example, for translocations of various proteins along DNA or protein (e.g., microtubule) lattices and translation of helical peptides along the coiled-coil interface. Two-dimensional (2D) diffusion has been shown for dynamics of proteins along membranes. The microscopic mechanisms of these 1-3D diffusions may vary significantly depending on the nature of the diffusing molecules, the substrate, and the interactions between them. In this review, we highlight some key examples of 1-3D biomolecular diffusion processes and illustrate the roles that electrostatic interactions and intrinsic disorder may play in modulating these processes.

Cation-dependent assembly of hexagonal DNA origami lattices on SiO2 surfaces.

DNA origami nanostructures have emerged as functional materials for applications in various areas of science and technology. In particular, the transfer of the DNA origami shape into inorganic materials using established silicon lithography methods holds great promise for the fabrication of nanostructured surfaces for nanoelectronics and nanophotonics. Using ordered DNA origami lattices directly assembled on the oxidized silicon surface instead of single nanostructures would enable the fabrication of functional nanopatterned surfaces with macroscopic dimensions. Here, we thus investigate the assembly of hexagonal DNA lattices from DNA origami triangles on RCA-cleaned silicon wafers with hydroxylated surface oxide by time-lapse atomic force microscopy (AFM). Lattice assembly on the SiO2 surface is achieved by a competition of monovalent and divalent cations at elevated temperatures. Ca2+ is found to be superior to Mg2+ in promoting the assembly of ordered lattices, while the presence of Mg2+ rather results in DNA origami aggregation and multilayer formation at the comparably high Na+ concentrations of 200 to 600 mM. Furthermore, Na+ concentration and temperature have a similar effect on lattice order, so that a reduction of temperature can be compensated to some extent by an increase in Na+ concentration. However, even under optimized conditions, the DNA origami lattices assembled on the SiO2 surface exhibit a lower degree of order than equivalent lattices assembled on mica, which is attributed to a higher desorption rate of the DNA origami nanostructures. Even though this high desorption rate also complicates any post-assembly treatment, the formed DNA origami lattices could successfully be transferred into the dry state, which is an important prerequisite for further processing steps.

Augmented DNA Nanoarchitectures: A Structural Library of 3D Self-Assembling Tensegrity Triangle Variants.

The DNA tensegrity triangle is known to reliably self-assemble into a 3D rhombohedral crystalline lattice via sticky-end cohesion. Here, the library of accessible motifs is expanded throughcovalent extensions of intertriangle regions and sticky-end-coordinated linkages of adjacent triangles with double helical segmentsusing both geometrically symmetric and asymmetric configurations. The molecular structures of 18self-assembled architectures at resolutions of 3.32-9.32Å are reported; the observed cell dimensions, cavity sizes, and cross-sectional areas agree with theoretical expectations. These data demonstrate that fine control over triclinic and rhombohedral crystal parameters and the customizability of more complex 3D DNA lattices are attainable via rational design. It is anticipated that augmented DNA architectures may be fine-tuned for the self-assembly of designer nanocages, guest-host complexes, and proscriptive 3D nanomaterials, as originally envisioned. Finally, designer asymmetric crystalline building blocks can be seen as a first step toward controlling and encoding information in three dimensions.

Nanoscale packing of DNA tiles into DNA macromolecular lattices

Nanoscale double-crossovers (DX), antiparallel (A), and even half-turns-perimeter (E) DNA tiles (DAE-tiles) with rectangular shapes can be packed into large arrays of micrometer-scale lattices. But the features and mechanical strength of DNA assembly made from differently shaped large-sized DAE DNA tiles and the effects of various geometries on the final DNA assembly are yet to be explored. Herein, we focused on examining DNA lattices synthesized from DX bi-triangular, DNA tiles (T) with concave and convex regions along the perimeter of the tiles. The bi-triangular DNA tiles “T(A) and T(B)” were synthesized by self-assembling the freshly prepared short circular scaffold (S) strands “S(A) and S(B)”, each of 106 nucleotides (NT) lengths. The tiles “T(A) and T(B)” were then coupled together to get assembled via sticky ends. It resulted in the polymerization of DNA tiles into large-sized DNA lattices with giant micrometer-scale dimensions to form the “T(A) + T(B)” assembly. These DNA macro-frameworks were visualized “in the air” under atomic force microscopy (AFM) employing tapping mode. We have characterized how curvature in DNA tiles may undergo transitions and transformations to adjust the overall torque, strain, twists, and the topology of the final self-assembly array of DNA tiles. According to our results, our large-span DX tiles assembly “T(A) + T(B)” despite the complicated curvatures and mechanics, was successfully packed into giant DNA lattices of the width of 30–500 nm and lengths of 500 nm to over 10 μm. Conclusively, the micrometer-scale “T(A) + T(B)” framework assembly was rigid, stable, stiff, and exhibited enough tensile strength to form monocrystalline lattices.

Binding feasibility and vibrational characteristics of single-strand spacer-added DNA and protein complexes

Two of the most important features in the field of nanotechnology are self-assembly with nanometre-scale precision, and the self-alignment of functionalised nanomaterials. Here, we discuss the binding feasibility of single-strand spacer-added DNA building blocks to biotin–streptavidin (SA) complexes. We use atomic force microscopy, photoluminescence (PL) spectroscopy, and dynamic simulation to study the topological, optical, and vibrational characteristics of DNA lattices. To construct the DNA lattices, we use two distinct DNA building blocks, i.e. a double-crossover tile with a biotin (DXB), and a double-crossover tile with a flexible single-strand spacer containing a biotin (DXSB). Biotinylated DXB and DXSB lattices grown on the substrate eventually attracted streptavidins (SA, a tetramer protein) and formed DXB + SA, and DXSB + SA lattices, respectively. Furthermore, we examine the feasibility of alignments of an individual DXB (DXSB) tile on SA-bound DXB (DXSB) lattices, and a SA-conjugated Au nanoparticle (NP) on DXB (DXSB) lattices. To use more than two binding sites of biotins on SA (to serve as a connector between biotinylated tiles), the introduction of flexible single-strand spacers in DX tiles helped to overcome geometrical hindrance. In addition, the PL spectra of DXB and DXSB lattices with SA–Au conjugates are analysed to understand the periodic bindings of Au NPs on DXB (DXSB) lattices. We also conduct dynamic simulations of modal analysis and molecular dynamics simulation, which provide the vibrational characteristics and evidence of the importance of single-strand spacer-added DNA samples. Patterning of nanomaterials with specific functionalities with high precision using a simple method would be useful for the manufacture of high-density nanoelectronic devices and extreme-sensitivity biosensors.

Suppressing high-dimensional crystallographic defects for ultra-scaled DNA arrays

While DNA-directed nano-fabrication enables the high-resolution patterning for conventional electronic materials and devices, the intrinsic self-assembly defects of DNA structures present challenges for further scaling into sub-1 nm technology nodes. The high-dimensional crystallographic defects, including line dislocations and grain boundaries, typically lead to the pattern defects of the DNA lattices. Using periodic line arrays as model systems, we discover that the sequence periodicity mainly determines the formation of line defects, and the defect rate reaches 74% at 8.2-nm line pitch. To suppress high-dimensional defects rate, we develop an effective approach by assigning the orthogonal sequence sets into neighboring unit cells, reducing line defect rate by two orders of magnitude at 7.5-nm line pitch. We further demonstrate densely aligned metal nano-line arrays by depositing metal layers onto the assembled DNA templates. The ultra-scaled critical pitches in the defect-free DNA arrays may further promote the dimension-dependent properties of DNA-templated materials.

2D DNA lattices assembled from DX-coupled tiles

HypothesisFormation of coupled double crossovers (DXs) in a circular 106-mer oligonucleotide (c106nt) could generate stable tiles with the tile core span of 10 half turns. The large-span tiles with complicated curvatures and mechanics could assemble 2D lattices under different environments. Hence, 2D DNA lattice structures based on tile types and sequences, tile packing modes of corrugation and non-corrugation, and assembly media of solution and the substrate-solution interface are yet to be explored. ExperimentsTwo c106nt scaffold strands with different sequences were synthesized. Four types of tiles, two rectilinear and two triangular tiles, were designed and their 2D assemblies were examined by atomic force microscopy (AFM). FindingsThe DX-coupled tiles provided fair strength and rigidity to assemble 2D lattices. Due to the complicated curvature and mechanics of tiles, the two-tile assemblies in solution displayed a few ripe lattices of ribbons, tubes, or polycrystalline aggregates as the minor products and tile oligomers as the major products; whereas the one-tile assemblies via substrate mediation exhibited well-organized monolayer lattices covering the whole mica disk. The herringbone packing patterns were first observed in DNA nanostructures. Based on the lattice constants and the surface coverages of lattices, we estimated the lattice yields for the substrate-mediated assemblies.

Enhanced neutrophil extracellular trap formation in COVID-19 is inhibited by the protein kinase C inhibitor ruboxistaurin.

BackgroundNeutrophil extracellular traps (NETs) are web-like DNA and protein lattices which are expelled by neutrophils to trap and kill pathogens, but which cause significant damage to the host tissue. NETs have emerged as critical mediators of lung damage, inflammation and thrombosis in coronavirus disease 2019 (COVID-19) and other diseases, but there are no therapeutics to prevent or reduce NETs that are available to patients.MethodsNeutrophils were isolated from healthy volunteers (n=9) and hospitalised patients with COVID-19 at the acute stage (n=39) and again at 3–4 months post-acute sampling (n=7). NETosis was measured by SYTOX green assays.ResultsHere, we show that neutrophils isolated from hospitalised patients with COVID-19 produce significantly more NETs in response to lipopolysaccharide (LPS) compared to cells from healthy control subjects. A subset of patients was captured at follow-up clinics (3–4 months post-acute sampling), and while LPS-induced NET formation is significantly lower at this time point, it remains elevated compared to healthy controls. LPS- and phorbol myristate acetate (PMA)-induced NETs were significantly inhibited by the protein kinase C (PKC) inhibitor ruboxistaurin. Ruboxistaurin-mediated inhibition of NETs in healthy neutrophils reduces NET-induced epithelial cell death.ConclusionOur findings suggest ruboxistaurin could reduce proinflammatory and tissue-damaging consequences of neutrophils during disease, and since it has completed phase III trials for other indications without safety concerns, it is a promising and novel therapeutic strategy for COVID-19.

Interaction of Prion Peptides with DNA Structures.

Prion protein aggregation is known to be modulated by macromolecules including nucleic acids. To clarify the role of nucleic acids in PrP pathology, we investigated the interaction between nucleic acids and the prion peptide (PrP)—a synthetic prion protein model peptide resembling a portion of the human prion protein in structure and function spanning amino acid residues 106–126. We used synthetic DNA lattices and natural DNA duplexes extracted from salmon (sDNA) bound with PrP and studied their interaction using distinct physical measurements. The formation of DNA lattices with PrP was visualized by atomic force microscopy (AFM) to investigate the influence of the PrP. PrP inhibited the growth of the double-crossover (DX) lattices significantly compared to the control peptide (CoP). We also conducted optical measurements such as ultraviolet–visible (UV–Vis), circular dichroism (CD), and Fourier transform infrared (FTIR) spectroscopies to validate the interaction between PrP and DNA immediately (D0) and after a 30-day incubation (D30) period. UV–Vis spectra showed variation in the absorbance intensities, specific for the binding of CoP and PrP to DNA. The CD analysis revealed the presence of various secondary structures, such as α-helices and β-sheets, in PrP- and PrP-bound sDNA complexes. The PrP–sDNA interaction was confirmed using FTIR by the change and shift of the absorption peak intensity and the alteration of PrP secondary structures in the presence of DNA. The cytotoxic effects of the PrP-bound sDNA complexes were assessed by a cytotoxicity assay in human neuroblastoma cells in culture. It confirmed that PrP with sDNA was less cytotoxic than CoP. This study provides new applications for DNA molecules by investigating their effect in complex with aggregated proteins. Our study unequivocally showed the beneficial effect of the interaction between DNA and the pathological prion protein. It therefore provides valuable information to exploit this effect in the development of potential therapeutics. Moreover, our work might serve as a basis for further studies investigating the role of DNA interactions with other amyloidogenic proteins.

Orienting an Organic Semiconductor into DNA 3D Arrays by Covalent Bonds.

A quasi-one-dimensional organic semiconductor, hepta(p-phenylene vinylene) (HPV), was incorporated into a DNA tensegrity triangle motif using a covalent strategy. 3D arrays were self-assembled from an HPV-DNA pseudo-rhombohedron edge by rational design and characterized by X-ray diffraction. Templated by the DNA motif, HPV molecules exist as single-molecule fluorescence emitters at the concentration of 8 mM within the crystal lattice. The anisotropic fluorescence emission from HPV-DNA crystals indicates HPV molecules are well aligned in the macroscopic 3D DNA lattices. Sophisticated nanodevices and functional materials constructed from DNA can be developed from this strategy by addressing functional components with molecular accuracy.

Orienting an Organic Semiconductor into DNA 3D Arrays by Covalent Bonds

AbstractA quasi‐one‐dimensional organic semiconductor, hepta(p‐phenylene vinylene) (HPV), was incorporated into a DNA tensegrity triangle motif using a covalent strategy. 3D arrays were self‐assembled from an HPV‐DNA pseudo‐rhombohedron edge by rational design and characterized by X‐ray diffraction. Templated by the DNA motif, HPV molecules exist as single‐molecule fluorescence emitters at the concentration of 8 mM within the crystal lattice. The anisotropic fluorescence emission from HPV‐DNA crystals indicates HPV molecules are well aligned in the macroscopic 3D DNA lattices. Sophisticated nanodevices and functional materials constructed from DNA can be developed from this strategy by addressing functional components with molecular accuracy.

Construction and Configuration Analysis of Zelkova Serrata Lenticel-Like Patterns Generated through DNA Algorithmic Self-Assembly.

Multiple models and simulations have been proposed and performed to understand the mechanism of the various pattern formations existing in nature. However, the logical implementation of those patterns through efficient building blocks such as nanomaterials and biological molecules is rarely discussed. This study adopts a cellular automata model to generate simulation patterns (SPs) and experimental patterns (EPs) obtained from DNA lattices similar to the discrete horizontal brown-color line-like patterns on the bark of the Zelkova serrata tree, known as lenticels [observation patterns (OPs)]. SPs and EPs are generated through the implementation of six representative rules (i.e., R004, R105, R108, R110, R126, and R218) in three-input/one-output algorithmic logic gates. The EPs obtained through DNA algorithmic self-assembly are visualized by atomic force microscopy. Three different modules (A, B, and C) are introduced to analyze the similarities between the SPs, EPs, and OPs of Zelkova serrata lenticels. Each module has unique configurations with specific orientations allowing the calculation of the deviation of the SPs and the EPs with respect to the OPs within each module. The findings show that both the SP and the EP generated under R105 and R126 and analyzed with module B provide a higher similarity of Zelkova serrata lenticel-like patterns than the other four rules. This study provides a perspective regarding the use of DNA algorithmic self-assembly for the construction of various complex natural patterns.

Reconfigurable Two‐Dimensional DNA Lattices: Static and Dynamic Angle Control

AbstractBranched DNA motifs serve as the basic construction elements for all synthetic DNA nanostructures. However, precise control of branching orientation remains a key challenge to further heighten the overall structural order. In this study, we use two strategies to control the branching orientation. The first one is based on immobile Holliday junctions which employ specific nucleotide sequences at the branch points which dictate their orientation. The second strategy is to use angle‐enforcing struts to fix the branching orientation with flexible spacers at the branch points. We have also demonstrated that the branching orientation control can be achieved dynamically, either by canonical Watson–Crick base pairing or non‐canonical nucleobase interactions (e.g., i‐motif and G‐quadruplex). With precise angle control and feedback from the chemical environment, these results will enable novel DNA nanomechanical sensing devices, and precisely‐ordered three‐dimensional architectures.

Reconfigurable Two-Dimensional DNA Lattices: Static and Dynamic Angle Control.

Branched DNA motifs serve as the basic construction elements for all synthetic DNA nanostructures. However, precise control of branching orientation remains a key challenge to further heighten the overall structural order. In this study, we use two strategies to control the branching orientation. The first one is based on immobile Holliday junctions which employ specific nucleotide sequences at the branch points which dictate their orientation. The second strategy is to use angle-enforcing struts to fix the branching orientation with flexible spacers at the branch points. We have also demonstrated that the branching orientation control can be achieved dynamically, either by canonical Watson-Crick base pairing or non-canonical nucleobase interactions (e.g., i-motif and G-quadruplex). With precise angle control and feedback from the chemical environment, these results will enable novel DNA nanomechanical sensing devices, and precisely-ordered three-dimensional architectures.

Modulational stability brought by cubic–quartic interactions of the nearest-neighbor in FK model subjected in a parametrized on-site potential

This work extends to higher-order interactions the results of Nguetcho (2017), in which we discussed only on modulational instability in one-dimensional chain made of atoms, harmonically coupled to their nearest neighbors and subjected to an external on-site potential. Here we investigate the competition between cubic–quartic nonlinearities interactions of the nearest-neighbor and substrate’s deformability, and mainly discuss its impact on the modulational instability of the system. This makes it possible to adapt the theoretical model to a real physical system such as atomic chains or DNA lattices. The governing equation, derived from the modified Frenkel–Kontorova model, is an extended nonlinear Schrödinger equation (eNLS) containing a new higher-order nonlinear term. By employing linear stability analysis, the generic properties of the MI gain spectra of the system are demonstrated. In the presence of the new quartic nonlinearity, the combinations of the system’s parameters open a large variety of gain profiles and instability domains that cannot be explored without the quartic nonlinearity. Direct numerical simulations are performed to support our analytical results, and an excellent agreement is found.

Configuration Analysis of a Lizard Skin-like Pattern Formed by DNA Self-Assembly.

Nature manifests diverse and complicated patterns through efficient physical, chemical, and biological processes. One of the approaches to generate complex patterns, as well as simple patterns, is the use of the cellular automata algorithm. However, there are certain limitations to produce such patterns experimentally due to the difficulty of finding candidate programmable building blocks. Here, we demonstrated the feasibility of generating an ocellated lizard skin-like pattern by simulation considering the probabilistic occurrence of cells and constructed the simulation results on DNA lattices via bottom-up self-assembly. To understand the similarity between the simulated pattern (SP) and the observed pattern (OP) of lizard skin, a unique configuration scheme (unit configuration was composed of 7 cells) was conceived. SPs were generated through a computer with a controlling population of gray and black cells in a given pattern. Experimental patterns (EPs) on DNA lattices, consisting of double-crossover (DX) tiles without and with protruding hairpins, were fabricated and verified through atomic force microscopy (AFM). For analyzing the similarity of the patterns, we introduced deviation of the average configuration occurrence for SP and EP with respect to OP, i.e., σα(SO) and σα(EO). The configuration and deviation provide characteristic information of patterns. We recognized that the minimum values of <σα(SO)> and <σα(EO)> occurred when 50% (55%) of black cells in given SPs (DX tiles with hairpins in given EPs) appeared to be most similar to the OP. Our study provides a novel platform for the applicability of DNA molecules to systematically demonstrate other naturally existing complex patterns or processes with ease.