Molecular architectonics of DNA for functional nanoarchitectures

A triple-aptamer tetrahedral DNA nanostructures based carbon-nanotube-array transistor biosensor for rapid virus detection

Outbreaks of infectious viruses cause enormous challenges to global public health. Recently, the coronavirus disease 2019 (COVID-19) induced by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has severely threatened human health and resulted in the global pandemic. A strategy to detect SARS-CoV-2 with both fast sensing speed and high accuracy is urgently required. Here, rapid detection of SARS-CoV-2 antigen using carbon-nanotube-array-based thin-film transistor (CNT-array-based TFT) biosensors merged with tetrahedral DNA nanostructures (TDNs) and triple aptamers is demonstrated for the first time. Compared with CNT-network-based TFT biosensors and metal-electrode-based CNT-TFT biosensors, the response of CNT-array-based TFT biosensors can be enhanced up to 102% for SARS-CoV-2 receptor-binding domain (RBD) detection, which is supported by its sensing mechanism. By combining TDNs with triple aptamers, the biosensor has realized the wildtype SARS-CoV-2 RBD detection in a broad detection range spanning eight orders of magnitude with a low limit of detection (LOD) of 10 aM (6 copies/μL) owing to the improved protein capture efficiency. Moreover, the triple-aptamer biosensor platform has achieved the detection of SARS-CoV-2 Omicron RBD in a low LOD of 6 aM (3.6 copies/μL). Additionally, the CNT-array-based TFT biosensors have exhibited excellent specificity, enabling identification among SARS-CoV-2 antigen, SARS-CoV antigen and MERS-CoV antigen. The platform of CNT-array-based TFT biosensors combined with TDNs and triple aptamers provides a high-performance and rapid approach for SARS-CoV-2 detection, and its versatility by altering specific aptamers enables the possibility for rapid virus detection.

Nanoclusters with specific DNA overhangs: modifying configurability, engineering contrary logic pairs and the parity generator/checker for error detection

The most promising alternative for next-generation molecular computers is biocomputing, which uses DNAs as its primary building blocks to perform a Boolean operation. DNA nanoclusters (NCs) have emerged as promising candidates for biosensing applications due to their unique self-assembly properties and programmability. It has been demonstrated that adding DNA overhangs to DNA NCs improves their adaptability in identifying specific biomolecular interactions. A recent proposal in DNA computing is the concept of "contrary logic pairs (CLPs)" executed by employing a DNA hybrid architecture as a universal platform. We have designed thymine overhang-modified DNA-templated NCs (T-Au/Ag NCs). These NCs serve as a chemosensing ensemble platform, where the presence of HgII ions mediates the formation of M-Au/Ag NCs. The resulting NCs exhibit the capability to drive elementary CLPs (YES, NOT, OR, NOR, INH and IMP) as well as complex logic operations (XOR and XNOR). Additionally, they can be utilized for advanced non-arithmetic DNA logic devices like a parity generator (pG) and a parity checker (pC) for "error detection". Bit errors are an unavoidable and common occurrence during any computing. A cascade of XOR operations was used to evaluate these errors by introducing the pG and pC at the transmitting (TX) and receiving (RX) ends in binary transmission, respectively, which has devastating implications for reliable logic circuits, especially in advanced logic computation. Moreover, an even/odd natural number from 0 to 9 distinguishable pC was designed based on a dual-source responsive computing platform. This work offers inspiring avenues for a cost-effective strategy to construct highly-intelligent DNA computing devices by enhancing the multi-input responsive single DNA platform concept.

Template-Assisted Assembly of Hybrid DNA/RNA Nanostructures Using Branched Oligodeoxy- and Oligoribonucleotides

A template-assisted assembly approach to a C24 fullerene-like double-stranded DNA polyhedral shell is proposed. The assembly employed a supramolecular oligonucleotide dendrimer as a 3D template that was obtained via the hybridization of siRNA strands and a single-stranded DNA oligonucleotide joined to three- or four-way branched junctions. A four-way branched oligonucleotide building block (a starlet) was designed for the assembly of the shell composed of three identical self-complementary DNA single strands and a single RNA strand for hybridization to the DNA oligonucleotides of the template. To prevent premature auto-hybridization of the self-complementary oligonucleotides in the starlet, a photolabile protecting group was introduced via the N3-substituted thymidine phosphoramidite. Cleavable linkers such as a disulfide linkage, RNase A sensitive triribonucleotides, and di- and trideoxynucleotides were incorporated into the starlet and template at specific points to guide the post-assembly disconnection of the shell from the template, and enzymatic disassembly of the template and the shell in biological media. At the same time, siRNA strands were modified with 2'-OMe ribonucleotides and phosphorothioate groups in certain positions to stabilize toward enzymatic digestion. We report herein a solid-phase synthesis of branched oligodeoxy and oligoribonucleotide building blocks for the DNA/RNA dendritic template and the branched DNA starlet for a template-assisted construction of a C24 fullerene-like DNA shell after initial molecular modeling, followed by the assembly of the shell around the DNA-coated RNA dendritic template, and visualization of the resulting nanostructure by transmission electron microscopy.

Mercury mediated DNA-Au/Ag nanocluster ensembles to generate a gray code encoder for biocomputing

Boolean operations utilizing DNA as a platform for biocomputing have become a promising tool for next-generation bio-molecular computers. In the whole process of any binary data transmission, bit errors are unavoidable and commonly occur. Cascades of exclusive-OR (XOR) operations show the great potential to evaluate these errors by introducing a parity generator (pG) and a parity checker (pC). Herein, we constructed a DNA hybrid architecture platform employing a chemosensing ensemble of mercury-mediated DNA-Au/Ag nanoclusters (M-Au/Ag NCs) to operate unconventional pG/pC for "error detection". Taking advantage of pG/pC, the transmitted and received data is converted to secure information using a binary to gray code encoder. To the best of our knowledge, this is the first molecular gray code encoder for biocomputing, which discovers an exciting avenue to protect information security through sophisticated logic circuits.

Photoswitchable architecture transformation of a DNA-hybrid assembly at the microscopic and macroscopic scale

Molecular recognition-driven self-assembly employing single-stranded DNA (ssDNA) as a template is a promising approach to access complex architectures from simple building blocks. Oligonucleotide-based nanotechnology and soft-materials benefit from the high information storage density, self-correction, and memory function of DNA. Here we control these beneficial properties with light in a photoresponsive biohybrid hydrogel, adding an extra level of function to the system. An ssDNA template was combined with a complementary photo-responsive unit to reversibly switch between various functional states of the supramolecular assembly using a combination of light and heat. We studied the structural response of the hydrogel at both the microscopic and macroscopic scale using a combination of UV-vis absorption and CD spectroscopy, as well as fluorescence, transmission electron, and atomic force microscopy. The hydrogels grown from these supramolecular self-assembly systems show remarkable shape-memory properties and imprinting shape-behavior while the macroscopic shape of the materials obtained can be further manipulated by irradiation.

Molecular recognition-driven self-assembly employing single-stranded DNA (ssDNA) as a template is a promising approach to access complex architectures from simple building blocks.

Nucleic Acid Architectonics for pH-Responsive DNA Systems and Devices

Nucleic acid-based architectures have opened up numerous opportunities for basic and applied research in the field of DNA nanotechnology. The scheme of molecular architectonics of nucleic acids exploits conventional and unconventional base pairing interactions to integrate molecular partners in constructing functional molecular architectures and devices. The pH-responsive functional nucleic acid systems and devices have gained interest in diagnostics and therapeutics because of their biocompatibility and structural programmability. In this Mini-Review, we discuss recent advancements in the area of nucleic acid architectonics with a special emphasis on pH-driven molecular systems including molecular and nanoarchitectures, templated architectures and nanoclusters, nanomachines, hydrogels, targeted bioimaging, and drug delivery architectures. Finally, the Mini-Review is concluded by highlighting the challenges and opportunities for future developments.

Porous carbon nanoarchitectonics for the environment: detection and adsorption

As a post-nanotechnology concept, nanoarchitectonics has emerged from the 20th century to the 21st century. This review summarizes the recent progress in the field of metal-free porous carbon nanoarchitectonics.

Metal Complexes as DNA Synthesis and/or Repair Inhibitors: Anticancer and Antimicrobial Agents

Medicinal inorganic chemistry involving the utilization of metal-based compounds as therapeutics has become a field showing distinct promise. DNA and RNA are ideal drug targets for therapeutic intervention in the case of various diseases, such as cancer and microbial infection. Metals play a vital role in medicine, with at least 10 metals known to be essential for human life and a further 46 nonessential metals having been involved in drug therapies and diagnosis. These metal-based complexes interact with DNA in various ways, and are often delivered as prodrugs which undergo activation in vivo. Metal complexes cause DNA crosslinking, leading to the inhibition of DNA synthesis and repair. In this review, the various interactions of metal complexes with DNA nucleic acids, as well as the underlying mechanism of action, were highlighted. Furthermore, we also discussed various tools used to investigate the interaction between metal complexes and the DNA. The tools included in vitro techniques such as spectroscopy and electrophoresis, and in silico studies such as protein docking and density-functional theory that are highlighted for preclinical development.

Sequence Does Not Matter: The Biomedical Applications of DNA-Based Coatings and Cores

Biomedical applications of DNA are diverse but are usually associated with specific recognition of target nucleotide sequences or proteins and with gene delivery for therapeutic or biotechnological purposes. However, other aspects of DNA functionalities, like its nontoxicity, biodegradability, polyelectrolyte nature, stability, thermo-responsivity and charge transfer ability that are rather independent of its sequence, have recently become highly appreciated in material science and biomedicine. Whereas the latest achievements in structural DNA nanotechnology associated with DNA sequence recognition and Watson–Crick base pairing between complementary nucleotides are regularly reviewed, the recent uses of DNA as a raw material in biomedicine have not been summarized. This review paper describes the main biomedical applications of DNA that do not involve any synthesis or extraction of oligo- or polynucleotides with specified sequences. These sequence-independent applications currently include some types of drug delivery systems, biocompatible coatings, fire retardant and antimicrobial coatings and biosensors. The reinforcement of DNA properties by DNA complexation with nanoparticles is also described as a field of further research.

Fractal-Percolation Structure Architectonics in Sol-Gel Synthesis

It was developed a new technique to assess micro- and mesopores with sizes below a few nanometers. The porous materials with hierarchical fractal-percolation structure were obtained with the sol-gel method. The tetraethoxysilane hydrolysis and polycondensation reactions were performed in the presence of salts as the sources of metal oxides. The porous materials were obtained under spinodal decomposition conditions during application of the polymer sol to the substrate surface and thermal treatment of the structures. The model is based on an enhanced Kepler net of the 4612 type with hexagonal cells filled with a quasi-two-dimensional projection of the Jullien fractal after the 2nd iteration. The materials obtained with the sol-gel method were studied using the atomic force microscopy, electron microscopy, thermal desorption, as well as an AutoCAD 2022 computer simulation of the percolation transition in a two-component system using the proposed multimodal model. Based on the results obtained, a new method was suggested to assess micro- and mesopores with sizes below a few nanometrs, which cannot be analyzed using the atomic force microscopy and electron microscopy.

The Architectonics Features of Heterostructures for IR Range Detectors Based on Polycrystalline Layers of Lead Chalcogenides

A model is developed for the formation of porous intragranular architectonics of nanostructured polycrystalline layers of lead chalcogenides for photodetectors and IR emitters. The layers are obtained under the conditions of thermal evaporation in a quasi-closed volume by the “hot wall” method followed by sensitizing heat treatment in an iodine-containing atmosphere. Model concepts are developed considering the experimental results of studying the intragranular structure of lead chalcogenides through original combined AFM methods over the cross-section of porous grains (cores) encapsulated by an oxide shell (lateral force microscopy and local tunneling I–V spectroscopy).

Free Charge Carriers in Homo-Sorted π-Stacks of Donor-Acceptor Conjugates

Inspired by the high photoconversion efficiency observed in natural light-harvesting systems, the hierarchical organization of molecular building blocks has gained impetus in the past few decades. Particularly, the molecular arrangement and packing in the active layer of organic solar cells (OSCs) have garnered significant attention due to the decisive role of the nature of donor/acceptor (D/A) heterojunctions in charge carrier generation and ultimately the power conversion efficiency. This review focuses on the recent developments in emergent optoelectronic properties exhibited by self-sorted donor-on-donor/acceptor-on-acceptor arrangement of covalently linked D-A systems, highlighting the ultrafast excited state dynamics of charge transfer and transport. Segregated organization of donors and acceptors promotes the delocalization of photoinduced charges among the stacks, engendering an enhanced charge separation lifetime and percolation pathways with ambipolar conductivity and charge carrier yield. Covalently linking donors and acceptors ensure a sufficient D-A interface and interchromophoric electronic coupling as required for faster charge separation while providing better control over their supramolecular assemblies. The design strategies to attain D-A conjugate assemblies with optimal charge carrier generation efficiency, the scope of their application compared to state-of-the-art OSCs, current challenges, and future opportunities are discussed in the review. An integrated overview of rational design approaches derived from the comprehension of underlying photoinduced processes can pave the way toward superior optoelectronic devices and bring in new possibilities to the avenue of functional supramolecular architectures.

Hydrogen Bonding in Natural and Unnatural Base Pairs-A Local Vibrational Mode Study

In this work hydrogen bonding in a diverse set of 36 unnatural and the three natural Watson Crick base pairs adenine (A)-thymine (T), adenine (A)-uracil (U) and guanine (G)-cytosine (C) was assessed utilizing local vibrational force constants derived from the local mode analysis, originally introduced by Konkoli and Cremer as a unique bond strength measure based on vibrational spectroscopy. The local mode analysis was complemented by the topological analysis of the electronic density and the natural bond orbital analysis. The most interesting findings of our study are that (i) hydrogen bonding in Watson Crick base pairs is not exceptionally strong and (ii) the N-H⋯N is the most favorable hydrogen bond in both unnatural and natural base pairs while O-H⋯N/O bonds are the less favorable in unnatural base pairs and not found at all in natural base pairs. In addition, the important role of non-classical C-H⋯N/O bonds for the stabilization of base pairs was revealed, especially the role of C-H⋯O bonds in Watson Crick base pairs. Hydrogen bonding in Watson Crick base pairs modeled in the DNA via a QM/MM approach showed that the DNA environment increases the strength of the central N-H⋯N bond and the C-H⋯O bonds, and at the same time decreases the strength of the N-H⋯O bond. However, the general trends observed in the gas phase calculations remain unchanged. The new methodology presented and tested in this work provides the bioengineering community with an efficient design tool to assess and predict the type and strength of hydrogen bonding in artificial base pairs.

Molecular Architectonics-guided Design of Biomaterials

The quest for mastering the controlled engineering of dynamic molecular assemblies is the basis of molecular architectonics. The rational use of noncovalent interactions to programme the molecular assemblies allow the construction of diverse molecular and material architectures with novel functional properties and applications. Understanding and controlling the assembly of molecular systems are daunting tasks owing to the complex factors that govern at the molecular level. Molecular architectures depend on the design of functional molecular modules through the judicious selection of functional core and auxiliary units to guide the precise molecular assembly and co-assembly patterns. Biomolecules with built-in information for molecular recognition are the ultimate examples of evolutionary guided molecular recognition systems that define the structure and functions of living organisms. Explicit use of biomolecules as auxiliary units to command the molecular assemblies of functional molecules is an intriguing exercise in the scheme of molecular architectonics. In this minireview, we discuss the implementation of the principles of molecular architectonics for the development of novel biomaterials with functional properties and applications ranging from sensing, drug delivery to neurogeneration and tissue engineering. We present the molecular designs pioneered by our group owing to the requirement and scope of the article while acknowledging the designs pursued by several research groups that befit the concept.

Toehold-Mediated Selective Assembly of Compact Discrete DNA Nanostructures

Production of small discrete DNA nanostructures containing covalent junctions requires reliable methods for the synthesis and assembly of branched oligodeoxynucleotide (ODN) conjugates. This study reports an approach for self-assembly of hard-to-obtain primitive discrete DNA nanostructures-"nanoethylenes", dimers formed by double-stranded oligonucleotides using V-shaped furcate blocks. We scaled up the synthesis of V-shaped oligonucleotide conjugates using pentaerythritol-based diazide and alkyne-modified oligonucleotides using copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) and optimized the conditions for "nanoethylene" formation. Next, we designed nanoethylene-based "nanomonomers" containing pendant adapters. They demonstrated smooth and high-yield spontaneous conversion into the smallest cyclic product, DNA tetragon aka "nano-methylcyclobutane". Formation of DNA nanostructures was confirmed using native polyacrylamide gel electrophoresis (PAGE) and atomic force microscopy (AFM) and additionally studied by molecular modeling. The proposed facile approach to discrete DNA nanostructures using precise adapter-directed association expands the toolkit for the realm of DNA origami.

Silver assisted stereo-directed assembly of branched peptide nucleic acids into four-point nanostars

Branched chiral peptide nucleic acids br(4S/R)-PNA with three arms of PNA-C4 strands were constructed on a central chiral core of 4(R/S)-aminoproline as the branching center. The addition of Ag+ triggered the self-assembly of branched PNAs through the formation of C-Ag+-C metallo base pairing of the three PNA C4 arms leading to non-covalent dendrimers, whose architecture is directed by the C4(R/S)-stereocenter of core 4-aminoproline. The 4S-aminoprolyl core enabled the precise formation of four-pointed nanostars that was not realised with 4R-aminoprolyl or acyclic, achiral aminoethyl glycyl PNA cores. The dendritic assembly of 4 pointed nanostars exhibited net chirality of base stacks in CD spectra, while the base stack assembly from br(4R)-PNA 2 was overall achiral. The results demonstrate that the silver assisted, 4S-aminoproline core stereo selective chiral assembly of branched PNAs manifests into nanostar morphology. The chiral branched PNAs open new vistas in the supramolecular organization of nucleic acids.

Threading Intercalator-Induced Nanocondensates and Role of Endogenous Metal Ions in Decondensation for DNA Delivery

The interplay of condensation and decondensation of DNA plays a crucial role in chromosome maintenance and gene expression. The molecular architectonics governing the chromatin condensation-decondensation cycle are worth studying, as DNA performs unique and distinct roles in each state and switches between two states without the loss of structural and functional integrity. This phenomenon has been adapted and implemented in transfection studies. Effective gene delivery into the cells to achieve respectable transfection efficiency has remained a challenge and emphasizes the need for understanding the steps involved in DNA delivery and transfection. Especially, recognizing the factors that effectively regulate DNA decondensation can provide logical solutions to the hurdles affecting the transfection efficiency. We designed a set of small molecule-based threading intercalation ligands as model condensing agents to study various factors influencing the DNA condensation and decondensation process. This study revealed condensation of DNA into nanocondensate by the threading intercalator and endogenous stimuli induced effective decondensation. Further, DNA nanocondensates are tracked using the intrinsic fluorescence in the lower pH of endocytic pathway and were evaluated as nonviral vectors for in cellulo delivery of plasmids. The correlation of decondensation of DNA nanocondensate with endogenous metal ions at their physiological concentrations provided valuable insights and implications for intracellular DNA delivery.

A multifunctional DNA nanostructure based on multicolor FRET for nuclease activity assay

We develop a four-color fluorescent probe for ratiometric detection of multiple nucleases based on multistep fluorescence resonance energy transfer.