Three-dimensional nanoscale metal, metal oxide, and semiconductor frameworks through DNA-programmable assembly and templating.

Controlling the three-dimensional (3D) nanoarchitecture of inorganic materials is imperative for enabling their novel mechanical, optical, and electronic properties. Here, by exploiting DNA-programmable assembly, we establish a general approach for realizing designed 3D ordered inorganic frameworks. Through inorganic templating of DNA frameworks by liquid- and vapor-phase infiltrations, we demonstrate successful nanofabrication of diverse classes of inorganic frameworks from metal, metal oxide and semiconductor materials, as well as their combinations, including zinc, aluminum, copper, molybdenum, tungsten, indium, tin, and platinum, and composites such as aluminum-doped zinc oxide, indium tin oxide, and platinum/aluminum-doped zinc oxide. The open 3D frameworks have features on the order of nanometers with architecture prescribed by the DNA frames and self-assembled lattice. Structural and spectroscopic studies reveal the composition and organization of diverse inorganic frameworks, as well as the optoelectronic properties of selected materials. The work paves the road toward establishing a 3D nanoscale lithography.

DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch Thermodynamic Parameters.

We show that in silico design of DNA secondary structures is improved by extending the base pairing alphabet beyond A-T and G-C to include the pair between 2-amino-8-(1'-ß-d-2'-deoxyribofuranosyl)-imidazo-[1,2-a]-1,3,5-triazin-(8H)-4-one and 6-amino-3-(1'-ß-d-2'-deoxyribofuranosyl)-5-nitro-(1H)-pyridin-2-one, abbreviated as P and Z. To obtain the thermodynamic parameters needed to include P-Z pairs in the designs, we performed 47 optical melting experiments and combined the results with previous work to fit free energy and enthalpy nearest neighbor folding parameters for P-Z pairs and G-Z wobble pairs. We find G-Z pairs have stability comparable to that of A-T pairs and should therefore be included as base pairs in structure prediction and design algorithms. Additionally, we extrapolated the set of loop, terminal mismatch, and dangling end parameters to include the P and Z nucleotides. These parameters were incorporated into the RNAstructure software package for secondary structure prediction and analysis. Using the RNAstructure Design program, we solved 99 of the 100 design problems posed by Eterna using the ACGT alphabet or supplementing it with P-Z pairs. Extending the alphabet reduced the propensity of sequences to fold into off-target structures, as evaluated by the normalized ensemble defect (NED). The NED values were improved relative to those from the Eterna example solutions in 91 of 99 cases in which Eterna-player solutions were provided. P-Z-containing designs had average NED values of 0.040, significantly below the 0.074 of standard-DNA-only designs, and inclusion of the P-Z pairs decreased the time needed to converge on a design. This work provides a sample pipeline for inclusion of any expanded alphabet nucleotides into prediction and design workflows.

DNA Structure Design Is Improved Using an Artificially Expanded Alphabet of Base Pairs Including Loop and Mismatch Thermodynamic Parameters.

We show that in silico design of DNA secondary structures is improved by extending the base pairing alphabet beyond A-T and G-C to include the pair between 2-amino-8-(1'-ß-D-2'-deoxyribofuranosyl)-imidazo-[1,2- a ]-1,3,5-triazin-(8 H )-4-one and 6-amino-3-(1'-ß-D-2'-deoxyribofuranosyl)-5-nitro-(1 H )-pyridin-2-one, simply P and Z. To obtain the thermodynamic parameters needed to include P-Z pairs in the designs, we performed 47 optical melting experiments and combined the results with previous work to fit a new set of free energy and enthalpy nearest neighbor folding parameters for P-Z pairs and G-Z wobble pairs. We find that G-Z pairs have stability comparable to A-T pairs and therefore should be considered quantitatively by structure prediction and design algorithms. Additionally, we extrapolated the set of loop, terminal mismatch, and dangling end parameters to include P and Z nucleotides. These parameters were incorporated into the RNAstructure software package for secondary structure prediction and analysis. Using the RNAstructure Design program, we solved 99 of the 100 design problems posed by Eterna using the ACGT alphabet or supplementing with P-Z pairs. Extending the alphabet reduced the propensity of sequences to fold into off-target structures, as evaluated by the normalized ensemble defect (NED). The NED values were improved relative to those from the Eterna example solutions in 91 of 99 cases where Eterna-player solutions were provided. P-Z-containing designs had average NED values of 0.040, significantly below the 0.074 of standard-DNA-only designs, and inclusion of the P-Z pairs decreased the time needed to converge on a design. This work provides a sample pipeline for inclusion of any expanded alphabet nucleotides into prediction and design workflows.

Biofeedback-Based Videogames: Fostering Emotion Regulation at a Diverse Community Summer Camp.

Implementing nonstigmatized mental health interventions and tools within community programs serving diverse populations may reduce inequities in access to mental health care and preventative emotional learning. One potentially impactful tool is Mightier, a heart rate biofeedback-based videogame that aims to foster emotion regulation skills and practice through game play. In a randomized controlled trial, the present study evaluated the efficacy of Mightier when utilized in a community setting. Seventy-two children (ages 7-12) from a low-cost community summer camp were randomly assigned to play Mightier for 6 weeks or continue camp activities as usual. All campers participated in biweekly social and emotional learning groups. Participants exhibited significantly greater levels of adaptive emotion regulation and lower levels of emotional dysregulation, internalizing symptoms, and externalizing behaviors after the intervention. Caregivers of participants in the intervention group also reported significantly less parenting-related stress after the intervention. When incorporated into community programs, biofeedback-based videogames can foster emotional intelligence competencies in children without access to traditional mental health services.

Evaluation of a scalable online videogame-based biofeedback program to improve emotion regulation: A descriptive study assessing parent perspectives.

Individuals and families increasingly turn to e-mental health apps for education, diagnosis, and treatment of mental health disorders and to promote mental wellness. These apps provide significant increases in convenience from existing services, since they can augment or replace services with on-demand access within the home. This raises important questions about self-selection of interventions. Who uses these applications? How do individuals perceive their own progress within applications? This study is a retrospective data analysis-based evaluation of a commercially available e-mental health program that includes biofeedback video games that help children build emotion regulation skills by demonstrating and prompting children to practice bodily focused emotion regulation techniques. The e-mental health program also provided parent psychoeducation-focused coaching at the time of the evaluation. Data collection instruments used to inform the retrospective study included parent intake surveys, gameplay engagement data, and notes from parent coaching calls. The evaluation revealed families presenting for common symptoms associated with emotion regulation deficits, as opposed to a wellness cohort looking for additional support. Families near-universally activated and engaged with the intervention, willing to carry out an extended "dose" of the e-mental health program in their home. Parents self-reported their perceptions of their children's emotion regulation progress, primarily in terms of children's increased use of emotion regulation skills, improved emotion awareness and communication, calmer demeanor, greater confidence, and improved relationships. More work is needed to understand the corresponding clinical progress from this in-home training, as well as its implications for how emotion regulation skills grow.

Cascaded Enzyme Reactions over a Three-Dimensional, Wireframe DNA Origami Scaffold.

DNA nanotechnology has increasingly been used as a platform to scaffold enzymes based on its unmatched ability to structure enzymes in a desired format. The capability to organize enzymes has taken many forms from more traditional 2D pairings on individual scaffolds to recent works introducing enzyme organizations in 3D lattices. As the ability to define nanoscale structure has grown, it is critical to fully deconstruct the impact of enzyme organization at the single-scaffold level. Here, we present an open, three-dimensional (3D) DNA wireframe octahedron which is used to create a library of spatially arranged organizations of glucose oxidase and horseradish peroxidase. We explore the contribution of enzyme spacing, arrangement, and location on the 3D scaffold to cascade activity. The experiments provide insight into enzyme scaffold design, including the insignificance of scaffold sequence makeup on activity, an increase in activity at small enzyme spacings of <10 nm, and activity changes that arise from discontinuities in scaffold architecture. Most notably, the experiments allow us to determine that enzyme colocalization itself on the DNA scaffold dominates over any specific enzyme arrangement.

Designer Nanomaterials through Programmable Assembly.

Nanoparticles have long been recognized for their unique properties, leading to exciting potential applications across optics, electronics, magnetism, and catalysis. These specific functions often require a designed organization of particles, which includes the type of order as well as placement and relative orientation of particles of the same or different kinds. DNA nanotechnology offers the ability to introduce highly addressable bonds, tailor particle interactions, and control the geometry of bindings motifs. Here, we discuss how developments in structural DNA nanotechnology have enabled greater control over 1D, 2D, and 3D particle organizations through programmable assembly. This Review focuses on how the use of DNA binding between nanocomponents and DNA structural motifs has progressively allowed the rational formation of prescribed particle organizations. We offer insight into how DNA-based motifs and elements can be further developed to control particle organizations and how particles and DNA can be integrated into nanoscale building blocks, so-called "material voxels", to realize designer nanomaterials with desired functions.

A "Proof of Concept" Randomized Controlled Trial of a Video Game Requiring Emotional Regulation to Augment Anger Control Training.

Emotional dysregulation leading to clinically significant anger and aggression is a common and substantial concern for youth and their families. While psychotropic medications and cognitive behavioral therapies can be effective, these modalities suffer from drawbacks such as significant side effects, high rates of attrition, and lack of real-world skill translation. Regulate and Gain Emotional Control (RAGE-Control) is a video game designed as an engaging augment to existing treatments. The game facilitates emotional regulation skill building through practice modulating physiological arousal while completing a challenging inhibitory task. We compared reduction in anger, aggression, oppositionality, and global severity between two treatment conditions: Anger Control Training (ACT) augmented with RAGE-Control and ACT with a sham version of the game, in a pilot double-blind randomized controlled trial. To begin to understand mechanisms of change, we examined heart rate during game play over the course of the study and explored associations between symptom changes and heart rate changes. Materials and Methods: Forty youth with clinically significant anger dyscontrol (age 10-17) were randomly assigned to 10 sessions of ACT with RAGE-Control or ACT with sham video game. Results: Both treatments similarly reduced self-reported anger. However, ACT with RAGE-Control led to larger improvements in aggression (CI: -17 to -1.0, ES: 0.55, p = 0.015); oppositionality (CI: -9.0 to -7e-6, ES: 0.48, p = 0.032); and global severity (CI: -1.0 to -5e-6, ES: 0.51, p = 0.023) relative to sham. Participants in the RAGE-Control group saw a decrease in median heart rate during game play (ß = 1.2, p < 0.001). Larger pre to post decreases in heart rate were significantly associated with larger pre to post decreases in aggression and oppositional behaviors. Discussion: Augmenting ACT with RAGE-Control reduced behavioral expression of anger, but not the experience of angry feelings, as compared to ACT with a sham version of the game. Increased heart rate control, demonstrated by reduction in median heart rate during gameplay, was associated with decreased aggression and oppositional behavior. Together these findings support that augmenting traditional treatment with technology facilitating heart rate control through skill practice translates to enhancements in real-life behavioral change. Therefore, further exploration into engaging skill-focused games such as RAGE-Control is warranted. Clinical Trial Registration:ClinicalTrials.gov, identifier: NCT01551732.

Stability of the pH-Dependent Parallel-Stranded d(CGA) Motif.

Noncanonical DNA structures that retain programmability and structural predictability are increasingly being used in DNA nanotechnology applications, in which they offer versatility beyond traditional Watson-Crick interactions. The d(CGA) triplet repeat motif is structurally dynamic and can transition between parallel-stranded homo-base paired duplex and antiparallel unimolecular hairpin in a pH-dependent manner. Here, we evaluate the thermodynamic stability and nuclease sensitivity of oligonucleotides composed of the d(CGA) motif and several structurally related sequence variants. These results show that the structural transition resulting from decreasing the pH is accompanied by both a significant energetic stabilization and decreased nuclease sensitivity as unimolecular hairpin structures are converted to parallel-stranded homo-base paired duplexes. Furthermore, the stability of the parallel-stranded duplex form can be altered by changing the 5'-nucleobase of the d(CGA) triplet and the frequency and position of the altered triplets within long stretches of d(CGA) triplets. This work offers insight into the stability and versatility of the d(CGA) triplet repeat motif and provides constraints for using this pH-adaptive structural motif for creating DNA-based nanomaterials.

Practitioner review: Co-design of digital mental health technologies with children and young people.

BACKGROUND: There is increasing interest in digital technologies to help improve children and young people's mental health, and the evidence for the effectiveness for these approaches is rising. However, there is concern regarding levels of user engagement, uptake and adherence. Key guidance regarding digital health interventions stress the importance of early user input in the development, evaluation and implementation of technologies to help ensure they are engaging, feasible, acceptable and potentially effective. Co-design is a process of active involvement of stakeholders, requiring a change from the traditional approaches to intervention development. However, there is a lack of literature to inform the co-design of digital technologies to help child and adolescent mental health. METHODS: We reviewed the literature and practice in the co-design of digital mental health technologies with children and young people. We searched Medline, PsycInfo and Web of Science databases, guidelines, reviews and reference lists, contacted key authors for relevant studies, and extracted key themes on aspects of co-design relevant to practice. We supplemented this with case studies and methods reported by researchers working in the field. RESULTS: We identified 25 original articles and 30 digital mental health technologies that were designed/developed with children and young people. The themes identified were as follows: principles of co-design (including potential stakeholders and stages of involvement), methods of involving and engaging the range of users, co-designing the prototype and the challenges of co-design. CONCLUSIONS: Co-design involves all relevant stakeholders throughout the life and research cycle of the programme. This review helps to inform practitioners and researchers interested in the development of digital health technologies for children and young people. Future work in this field will need to consider the changing face of technology, methods of engaging with the diversity in the user group, and the evaluation of the co-design process and its impact on the technology.

Nucleic acid-cleaving catalytic DNA for sensing and therapeutics.

DNAzymes with nucleic acid-cleaving catalytic activity are increasing in versatility through concerted efforts to discover new sequences with unique functions, and they are generating excitement in the sensing community as cheap, stable, amplifiable detection elements. This review provides a comprehensive list and detailed descriptions of the DNAzymes identified to date, classified by their associated small molecule or ion needed for catalysis; of note, this classification clarifies conserved regions of various DNAzymes that are not obvious in the literature. Furthermore, we detail the breadth of functionality of these DNA sequences as well as the range of reaction conditions under which they are useful. In addition, the utility of the DNAzymes in a variety of sensing and therapeutic applications is presented, detailing both their advantages and disadvantages.

Ordered three-dimensional nanomaterials using DNA-prescribed and valence-controlled material voxels.

The ability to organize nanoscale objects into well-defined three-dimensional (3D) arrays can translate advances in nanoscale synthesis into targeted material fabrication. Despite successes in nanoparticle assembly, most extant methods are system specific and not fully compatible with biomolecules. Here, we report a platform for creating distinct 3D ordered arrays from different nanomaterials using DNA-prescribed and valence-controlled material voxels. These material voxels consist of 3D DNA frames that integrate nano-objects within their scaffold, thus enabling the object's valence and coordination to be determined by the frame's vertices, which can bind to each other through hybridization. Such DNA material voxels define the lattice symmetry through the spatially prescribed valence decoupling the 3D assembly process from the nature of the nanocomponents, such as their intrinsic properties and shapes. We show this by assembling metallic and semiconductor nanoparticles and also protein superlattices. We support the technological potential of such an assembly approach by fabricating light-emitting 3D arrays with diffraction-limited spectral purity and 3D enzymatic arrays with increased activity.

Light-Induced Reversible DNA Ligation of Gold Nanoparticle Superlattices.

DNA-mediated self-assembly of nanoparticles has been of great interest because it enables access to nanoparticle superstructures that cannot be synthesized otherwise. However, the programmability of higher order nanoparticle structures can be easily lost under DNA denaturing conditions. Here, we demonstrate that light can be employed as an external stimulus to master the stability of nanoparticle superlattices (SLs) via the promotion of a reversible photoligation of DNA in SLs. The oligonucleotides attached to the nanoparticles are encoded to ligate using 365 nm light, effectively locking the SLs and rendering them stable under DNA denaturing conditions. The reversible process of unlocking these structures is possible by irradiation with light at 315 nm, recovering the structures to their natural state. Our work inspires an alternative research direction toward postassembly manipulation of nanoparticle superstructures using external stimuli as a tool to enrich the library of additional material forms and their application in different media and environments.

Controlling the Catalytic Functions of DNAzymes within Constitutional Dynamic Networks of DNA Nanostructures.

Mimicking complex cellular dynamic chemical networks being up-regulated or down-regulated by external triggers is one of the challenges in systems chemistry. Constitutional dynamic networks (CDNs), composed of exchangeable components that respond to environmental triggers by self-adaption, provide general means to mimic biosystems. We use the structural and functional information encoded in nucleic acid nanostructures to construct effector (input)-triggered constitutional dynamic networks that reveal adaptable catalytic properties. Specifically, CDNs composed of four exchangeable constituents, AA', BA', AB', and BB', are constructed. In the presence of an effector (input) that controls the stability of one of the constituents, the input-guided up-regulation or down-regulation of the CDN's constituents proceeds. As effectors we apply the fuel-strand stabilization of one of the CDN constituents by the formation of the T-A·T triplex structure, or by the K+-ion-induced stabilization of one of the CDN constituents, via the formation of a K+-ion-stabilized G-quadruplex. Energetic stabilization of one of the CDN constituents leads to a new dynamically adapted network composed of up-regulated and down-regulated constituents. By applying counter triggers to the effector units, e.g., an antifuel strand or 18-crown-6-ether, reconfiguration to the original CDNs is demonstrated. The performance of the CDNs is followed by the catalytic activities of the constituents and by complementary quantitative gel electrophoresis experiments. The orthogonal triggered and switchable operation of the CDNs is highlighted.

pH- and ligand-induced release of loads from DNA-acrylamide hydrogel microcapsules.

Herein, a method to construct stimuli-responsive DNA-acrylamide-based hydrogel microcapsules has been presented. This method involves the use of polyacrylamide chains modified with predesigned nucleic acid hairpin units and optionally single-strand tethers that provide the required hybridization and recognition functions to yield substrate-loaded stimuli-responsive hydrogel-based microcapsules. The synthesis of the microcapsules involves the loading of CaCO3 microparticles with the respective load substrates and the functionalization of the CaCO3 template particles with nucleic acid promoter units. In the presence of the hairpin-modified acrylamide chains, the promoter units induce the hybridization chain reaction (HCR), which leads to the formation of a hydrogel coating, which, after the dissociation of the CaCO3 cores, yields substrate-loaded stimuli-responsive hydrogel microcapsules. One of the microcapsule systems includes, in the hairpin-modified acrylamide constructs, and in the subsequent HCR-generated hydrogel shells, the caged sequences of anti-ATP or anti-cocaine aptamers. In the presence of ATP or cocaine, the duplex-caged aptamer sequences are separated via the formation of ATP- or cocaine-aptamer complexes, which results in the partial separation of the microcapsules and the release of the loads. The second type of microcapsule is cooperatively stabilized by bridges generated by HCR and pH-sensitive duplex units. Under acidic conditions, the pH-sensitive bridges dissociate via the formation of i-motif structures, which results in an increase in the fluidity of the microcapsule shells and the release of the loads. Preliminary studies indicate that ATP- or pH-responsive microcapsules loaded with the anticancer drug, doxorubicin, have a selective cytotoxic effect on MDA-MB-231 cancer cells.

Stimuli-Responsive DNA-Based Hydrogels: From Basic Principles to Applications.

The base sequence of nucleic acids encodes structural and functional information into the DNA biopolymer. External stimuli such as metal ions, pH, light, or added nucleic acid fuel strands provide triggers to reversibly switch nucleic acid structures such as metal-ion-bridged duplexes, i-motifs, triplex nucleic acids, G-quadruplexes, or programmed double-stranded hybrids of oligonucleotides (DNA). The signal-triggered oligonucleotide structures have been broadly applied to develop switchable DNA nanostructures and DNA machines, and these stimuli-responsive assemblies provide functional scaffolds for the rapidly developing area of DNA nanotechnology. Stimuli-responsive hydrogels undergoing signal-triggered hydrogel-to-solution transitions or signal-controlled stiffness changes attract substantial interest as functional matrices for controlled drug delivery, materials exhibiting switchable mechanical properties, acting as valves or actuators, and "smart" materials for sensing and information processing. The integration of stimuli-responsive oligonucleotides with hydrogel-forming polymers provides versatile means to exploit the functional information encoded in the nucleic acid sequences to yield stimuli-responsive hydrogels exhibiting switchable physical, structural, and chemical properties. Stimuli-responsive DNA-based nucleic acid structures are integrated in acrylamide polymer chains and reversible, switchable hydrogel-to-solution transitions of the systems are demonstrated by applying external triggers, such as metal ions, pH-responsive strands, G-quadruplex, and appropriate counter triggers that bridge and dissociate the polymer chains. By combining stimuli-responsive nucleic acid bridges with thermosensitive poly(N-isopropylacrylamide) (pNIPAM) chains, systems undergoing reversible solution ↔ hydrogel ↔ solid transitions are demonstrated. Specifically, by bridging acrylamide polymer chains by two nucleic acid functionalities, where one type of bridging unit provides a stimuli-responsive element and the second unit acts as internal "bridging memory", shape-memory hydrogels undergoing reversible and switchable transitions between shaped hydrogels and shapeless quasi-liquid states are demonstrated. By using stimuli-responsive hydrogel cross-linking units that can assemble the bridging units by two different input signals, the orthogonally-triggered functions of the shape-memory were shown. Furthermore, a versatile approach to assemble stimuli-responsive DNA-based acrylamide hydrogel films on surfaces is presented. The method involves the activation of the hybridization chain-reaction (HCR) by a surface-confined promoter strand, in the presence of acrylamide chains modified with two DNA hairpin structures and appropriate stimuli-responsive tethers. The resulting hydrogel-modified surfaces revealed switchable stiffness properties and signal-triggered catalytic functions. By applying the method to assemble the hydrogel microparticles, substrate-loaded, stimuli-responsive microcapsules are prepared. The signal-triggered DNA-based hydrogel microcapsules are applied as drug carriers for controlled release. The different potential applications and future perspectives of stimuli responsive hydrogels are discussed. Specifically, the use of these smart materials and assemblies as carriers for controlled drug release and as shape-memory matrices for information storage and inscription and the use of surface-confined stimuli-responsive hydrogels, exhibiting switchable stiffness properties, for catalysis and controlled growth of cells are discussed.

Biophysics of Artificially Expanded Genetic Information Systems. Thermodynamics of DNA Duplexes Containing Matches and Mismatches Involving 2-Amino-3-nitropyridin-6-one (Z) and Imidazo[1,2-a]-1,3,5-triazin-4(8H)one (P).

Synthetic nucleobases presenting non-Watson-Crick arrangements of hydrogen bond donor and acceptor groups can form additional nucleotide pairs that stabilize duplex DNA independent of the standard A:T and G:C pairs. The pair between 2-amino-3-nitropyridin-6-one 2'-deoxyriboside (presenting a {donor-donor-acceptor} hydrogen bonding pattern on the Watson-Crick face of the small component, trivially designated Z) and imidazo[1,2-a]-1,3,5-triazin-4(8H)one 2'-deoxyriboside (presenting an {acceptor-acceptor-donor} hydrogen bonding pattern on the large component, trivially designated P) is one of these extra pairs for which a substantial amount of molecular biology has been developed. Here, we report the results of UV absorbance melting measurements and determine the energetics of binding of DNA strands containing Z and P to give short duplexes containing Z:P pairs as well as various mismatches comprising Z and P. All measurements were done at 1 M NaCl in buffer (10 mM Na cacodylate, 0.5 mM EDTA, pH 7.0). Thermodynamic parameters (ΔH°, ΔS°, and ΔG°37) for oligonucleotide hybridization were extracted. Consistent with the Watson-Crick model that considers both geometric and hydrogen bonding complementarity, the Z:P pair was found to contribute more to duplex stability than any mismatches involving either nonstandard nucleotide. Further, the Z:P pair is more stable than a C:G pair. The Z:G pair was found to be the most stable mismatch, forming either a deprotonated mismatched pair or a wobble base pair analogous to the stable T:G mismatch. The C:P pair is less stable, perhaps analogous to the wobble pair observed for C:O6-methyl-G, in which the pyrimidine is displaced into the minor groove. The Z:A and T:P mismatches are much less stable. Parameters for predicting the thermodynamics of oligonucleotides containing Z and P bases are provided. This represents the first case where this has been done for a synthetic genetic system.