Encoding Carbon Nanotubes with Tubular Nucleic Acids for Information Storage

DNA Origami Plasmonic Nanoantenna for Programmable Biosensing of Multiple Cytokines in Cancer Immunotherapy

Herein, we report a DNA origami plasmonic nanoantenna for the programmable surface-enhanced Raman scattering (SERS) detection of cytokine release syndrome (CRS)-associated cytokines (e.g., tumor necrosis factor-α (TNF-α) and interferon-γ (IFN-γ)) in cancer immunotherapy. Typically, the nanoantenna was made of self-assembled DNA origami nanotubes (diameter: ∼19 nm; length: ∼90 nm) attached to a silver nanoparticle-modified silicon wafer (AgNP/Si). Each DNA origami nanotube contains one miniature gold nanorod (AuNR) inside (e.g., length: ∼35 nm; width: ∼7 nm). Intriguingly, TNF-α and IFN-γ logically regulate the opening of the nanotubes and the dissociation of the AuNRs from the origami structure upon binding to their corresponding aptamers. On this basis, we constructed a complete set of Boolean logic gates that read cytokine molecules as inputs and return changes in Raman signals as outputs. Significantly, we demonstrated that the presented system enables the quantification of TNF-α and IFN-γ in the serum of tumor-bearing mice receiving different types of immunotherapies (e.g., PD1/PD-L1 complex inhibitors and STING agonists). The sensing results are consistent with those of the ELISA. This strategy fills a gap in the use of DNA origami for the detection of multiple cytokines in real systems.

Efficient data reconstruction: The bottleneck of large-scale application of DNA storage

Over the past decade, the rapid development of DNA synthesis and sequencing technologies has enabled preliminary use of DNA molecules for digital data storage, overcoming the capacity and persistence bottlenecks of silicon-based storage media. DNA storage has now been fully accomplished in the laboratory through existing biotechnology, which again demonstrates the viability of carbon-based storage media. However, the high cost and latency of data reconstruction pose challenges that hinder the practical implementation of DNA storage beyond the laboratory. In this article, we review existing advanced DNA storage methods, analyze the characteristics and performance of biotechnological approaches at various stages of data writing and reading, and discuss potential factors influencing DNA storage from the perspective of data reconstruction.

One-pot asymmetric living copolymerization-induced chiral self-assemblies and circularly polarized luminescence

Controlled synthesis of conjugated block polymers enables the optimization of their self-assembly and may lead to distinct optical properties and functionalities. Herein, we report a direct chain extension of one-handed helical poly(acyl methane) with 1-ethynyl-4-iodo-2,5-bis(octyloxy)benzene, affording well-defined π-conjugated poly(acyl methane)-b-poly(phenylene ethynylene) copolymers. Although the distinct monomers are polymerized via different mechanisms, the one-pot copolymerization follows a living polymerization manner, giving the desired optically active block copolymers with controllable molar mass and low distribution. The block copolymerization induced chiral self-assembly simultaneously due to the one-handed helicity of the poly(acyl methane) block, giving spherical nanoparticles, one-handed helices, and chiral micelles with controlled dimensions regarding the composition of the generated copolymers. Interestingly, the chiral assemblies exhibit clear circularly polarized luminescence with tunable handedness and a high dissymmetric factor.

Data Storage Using DNA

The exponential growth of global data has outpaced the storage capacities of current technologies, necessitating innovative storage strategies. DNA, as a natural medium for preserving genetic information, has emerged as a highly promising candidate for next-generation storage medium. Storing data in DNA offers several advantages, including ultrahigh physical density and exceptional durability. Facilitated by significant advancements in various technologies, such as DNA synthesis, DNA sequencing, and DNA nanotechnology, remarkable progress has been made in the field of DNA data storage over the past decade. However, several challenges still need to be addressed to realize practical applications of DNA data storage. In this review, the processes and strategies of in vitro DNA data storage are first introduced, highlighting recent advancements. Next, a brief overview of in vivo DNA data storage is provided, with a focus on the various writing strategies developed to date. At last, the challenges encountered in each step of DNA data storage are summarized and promising techniques are discussed that hold great promise in overcoming these obstacles.

Enthalpy and entropy synergistic regulation-based programmable DNA motifs for biosensing and information encryption

Deoxyribonucleic acid (DNA) provides a collection of intelligent tools for the development of information cryptography and biosensors. However, most conventional DNA regulation strategies rely solely on enthalpy regulation, which suffers from unpredictable stimuli-responsive performance and unsatisfactory accuracy due to relatively large energy fluctuations. Here, we report an enthalpy and entropy synergistic regulation-based pH-responsive A⁺/C DNA motif for programmable biosensing and information encryption. In the DNA motif, the variation in loop length alters entropic contribution, and the number of A⁺/C bases regulates enthalpy, which is verified through thermodynamic characterizations and analyses. On the basis of this straightforward strategy, the performances, such as pK_a, of the DNA motif can be precisely and predictably tuned. The DNA motifs are finally successfully applied for glucose biosensing and crypto-steganography systems, highlighting their potential in the field of biosensing and information encryption.

Surface engineering of colloidal nanoparticles

Synthesis of engineered colloidal nanoparticles (NPs) with delicate surface characteristics leads to well-defined physicochemical properties and contributes to multifunctional applications. Surface engineering of colloidal NPs can improve their stability in diverse solvents by inhibiting the interparticle attractive forces, thus providing a prerequisite for further particle manipulation, fabrication of the following materials and biological applications. During the last decades, surface engineering methods for colloidal NPs have been well-developed by numerous researchers. However, accurate control of surface properties is still an important topic. The emerging DNA/protein nanotechnology offers additional possibility of surface modification of NPs and programmable particle self-assembly. Here, we first briefly review the recent progress in surface engineering of colloidal NPs, focusing on the improved stability by grafting suitable small molecules, polymers or biological macromolecules. We then present the practical strategies for nucleic acid surface encoding of NPs and subsequent programmable assembly. Various exciting applications of these unique materials are summarized with a specific focus on the cellular uptake, bio-toxicity, imaging and diagnosis of colloidal NPs in vivo. With the growing interest in colloidal NPs in nano-biological research, we expect that this review can play an instructive role in engineering the surface properties for desired applications.

Metal-Organic Frameworks in Microfluidics Enable Fast Encapsulation/Extraction of DNA for Automated and Integrated Data Storage

DNA as an exceptional data storage medium offers high information density. However, DNA storage requires specialized equipment and tightly controlled environments for storage. Fast encapsulation within minutes for enhanced DNA stability to do away with specialized equipment and fast DNA extraction remain a challenge. Here, we report a DNA microlibrary that can be encapsulated by metal-organic frameworks (MOFs) within 10 min and extracted (5 min) in a single microfluidic chip for automated and integrated DNA-based data storage. The DNA microlibrary@MOFs enhances the stability of data-encoded DNA against harsh environments. The encoded information can be read out perfectly after accelerated aging, equivalent to being readable after 10 years of storage at 25 °C, 50% relative humidity, and 10 000 lx sunlight radiation. Moreover, the library enables fast retrieval of target data via flow cytometry and can be reproduced after each access.

Dual Lewis Acid- and Base-Responsive Terpyridine-Based Hydrogel: Programmable and Spatiotemporal Regulation of Fluorescence for Chemical-Based Information Security

A huge amount of data inundated in our daily life; there is an ever-increasing need to develop a new strategy of information encryption-decryption-erasing. Herein, a polymeric DCTpy/PAM hydrogel has been fabricated to store information via controllable Eu³⁺/Zn²⁺ ionoprinting for hierarchical and multidimensional information decryption. Eu³⁺ and Zn²⁺ have a competition and dynamic interaction toward DCTpy under NH₃ stimuli in the polymeric DCTpy/PAM hydrogel network. The Eu(III)/Zn(II)@DCTpy/PAM hydrogel exhibits light red fluorescence of Eu³⁺ due to the antenna effect. Upon the addition of NH₃, dissociation of the Eu³⁺-DCTpy complex takes place, and the Zn(II)/DCTpy/NH₃ complex is formed with both ICT (intramolecular charge-transfer) and PET (photo-induced electron-transfer) process characteristics that exhibits yellow emission color. Subsequently, HCl can quench the fluorescence of the resulting hydrogel. By integrating transparency, adhesiveness, and programmable stimuli responsiveness of the hydrogel blocks in to one system, complex, multistage, and time-controlled information storage-encryption-decryption-erasing in sequence with multidimensions is illustrated via the molecule diffusion method. This work provides a novel and representative strategy in fabricating information encryption-decryption-erasing materials with high capacity and complexity by a simple terpyridine-based hydrogel.

Emerging Approaches to DNA Data Storage: Challenges and Prospects

With the total amount of worldwide data skyrocketing, the global data storage demand is predicted to grow to 1.75 × 10¹⁴ GB by 2025. Traditional storage methods have difficulties keeping pace given that current storage media have a maximum density of 10³ GB/mm³. As such, data production will far exceed the capacity of currently available storage methods. The costs of maintaining and transferring data, as well as the limited lifespans and significant data losses associated with current technologies also demand advanced solutions for information storage. Nature offers a powerful alternative through the storage of information that defines living organisms in unique orders of four bases (A, T, C, G) located in molecules called deoxyribonucleic acid (DNA). DNA molecules as information carriers have many advantages over traditional storage media. Their high storage density, potentially low maintenance cost, ease of synthesis, and chemical modification make them an ideal alternative for information storage. To this end, rapid progress has been made over the past decade by exploiting user-defined DNA materials to encode information. In this review, we discuss the most recent advances of DNA-based data storage with a major focus on the challenges that remain in this promising field, including the current intrinsic low speed in data writing and reading and the high cost per byte stored. Alternatively, data storage relying on DNA nanostructures (as opposed to DNA sequence) as well as on other combinations of nanomaterials and biomolecules are proposed with promising technological and economic advantages. In summarizing the advances that have been made and underlining the challenges that remain, we provide a roadmap for the ongoing research in this rapidly growing field, which will enable the development of technological solutions to the global demand for superior storage methodologies.

Protein-Mimicking Nanoparticles in Biosystems

Proteins are essential elements for almost all life activities. The emergence of nanotechnology offers innovative strategies to create a diversity of nanoparticles (NPs) with intrinsic capacities of mimicking the functions of proteins. These artificial mimics are produced in a cost-efficient and controllable manner, with their protein-mimicking performances comparable or superior to those of natural proteins. Moreover, they can be endowed with additional functionalities that are absent in natural proteins, such as cargo loading, active targeting, membrane penetrating, and multistimuli responding. Therefore, protein-mimicking NPs have been utilized more and more often in biosystems for a wide range of applications including detection, imaging, diagnosis, and therapy. To highlight recent progress in this broad field, herein, representative protein-mimicking NPs that fall into one of the four distinct categories are summarized: mimics of enzymes (nanozymes), mimics of fluorescent proteins, NPs with high affinity binding to specific proteins or DNA sequences, and mimics of protein scaffolds. This review covers their subclassifications, characteristic features, functioning mechanisms, as well as the extensive exploitation of their great potential for biological and biomedical purposes. Finally, the challenges and prospects in future development of protein-mimicking NPs are discussed.

Preservation and Encryption in DNA Digital Data Storage

The exponential growth of the total amount of global data presents a huge challenge to mainstream storage media. The emergence of molecular digital storage inspires the development of the new-generation higher-density digital data storage. In particular, DNA with high storage density, reproducibility, and long recoverable lifetime behaves the ideal representative of molecular digital storage media. With the development of DNA synthesis and sequencing technologies and the reduction of cost, DNA digital storage has attracted more and more attention and achieved significant breakthroughs. Herein, this Review briefly describes the workflow of DNA storage, and highlights the storage step of DNA digital data storage. Then, according to different information storage forms, the current DNA information encryption methods are emphatically expounded. Finally, the brief perspectives on the current challenges and optimizing proposals in DNA information preservation and encryption are presented.

Continuously Multiplexed Ultrastrong Raman Probes by Precise Isotopic Polymer Backbone Doping for Multidimensional Information Storage and Encryption

Raman-based super multiplexing has attracted great interest in imaging, biological analysis, identity security, and information storage. It still remains a great challenge to synthesize a large number of different Raman-active molecules to fulfill the Raman color palette. Here, we report a facile and systematic strategy to construct continuously multiplexed ultrastrong Raman probes. By precisely incorporating different ratios of ¹³C isotope into the backbone of poly(deca-4,6-diynedioic acid) (PDDA), we can obtain a library of PDDAs with tunable double-bond Raman frequencies and adjustable intensity ratios of two triple-bond (¹³C≡¹³C and ¹²C≡¹²C) Raman peaks, while retaining the ultrastrong Raman signals and physicochemical properties of the polymer. We also demonstrate the successful application of ¹³C-doped PDDAs as security inks to generate a novel 3D matrix barcode system for information encryption and high-density data storage. The isotopically doped PDDA series herein pave a new way to advance Raman-based super multiplexing for diverse applications.

A six-plex switchable DNA origami cipher disk for tandem-in-time cryptography

We report a DNA origami cipher disk (DOCD) allowing random, continuous and reversible switchover between six visibly different patterns in response to the input DNA strands. A DOCD-enabled tandem-in-time cryptographic protocol was thereby established by using a string of DNA strands as a carrier for accurate information encoding and transmission.

Unlocking Chemically Encrypted Information Using Three Types of External Stimuli

Encryption is critical to information security; however, existing chemical-based information encryption strategies are still in their infancy. We report here a new approach to chemical encryption involving a supramolecular gel QR (quick response) code with multiple encryption functions. Three color "turn-on" supramolecular polymer gels, G1-G3, were prepared that produce pink, purple, and yellow colors when subject to treatment with acetic acid vapor, UV light, and methanolic FeCl₃, respectively. As the result of hydrogen-bonding interactions at the gel interfaces, the three gels can be assembled to produce gel G4. Engraving a QR code pattern onto G4 then gave gel G5. When one or two stimuli are applied to the individual pieces corresponding to the QR engraved versions of the gels G1-G3 making up G5, a complete scannable pattern is not displayed, and the stored information cannot be recognized. Only when three different stimuli are applied at the same time does G5 give a complete recognizable pattern allowing the stored information to be retrieved. This strategy was applied to the decryption-based opening of a coded lock.

Design Approaches and Computational Tools for DNA Nanostructures

Designing a structure in nanoscale with desired shape and properties has been enabled by structural DNA nanotechnology. Design strategies in this research field have evolved to interpret various aspects of increasingly more complex nanoscale assembly and to realize molecular-level functionality by exploring static to dynamic characteristics of the target structure. Computational tools have naturally been of significant interest as they are essential to achieve a fine control over both shape and physicochemical properties of the structure. Here, we review the basic design principles of structural DNA nanotechnology together with its computational analysis and design tools.

Functionalized carbon nanotubes: synthesis, properties and applications in water purification, drug delivery, and material and biomedical sciences

Carbon nanotubes (CNTs) are considered as one of the ideal materials due to their high surface area, high aspect ratio, and impressive material properties, such as mechanical strength, and thermal and electrical conductivity, for the manufacture of next generation composite materials. In spite of the mentioned attractive features, they tend to agglomerate due to their inherent chemical structure which limits their application. Surface modification is required to overcome the agglomeration and increase their dispersability leading to enhanced interactions of the functionalized CNTs with matrix materials/polymer matrices. Recent developments concerning reliable methods for the functionalization of carbon nanotubes offer an additional thrust towards extending their application areas. By chemical functionalization, organic functional groups are generated/attached to the surfaces as well as the tip of CNTs which opens up the possibilities for tailoring the properties of nanotubes and extending their application areas. Different research efforts have been devoted towards both covalent and non-covalent functionalization for different applications. Functionalized CNTs have been used successfully for the development of high quality nanocomposites, finding wide application as chemical and biological sensors, in optoelectronics and catalysis. Non covalently functionalized carbon nanotubes have been used as a substrate for the immobilization of a large variety of biomolecules to impart specific recognition properties for the development of miniaturized biosensors as well as designing of novel bioactive nanomaterials. Functionalized CNTs have also been demonstrated as one of the promising nanomaterials for the decontamination of water due to their high adsorption capacity and specificity for various contaminants. Specifically modified CNTs have been utilized for bone tissue engineering and as a novel and versatile drug delivery vehicle. This review article discusses in short the synthesis, properties and applications of CNTs. This includes the need for functionalization of CNTs, methods and types of functionalization, and properties of functionalized CNTs and their applications especially with respect to material and biomedical sciences, water purification, and drug delivery systems.

Combinatorial constraint coding based on the EORS algorithm in DNA storage

The development of information technology has produced massive amounts of data, which has brought severe challenges to information storage. Traditional electronic storage media cannot keep up with the ever-increasing demand for data storage, but in its place DNA has emerged as a feasible storage medium with high density, large storage capacity and strong durability. In DNA data storage, many different approaches can be used to encode data into codewords. DNA coding is a key step in DNA storage and can directly affect storage performance and data integrity. However, since errors are prone to occur in DNA synthesis and sequencing, and non-specific hybridization is prone to occur in the solution, how to effectively encode DNA has become an urgent problem to be solved. In this article, we propose a DNA storage coding method based on the equilibrium optimization random search (EORS) algorithm, which meets the Hamming distance, GC content and no-runlength constraints and can reduce the error rate in storage. Simulation experiments have shown that the size of the DNA storage code set constructed by the EORS algorithm that meets the combination constraints has increased by an average of 11% compared with previous work. The increase in the code set means that shorter DNA chains can be used to store more data.

Bottom-Up Fabrication of DNA-Templated Electronic Nanomaterials and Their Characterization

Bottom-up fabrication using DNA is a promising approach for the creation of nanoarchitectures. Accordingly, nanomaterials with specific electronic, photonic, or other functions are precisely and programmably positioned on DNA nanostructures from a disordered collection of smaller parts. These self-assembled structures offer significant potential in many domains such as sensing, drug delivery, and electronic device manufacturing. This review describes recent progress in organizing nanoscale morphologies of metals, semiconductors, and carbon nanotubes using DNA templates. We describe common substrates, DNA templates, seeding, plating, nanomaterial placement, and methods for structural and electrical characterization. Finally, our outlook for DNA-enabled bottom-up nanofabrication of materials is presented.

Minimum Free Energy Coding for DNA Storage

With the development of information technology, huge amounts of data are produced at the same time. How to store data efficiently and at low cost has become an urgent problem. DNA is a high-density and persistent medium, making DNA storage a viable solution. In a DNA data storage system, the first consideration is how to encode the data effectively into code words. However, DNA strands are prone to non-specific hybridization during the hybridization reaction process and are prone to errors during synthesis and sequencing. In order to reduce the error rate, a thermodynamic minimum free energy (MFE) constraint is proposed and applied to the construction of coding sets for DNA storage. The Brownian multi-verse optimizer (BMVO) algorithm, based on the Multi-verse optimizer (MVO) algorithm, incorporates the idea of Brownian motion and Nelder-Mead method, and it is used to design a better DNA storage coding set. In addition, compared with previous works, the coding set has been increasing by 4%-50% in size and has better thermodynamic properties. With the improvement of the quality of the DNA coding set, the accuracy of reading and writing and the robustness of the DNA storage system are also enhanced.

Construction of Molecular Sensing and Logic Systems Based on Site-Occupying Effect-Modulated MOF-DNA Interaction

Interactions between metal-organic frameworks (MOFs) and nucleic acids are of great importance in molecular assembly. However, current MOF-nucleic acid interactions lack diversity and are normally realized in an uncontrollable manner. Herein, the interaction of zirconium-based MOFs (Zr-MOFs) with nucleic acids is enabled by the formation of Zr-O-P bonds and further manipulated by a phosphate-induced site-occupying effect. Covering Zr ions in clusters of MOFs with phosphates impedes the formation of Zr-O-P bonds with nucleic acids, rendering the MOF-nucleic acid interaction tunable and stimulus-responsive. Notably, the experimental results demonstrate that various phosphates, Zr-MOFs, and nucleic acids can all be adopted in the tunable interaction. On the basis of these findings, fluorescent DNA and typical Zr-MOFs are proposed as functional probe-quencher pairs to establish molecular sensing and logic systems. Accordingly, alkaline phosphatase and inorganic pyrophosphatase can be quantified simultaneously, and the overall relation of different phosphates and phosphatases is facilely displayed. The work provides a general strategy for modulating MOF-nucleic acid interactions, which is conducive to the development of molecular intelligent systems.

Propelling DNA Computing with Materials' Power: Recent Advancements in Innovative DNA Logic Computing Systems and Smart Bio-Applications

DNA computing is recognized as one of the most outstanding candidates of next-generation molecular computers that perform Boolean logic using DNAs as basic elements. Benefiting from DNAs' inherent merits of low-cost, easy-synthesis, excellent biocompatibility, and high programmability, DNA computing has evoked substantial interests and gained burgeoning advancements in recent decades, and also exhibited amazing magic in smart bio-applications. In this review, recent achievements of DNA logic computing systems using multifarious materials as building blocks are summarized. Initially, the operating principles and functions of different logic devices (common logic gates, advanced arithmetic and non-arithmetic logic devices, versatile logic library, etc.) are elaborated. Afterward, state-of-the-art DNA computing systems based on diverse "toolbox" materials, including typical functional DNA motifs (aptamer, metal-ion dependent DNAzyme, G-quadruplex, i-motif, triplex, etc.), DNA tool-enzymes, non-DNA biomaterials (natural enzyme, protein, antibody), nanomaterials (AuNPs, magnetic beads, graphene oxide, polydopamine nanoparticles, carbon nanotubes, DNA-templated nanoclusters, upconversion nanoparticles, quantum dots, etc.) or polymers, 2D/3D DNA nanostructures (circular/interlocked DNA, DNA tetrahedron/polyhedron, DNA origami, etc.) are reviewed. The smart bio-applications of DNA computing to the fields of intelligent analysis/diagnosis, cell imaging/therapy, amongst others, are further outlined. More importantly, current "Achilles' heels" and challenges are discussed, and future promising directions of this field are also recommended.

Dynamic Covalent Formation of Concave Disulfide Macrocycles Mechanically Interlocked with Single-Walled Carbon Nanotubes

The formation of discrete macrocycles wrapped around single-walled carbon nanotubes (SWCNTs) has recently emerged as an appealing strategy to functionalize these carbon nanomaterials and modify their properties. Here, we demonstrate that the reversible disulfide exchange reaction, which proceeds under mild conditions, can install relatively large amounts of mechanically interlocked disulfide macrocycles on the one-dimensional nanotubes. Size-selective functionalization of a mixture of SWCNTs of different diameters were observed, presumably arising from error correction and the presence of relatively rigid, curved π-systems in the key building blocks. A combination of UV/Vis/NIR, Raman, photoluminescence excitation, and transient absorption spectroscopy indicated that the small (6,4)-SWCNTs were predominantly functionalized by the small macrocycles 1₂ , whereas the larger (6,5)-SWCNTs were an ideal match for the larger macrocycles 2₂ . This size selectivity, which was rationalized computationally, could prove useful for the purification of nanotube mixtures, since the disulfide macrocycles can be removed quantitatively under mild reductive conditions.

Carbon Nanotubes and Short Cytosine-Rich Telomeric DNA Oligomeres as Platforms for Controlled Release of Doxorubicin-A Molecular Dynamics Study

This work deals with molecular dynamics analysis of properties of systems composed of carbon nanotubes and short telomeric DNA strands able to fold into i-motif structures at slightly acidic pH conditions. The studies are focused on possible application of such constructs as pH-controlled drug delivery and release systems. We study two different approaches. The first assumes that folding/unfolding property of these DNA strands might realize a gate closing/opening mechanism with carbon nanotube as a container for drug molecules. The second approach assumes that these DNA strands can modulate the drug intercalating property as a function of pH. As a model drug molecule we used doxorubicin. We found that the first approach is impossible to realize because doxorubicin is not effectively locked in the nanotube interior by DNA oligonuceotides. The second approach is more promising though direct drug release was not observed in unbiased molecular dynamics simulations. However, by applying detailed analysis of pair interaction energies, mobilities and potential of mean force we can show that doxorubicin can be released when the DNA strands fold into i-motifs. Carbon nanotube in that latter case acts mainly as a carrier for active phase which is composed of DNA fragments able to fold into noncanonical tetraplexes (i-motif).

Deformation-Resistant, Double-Layer DNA Self-Assembled Nanoraft with High Positioning Precision

The precise control and localization of a single entity on a stiff and rigid interface are crucial for exploring interentity interactions. A critical challenge for the precise positioning of a single entity on a substrate lies in how to construct a solid and flat interface with high positioning precision. Herein, we developed a solid DNA self-assembled nanoraft with high conformational stability by constructing a double-layer DNA origami. Compared with conventional single-layer DNA origami, the double-layer nanoraft showed higher deformation resistance capability with the nanorafts possessing higher structural integrity. Further, we analyzed the deformability of these two DNA origamis by structural reconstruction simulation, the results of which were significantly consistent with transmission electron microscopy experimental results. Using the deformation-resistant DNA self-assembled nanoraft, we achieved the precise positioning of single-stranded DNA probes on the DNA nanointerface by visualizing the AuNPs captured by the probes. Compared with the interface constructed by single-layer DNA origami, the distance between AuNPs on the two-layer DNA origami was more approximate to the theoretical value that we designed. The rigid nanointerface with high deformation resistance capability thus provides a powerful means for facilitating the self-assembly of heterogeneous elements with precisely controlled spacing and position.

Molecular Dynamics Study of the Interaction of Carbon Nanotubes With Telomeric DNA Fragment Containing Noncanonical G-quadruplex and i-Motif Forms

This work deals with molecular dynamics simulations of systems composed of telomeric dsDNA fragments, iG, and functionalized carbon nanotubes, fCNT. The iG contains 90 nucleotides in total and in its middle part the noncanonical i-motif and G-quadruplex are formed. Two chiralities of the fCNT were used, i.e., (10,0) and (20,0) and these nanotubes were either on-tip functionalized by guanine containing functional groups or left without functionalization. We proposed a dedicated computational procedure, based on the replica exchange concept, for finding a thermodynamically optimal conformation of iG and fCNT without destroying the very fragile noncanonical parts of the iG. We found that iG forms a V-shape spatial structure with the noncanonical fragments located at the edge and the remaining dsDNA strands forming the arms of V letter. The optimal configuration of iG in reference to fCNT strongly depends on the on-tip functionalization of the fCNT. The carbon nanotube without functionalization moves freely between the dsDNA arms, while the presence of guanine residues leads to immobilization of the fCNT and preferential location of the nanotube tip near the junction between the dsDNA duplex and i-motif and G-quadruplex. We also studied how the presence of fCNT affects the stability of the i-motif at the neutral pH when the cytosine pairs are nonprotonated. We concluded that carbon nanotubes do not improve the stability of the spatial structure of i-motif also when it is a part of a bigger structure like the iG. Such an effect was described in literature in reference to carboxylated nanotubes. Our current results suggest that the stabilization of i-motif is most probably related to easy formation of semiprotonated cytosine pairs at neutral pH due to interaction with carboxylated carbon nanotubes.