Structural DNA nanotechnology at the nexus of next-generation bio-applications: challenges and perspectives

DNA nanotechnology has significantly progressed in the last four decades, creating nucleic acid structures widely used in various biological applications. The structural flexibility, programmability, and multiform customization of DNA-based nanostructures make them ideal for creating structures of all sizes and shapes and multivalent drug delivery systems. Since then, DNA nanotechnology has advanced significantly, and numerous DNA nanostructures have been used in biology and other scientific disciplines. Despite the progress made in DNA nanotechnology, challenges still need to be addressed before DNA nanostructures can be widely used in biological interfaces. We can open the door for upcoming uses of DNA nanoparticles by tackling these issues and looking into new avenues. The historical development of various DNA nanomaterials has been thoroughly examined in this review, along with the underlying theoretical underpinnings, a summary of their applications in various fields, and an examination of the current roadblocks and potential future directions.

Outward Movement of Targeting Ligands from a Built-In Reserve Pool in Nuclease-Resistant 3D Hierarchical DNA Nanocluster for in Vivo High-Precision Cancer Therapy

Nanostructures made entirely of DNAs display great potential as chemotherapeutic drug carriers but so far cannot achieve sufficient clinic therapy outcomes due to off-target toxicity. In this contribution, an aptamer-embedded hierarchical DNA nanocluster (Apt-eNC) is constructed as an intelligent carrier for cancer-targeted drug delivery. Specifically, Apt-eNC is designed to have a built-in reserve pool in the interior cavity from which aptamers may move outward to function as needed. When surface aptamers are degraded, ones in reserve pool can move outward to offer the compensation, thereby magically preserving tumor-targeting performance in vivo. Even if withstanding extensive aptamer depletion, Apt-eNC displays a 115-fold enhanced cell targeting compared with traditional counterparts and at least 60-fold improved tumor accumulation. Moreover, one Apt-eNC accommodates 5670 chemotherapeutic agents. As such, when systemically administrated into HeLa tumor-bearing BALB/c nude mouse model, drug-loaded Apt-eNC significantly inhibits tumor growth without systemic toxicity, holding great promise for high precision therapy.

Integrated DNA triangular prism nanomachines for two-stage dynamic recognizing and bio-imaging from surface to the inside of living cells

The identification and detection of biomarkers in cancer cells play an essential role in the early detection of diseases, especially the detection of dual-biomarker. However, one of the most important limiting factors is how to realize the identification and labeling of biomarkers dynamically from the plasma membrane to the cytoplasm in living cells. In this study, integrated DNA triangular prism nanomachines (IDTPNs), a two-stage identification and dynamic bio-imaging strategy, recognize biomarkers from the plasma membrane to the cytoplasm have been designed. DNA triangular prism (DTP) was selected to act as a delivery platform with the aptamer Sgc8c and P53 modified on the side as the recognition molecules. Through the specific recognition of aptamers and the superior internalization of DTP, the IDTPNs realize the dynamic responses to PTK7 and p53 from the membrane to the cytoplasm in living cells. It is proved that the IDTPNs can be used for dynamic dual-biomarker recognition and bio-image from the surface to the inside of tumor cells automatically. Therefore, the strategy we developed provides a reliable platform for tumor diagnosis and biomarker research.

Deciphering the RNA universe in sperm in its role as a vertical information carrier

The inheritance of neurophysiologic and neuropsychologic complex diseases can only partly be explained by the Mendelian concept of genetic inheritance. Previous research showed that both psychological disorders like post-traumatic stress disorder and metabolic diseases are more prevalent in the progeny of affected parents. This could suggest an epigenetic mode of transmission. Human studies give first insight into the scope of intergenerational influence of stressors but are limited in exploring the underlying mechanisms. Animal models have elucidated the mechanistic underpinnings of epigenetic transmission. In this review, we summarize progress on the mechanisms of paternal intergenerational transmission by means of sperm RNA in mouse models. We discuss relevant details for the modelling of RNA-mediated transmission, point towards currently unanswered questions and propose experimental considerations for tackling these questions.

The biological applications of DNA nanomaterials: current challenges and future directions

DNA, a genetic material, has been employed in different scientific directions for various biological applications as driven by DNA nanotechnology in the past decades, including tissue regeneration, disease prevention, inflammation inhibition, bioimaging, biosensing, diagnosis, antitumor drug delivery, and therapeutics. With the rapid progress in DNA nanotechnology, multitudinous DNA nanomaterials have been designed with different shape and size based on the classic Watson-Crick base-pairing for molecular self-assembly. Some DNA materials could functionally change cell biological behaviors, such as cell migration, cell proliferation, cell differentiation, autophagy, and anti-inflammatory effects. Some single-stranded DNAs (ssDNAs) or RNAs with secondary structures via self-pairing, named aptamer, possess the ability of targeting, which are selected by systematic evolution of ligands by exponential enrichment (SELEX) and applied for tumor targeted diagnosis and treatment. Some DNA nanomaterials with three-dimensional (3D) nanostructures and stable structures are investigated as drug carrier systems to delivery multiple antitumor medicine or gene therapeutic agents. While the functional DNA nanostructures have promoted the development of the DNA nanotechnology with innovative designs and preparation strategies, and also proved with great potential in the biological and medical use, there is still a long way to go for the eventual application of DNA materials in real life. Here in this review, we conducted a comprehensive survey of the structural development history of various DNA nanomaterials, introduced the principles of different DNA nanomaterials, summarized their biological applications in different fields, and discussed the current challenges and further directions that could help to achieve their applications in the future.

DNA origami-based protein networks: from basic construction to emerging applications

Natural living systems are driven by delicate protein networks whose functions are precisely controlled by many parameters, such as number, distance, orientation, and position. Focusing on regulation rather than just imitation, the construction of artificial protein networks is important in many research areas, including biomedicine, synthetic biology and chemical biology. DNA origami, sophisticated nanostructures with rational design, can offer predictable, programmable, and addressable scaffolds for protein assembly with nanometer precision. Recently, many interdisciplinary efforts have achieved the precise construction of DNA origami-based protein networks, and their emerging application in many areas. To inspire more fantastic research and applications, herein we highlight the applicability and potentiality of DNA origami-based protein networks. After a brief introduction to the development and features of DNA origami, some important factors for the precise construction of DNA origami-based protein networks are discussed, including protein-DNA conjugation methods, networks with different patterns and the controllable parameters in the networks. The discussion then focuses on the emerging application of DNA origami-based protein networks in several areas, including enzymatic reaction regulation, sensing, bionics, biophysics, and biomedicine. Finally, current challenges and opportunities in this research field are discussed.

When Nanoworlds Collide: Implementing DNA Amplification, Nanoparticles, Molecules, and FRET into a Single MicroRNA Biosensor

Isothermal nucleic acid amplification strategies have been combined with nanotechnology for advanced biosensing, material design, and biomedical applications. However, merging phenomena and materials of different nanoscales with the aim of exploiting all their benefits at once has remained a challenging endeavor. Here, we exemplify the various problems one can encounter when combining the nanodimensions of lanthanide complexes (∼2 nm), Förster resonance energy transfer (FRET, ∼5 nm), quantum dots (QDs, ∼20 nm), and rolling circle amplification (RCA, ∼250 nm) into a single microRNA biosensor and how these challenges can be overcome. Six different approaches, including simple FRET-RCA, enzyme-digesting FRET-RCA, and FRET-hyperbranched-RCA were investigated. We demonstrated specific miR-21 detection with 80 fM limit of detection and multiplexing capability with FRET from a Tb complex to different QDs. The detailed view on the various complex multi-nanodimensional assay systems elucidated the limited clinical translation of such sophisticated multicomponent nanobiosensors.

DNA nanotechnology: A recent advancement in the monitoring of microcystin-LR

The Microcystin-Leucine-Arginine (MC-LR) is the most toxic and widely distributed microcystin, which originates from cyanobacteria produced by water eutrophication. The MC-LR has deleterious effects on the aquatic lives and agriculture, and this highly toxic chemical could severely endanger human health when the polluted food was intaken. Therefore, the monitoring of MC-LR is of vital importance in the fields including environment, food, and public health. Utilizing the complementary base pairing between DNA molecules, DNA nanotechnology can realize the programmable and predictable regulation of DNA molecules. In analytical applications, DNA nanotechnology can be used to detect targets via target-induced conformation change and the nano-assemblies of nucleic acids. Compared with the conventional analytical technologies, DNA nanotechnology has the advantages of sensitive, versatile, and high potential in real-time and on-site applications. According to the molecular basis for recognizing MC-LR, the strategies of applying DNA nanotechnology in the MC-LR monitoring are divided into two categories in this review: DNA as a recognition element and DNA-assisted signal processing. This paper introduces state-of-the-art analytical methods for the detection of MC-LR based on DNA nanotechnology and provides critical perspectives on the challenges and development in this field.

Multiplex real-time PCR using double-strand primers and probes for the detection of nucleic acids

Multiplex PCR encounters difficulties in primer designing with all the primer pairs working at the same annealing temperature. In this study, we have developed a double-strand primer-mediated multiple strand displacement reaction for the detection of SARS-COV-2 ORF, N and E genes (as examples). The double primer is composed of a 5'-modified fluorophore strand, which does not impact polymerase extension and a 3'-modified quencher strand, which cannot impact elongation. At the annealing temperature, the fluorophore strand combined with the template, extended and resulted in fluorescence signal release. Results showed that the double-strand primer relatively exhibits a wide annealing temperature range and good compatibility between three pairs of primers and probes. These merits allow the simple and multiplex real-time fluorescence quantification of nucleic acids. The detection limit was 400 copies/mL, and the detection time was approximately 2 h. In addition to its extreme specificity and simplicity, this method has a wide range of applications such as multiple PCR and SNP detection.

Mastering the Tools: Natural versus Artificial Vesicles in Nanomedicine

Naturally occurring extracellular vesicles and artificially made vesicles represent important tools in nanomedicine for the efficient delivery of biomolecules and drugs. Since its first appearance in the literature 50 years ago, the research on vesicles is progressing at a fast pace, with the main goal of developing carriers able to protect cargoes from degradation, as well as to deliver them in a time- and space-controlled fashion. While natural occurring vesicles have the advantage of being fully compatible with their host, artificial vesicles can be easily synthetized and functionalized according to the target to reach. Research is striving to merge the advantages of natural and artificial vesicles, in order to provide a new generation of highly performing vesicles, which would improve the therapeutic index of transported molecules. This progress report summarizes current manufacturing techniques used to produce both natural and artificial vesicles, exploring the promises and pitfalls of the different production processes. Finally, pros and cons of natural versus artificial vesicles are discussed and compared, with special regard toward the current applications of both kinds of vesicles in the healthcare field.

Layered Double Hydroxides in Bioinspired Nanotechnology

Layered Double Hydroxides (LDHs) are a relevant class of inorganic lamellar nanomaterials that have attracted significant interest in life science-related applications, due to their highly controllable synthesis and high biocompatibility. Under a general point of view, this class of materials might have played an important role for the origin of life on planet Earth, given their ability to adsorb and concentrate life-relevant molecules in sea environments. It has been speculated that the organic–mineral interactions could have permitted to organize the adsorbed molecules, leading to an increase in their local concentration and finally to the emergence of life. Inspired by nature, material scientists, engineers and chemists have started to leverage the ability of LDHs to absorb and concentrate molecules and biomolecules within life-like compartments, allowing to realize highly-efficient bioinspired platforms, usable for bioanalysis, therapeutics, sensors and bioremediation. This review aims at summarizing the latest evolution of LDHs in this research field under an unprecedented perspective, finally providing possible challenges and directions for future research.

Artificial Biosystems by Printing Biology

The continuous progress of printing technologies over the past 20 years has fueled the development of a plethora of applications in materials sciences, flexible electronics, and biotechnologies. More recently, printing methodologies have started up to explore the world of Artificial Biology, offering new paradigms in the direct assembly of Artificial Biosystems (small condensates, compartments, networks, tissues, and organs) by mimicking the result of the evolution of living systems and also by redesigning natural biological systems, taking inspiration from them. This recent progress is reported in terms of a new field here defined as Printing Biology, resulting from the intersection between the field of printing and the bottom up Synthetic Biology. Printing Biology explores new approaches for the reconfigurable assembly of designed life-like or life-inspired structures. This work presents this emerging field, highlighting its main features, i.e., printing methodologies (from 2D to 3D), molecular ink properties, deposition mechanisms, and finally the applications and future challenges. Printing Biology is expected to show a growing impact on the development of biotechnology and life-inspired fabrication.

On the Interaction between 1D Materials and Living Cells

One-dimensional (1D) materials allow for cutting-edge applications in biology, such as single-cell bioelectronics investigations, stimulation of the cellular membrane or the cytosol, cellular capture, tissue regeneration, antibacterial action, traction force investigation, and cellular lysis among others. The extraordinary development of this research field in the last ten years has been promoted by the possibility to engineer new classes of biointerfaces that integrate 1D materials as tools to trigger reconfigurable stimuli/probes at the sub-cellular resolution, mimicking the in vivo protein fibres organization of the extracellular matrix. After a brief overview of the theoretical models relevant for a quantitative description of the 1D material/cell interface, this work offers an unprecedented review of 1D nano- and microscale materials (inorganic, organic, biomolecular) explored so far in this vibrant research field, highlighting their emerging biological applications. The correlation between each 1D material chemistry and the resulting biological response is investigated, allowing to emphasize the advantages and the issues that each class presents. Finally, current challenges and future perspectives are discussed.

Competitive aptasensor for the ultrasensitive multiplexed detection of cancer biomarkers by fluorescent nanoparticle counting

Cancer biomarker quantification in human serum is of great importance for accurate patient diagnosis and informed clinical management. To date, ultrasensitive multiplexed detection of proteins without amplification is still a major challenge. Herein, we proposed a competitive aptasensor strategy for ultrasensitive multiplexed cancer biomarker detection by fluorescent nanoparticle (FNP) counting. The sequences are designed such that the binding abilities of linker DNA (L-DNA) with DNA-functionalized FNPs (DNA-FNPs) and aptamer are comparable. As long as one target binds with one molecule of aptamer, a signalling FNP forms a sandwich-structured nanocomposite, which was subsequently observed and enumerated with a fluorescence microscope. This 1 : 1 target-to-signal FNP production assured an improved sensitivity, benefiting from the reasonably good brightness and photostability of FNPs. For both singleplexed and multiplexed detection, this proposed strategy achieved an approximately 1000-fold improved limit of detection than the conventional method with the detection volume of 3.2 μL. Notably, the results for carcinoembryonic antigen (CEA) detection obtained directly from 9 human serum samples (colorectal/lung/healthy individuals) were consistent with that obtained by ELISA, showing potential application in clinical diagnosis.

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.

Imbibition of Femtoliter-Scale DNA-Rich Aqueous Droplets into Porous Nylon Substrates by Molecular Printing

This work presents the first reported imbibition mechanism of femtoliter (fL)-scale droplets produced by microchannel cantilever spotting (μCS) of DNA molecular inks into porous substrates (hydrophilic nylon). Differently from macroscopic or picoliter droplets, the downscaling to the fL-size leads to an imbibition process controlled by the subtle interplay of evaporation, spreading, viscosity, and capillarity, with gravitational forces being quasi-negligible. In particular, the minimization of droplet evaporation, surface tension, and viscosity allows for a reproducible droplet imbibition process. The dwell time on the nylon surface permits further tuning of the droplet lateral size, in accord with liquid ink diffusion mechanisms. The functionality of the printed DNA molecules is demonstrated at different imbibed oligonucleotide concentrations by hybridization with a fluorolabeled complementary sequence, resulting in a homogeneous coverage of DNA within the imbibed droplet. This study represents a first step toward the μCS-enabled fabrication of DNA-based biosensors and microarrays into porous substrates.

DNA nanotechnology approaches for microRNA detection and diagnosis

MicroRNAs are involved in the crucial processes of development and diseases and have emerged as a new class of biomarkers. The field of DNA nanotechnology has shown great promise in the creation of novel microRNA biosensors that have utility in lab-based biosensing and potential for disease diagnostics. In this Survey and Summary, we explore and review DNA nanotechnology approaches for microRNA detection, surveying the literature for microRNA detection in three main areas of DNA nanostructures: DNA tetrahedra, DNA origami, and DNA devices and motifs. We take a critical look at the reviewed approaches, advantages and disadvantages of these methods in general, and a critical comparison of specific approaches. We conclude with a brief outlook on the future of DNA nanotechnology in biosensing for microRNA and beyond.

Flexibility and thermal dynamic stability increase of dsDNA induced by Ru(bpy)2dppz2+ based on AFM and HRM technique

Ru(bpy)₂dppz²⁺ has been widely used as a probe for exploring the structure of double-stranded DNA (dsDNA). The flexibility change of DNA helix is important in many of its biological functions but not well understood. Here, flexibility change of dsDNA helix caused by intercalation with Ru(bpy)₂dppz²⁺ was investigated using the atomic force microscopy. At first, the interactions between ruthenium complex and dsDNA helix were characterized and the binding site size (p = 2.87 bp) and binding constant (K_a = 5.9 * 10⁷ M⁻¹) were determined by the relative extension of DNA helix using the equation of McGhee and von Hippel. By measuring intercalator-induced DNA elongation and the mean square of end-to-end distance at different molar ratios of Ru(bpy)₂dppz²⁺ to dsDNA, the changes of persistence length under different ruthenium concentrations were determined by the worm-like chain model. We found that the persistence length of dsDNA decreased with increasing Ru(bpy)₂dppz²⁺ concentration, demonstrating that the flexibility of dsDNA obviously enhanced due to the intercalation. Especially, the persistence length changed greatly from 54 to 34 nm on changing the molar ratio of ruthenium to dsDNA from 0 to 0.2. We speculated that the intercalation of dsDNA with Ru(bpy)₂dppz²⁺ resulted in local deformation or bending of the DNA duplex. In addition, the thermal dynamic stability of DNA helix was measured with high resolution melting method which revealed the increase in thermal dynamic stability of DNA helix due to the ruthenium intercalation.

Dual sensing reporter system of assembled gold nanoparticles toward the sequential colorimetric detection of adenosine and Cr(III)

A facile and sensitive sequential colorimetric detection strategy for adenosine and Cr³⁺ has been presented by using the aptamer and 11-mercaptoundecanoic acid assembled gold nanoparticles. The thiolated DNA and 11-mercaptoundecanoic acid was simultaneously assembled to the surface of gold nanoparticles in one step by gold-sulfur interaction. Adenosine aptamer was linked to functionalized gold nanaoparticles based on the strict complementary nature of the DNA base pairs. Conformational change of aptamer will be induced due to its specific binding with targets. As a result, this aptamer tethered aggregated nanoparticles underwent fast disassembly into dispersed nanoparticles upon binding of adenosine, and this distance change between particles induced a distinct solution color changing from blue to red. The dispersed particles were sensitive to Cr³⁺ due to the chelation effect between the carboxyl group of 11-mercaptoundecanoic acid and metal ions, and further occurred obvious aggregation accompanying with a color change from red to blue. Depended on this principle, a sensitive and selective sequential colorimetric sensor for detection of adenosine and Cr³⁺ was developed. The proposed colorimetric sensor exhibited wide linear ranges and low detection limits towards the detection of adenosine and Cr³⁺. Regarding adenosine, linear range was 1 × 10^-7 ∼ 1 × 10^-4 M with low detection limit of 1.8 × 10^-8 M, and the naked eye detection limit was estimated as 20 μM. With regard to Cr³⁺, good linear relationship was ranged from 1 × 10^-10 to 1 × 10^-6 M with low detection limit of 1.7 × 10^-11 M，and the naked eye detection limit was as low as 0.1 nM. Meanwhile, bifunctional recognition was successfully used for practical human urine samples with good recoveries from 89.0% to 112.6% for adenosine and 90.2%-113.4% for Cr³⁺. It also highlights the potential applications of other aptamers and ligands in cascade analysis of other analytes.

Printing Life-Inspired Subcellular Scale Compartments with Autonomous Molecularly Crowded Confinement

A simple, rapid, and highly controlled platform to prepare life-inspired subcellular scale compartments by inkjet printing has been developed. These compartments consist of fL-scale aqueous droplets (few µm in diameter) incorporating biologically relevant molecular entities with programmed composition and concentration. These droplets are ink-jetted in nL mineral oil drop arrays allowing for lab-on-chip studies by fluorescence microscopy and fluorescence life time imaging. Once formed, fL-droplets are stable for several hours, thus giving the possibility of readily analyze molecular reactions and their kinetics and to verify molecular behavior and intermolecular interactions. Here, this platform is exploited to unravel the behavior of different molecular probes and biomolecular systems (DNA hairpins, enzymatic cascades, protein-ligand couples) within the compartments. The fL-scale size induces the formation of molecularly crowded confined shell structures (hundreds of nanometers in thickness) at the droplet surface, allowing discovery of specific features (e.g., heterogeneity, responsivity to molecular triggers) that are mediated by the intermolecular interactions in these peculiar environments. The presented results indicate the possibility of using this platform for designing nature-inspired confined reactors allowing for a deepened understanding of molecular confinement effects in living subcellular compartments.

New copolymers as hosts of ribosomal RNA

Functionalized copolymers were synthesized and are proposed as hosts of RNA. The copolymers are based on carboxymethyl cellulose and poly-(ethylene glycol)-OH. These copolymers were functionalized with two amino acids, either lysine or histidine, through amide bond formation. The functionalized copolymer was then used to adsorb ribosomal RNA. The RNA loading was based on the nature of the amino acid functionalization of the copolymer. The array of RNA-copolymers was observed to be soft sphere-like, where the density of spheres was a function of the molecular weight of the carboxymethyl cellulose and the nature of the amino acid. Such RNA-copolymer systems are very sensitive to changes in pH.

Instant hydrogel formation of terpyridine-based complexes triggered by DNA via non-covalent interaction

Biomolecule-based hydrogels have potential use in a wide range of applications such as controlled drug release, tissue engineering, and biofabrication. Herein, driven by specific interactions between ds-DNA (double-stranded DNA) and Zn2+ based metal-complexes, we report that the use of DNA as cross-linkers can enhance interactions between self-assembling Zn2+ complexes containing terpyridine and sugar groups in the generation of bioinspired hydrogels from solutions or suspensions. The gelation process is fast and straightforward without tedious steps and happens at room temperature. Such a hydrogelation process of different Zn2+ complexes endows the visualized and selective DNA analogue discrimination. Several experiments suggest that the strong intercalation binding of Zn2+ complexes with ds-DNA results in the unzipping of ds-DNA into ss-DNA (single-stranded DNA), which further behave as linkers to enhance the intermolecular interactions of self-assembling Zn2+ complex molecules via coordination interactions. This work demonstrates an efficient and universal strategy to prepare hydrogels based on biomolecular recognition. Moreover, the DNA responsive behaviors of Zn2+ complexes are further compared with that of solutions and cells.

DNA nanotechnology for nucleic acid analysis: multifunctional molecular DNA machine for RNA detection

The Nobel prize in chemistry in 2016 was awarded for 'the design and synthesis of molecular machines'. Here we designed and assembled a molecular machine for the detection of specific RNA molecules. An association of several DNA strands, named multifunctional DNA machine for RNA analysis (MDMR1), was designed to (i) unwind RNA with the help of RNA-binding arms, (ii) selectively recognize a targeted RNA fragment, (iii) attract a signal-producing substrate and (iv) amplify the fluorescent signal by catalysis. MDMR1 enabled detection of 16S rRNA at concentrations ∼24 times lower than that by a traditional deoxyribozyme probe.

Conceptual design of tetraazaporphyrin- and subtetraazaporphyrin-based functional nanocarbon materials: electronic structures, topologies, optical properties, and methane storage capacities

A large variety of conceptual three- and fourfold tetraazaporphyrin- and subtetraazaporphyrin-based functional 3D nanocage and nanobarrel structures have been proposed on the basis of in silico design. The designed structures differ in their sizes, topology, porosity, and conjugation properties. The stability of nanocages of Oh symmetry and nanobarrels of D4h symmetry was revealed on the basis of DFT and MD calculations, whereas their optical properties were assessed using a TDDFT approach and a long-range corrected LC-wPBE exchange-correlation functional. It was shown that the electronic structures and vertical excitation energies of the functional nanocage and nanobarrel structures could be easily tuned via their size, topology, and the presence of bridging sp(3) carbon atoms. TDDFT calculations suggest significantly lower excitation energies in fully conjugated nanocages and nanobarrels compared with systems with bridging sp(3) carbon fragments. Based on DFT and TDDFT calculations, the optical properties of the new materials can rival those of known quantum dots and are superior to those of monomeric phthalocyanines and their analogues. The methane gas adsorption properties of the new nanostructures and nanotubes generated by conversion from nanobarrels were studied using an MD simulation approach. The ability to store large quantities of methane (106-216 cm(3) (STP) cm(-3)) was observed in all cases with several compounds being close to or exceeding the DOE target of 180 cm(3) (STP) cm(-3) for material-based methane storage at a pressure of 3.5 MPa and room temperature.