Thermostable branched DNA nanostructures as modular primers for polymerase chain reaction

Polymeric DNA Hydrogels and Their Applications in Drug Delivery for Cancer Therapy

The biomolecule deoxyribonucleic acid (DNA), which acts as the carrier of genetic information, is also regarded as a block copolymer for the construction of biomaterials. DNA hydrogels, composed of three-dimensional networks of DNA chains, have received considerable attention as a promising biomaterial due to their good biocompatibility and biodegradability. DNA hydrogels with specific functions can be prepared via assembly of various functional sequences containing DNA modules. In recent years, DNA hydrogels have been widely used for drug delivery, particularly in cancer therapy. Benefiting from the sequence programmability and molecular recognition ability of DNA molecules, DNA hydrogels prepared using functional DNA modules can achieve efficient loading of anti-cancer drugs and integration of specific DNA sequences with cancer therapeutic effects, thus achieving targeted drug delivery and controlled drug release, which are conducive to cancer therapy. In this review, we summarized the assembly strategies for the preparation of DNA hydrogels on the basis of branched DNA modules, hybrid chain reaction (HCR)-synthesized DNA networks and rolling circle amplification (RCA)-produced DNA chains, respectively. The application of DNA hydrogels as drug delivery carriers in cancer therapy has been discussed. Finally, the future development directions of DNA hydrogels in cancer therapy are prospected.

Fast Transport and Transformation of Biomacromolecular Substances via Thermo-Stimulated Active "Inhalation-Exhalation" Cycles of Hierarchically Structured Smart pNIPAM-DNA Hydrogels

Although smart hydrogels hold great promise in biosensing and biomedical applications, their response to external stimuli is governed by the passive diffusion-dependent substance transport between hydrogels and environments and within the 3D hydrogel matrices, resulting in slow response to biomacromolecules and limiting their extensive applications. Herein, inspired by the respiration systems of organisms, an active strategy to achieve highly efficient biomolecular substance transport through the thermo-stimulated "inhalation-exhalation" cycles of hydrogel matrices is demonstrated. The cryo-structured poly(N-isopropylacrylamide) (pNIPAM)-DNA hydrogels, composed of functional DNA-tethered pNIPAM networks and free-water-containing macroporous channels, exhibit thermally triggered fast and reversible shrinking/swelling cycles with high-volume changes, which drive the formation of dynamic water stream to accelerate the intake of external substances and expelling of endogenous substances, thus promoting the functional properties of hydrogel systems. Demonstrated by catalytic DNAzyme and CRISPR-Cas12a-incorporating hydrogels, significantly enhanced catalytic efficiency with up to 280% and 390% is achieved, upon the introduction of active "inhalation-exhalation" cycles, respectively. Moreover, remotely near-infrared (NIR)-triggering of "inhalation-exhalation" cycles is achieved after the introduction of NIR-responsive MXene nanosheets into the hydrogel matrix. These hydrogel systems with enhanced substance transport and transformation properties hold promise in the development of more effective biosensing and therapeutic systems.

Programmable DNA Hydrogels as Artificial Extracellular Matrix

The cell microenvironment plays a crucial role in regulating cell behavior and fate in physiological and pathological processes. As the fundamental component of the cell microenvironment, extracellular matrix (ECM) typically possesses complex ordered structures and provides essential physical and chemical cues to the cells. Hydrogels have attracted much attention in recapitulating the ECM. Compared to natural and synthetic polymer hydrogels, DNA hydrogels have unique programmable capability, which endows the material precise structural customization and tunable properties. This review focuses on recent advances in programmable DNA hydrogels as artificial extracellular matrix, particularly the pure DNA hydrogels. It introduces the classification, design, and assembly of DNA hydrogels, and then summarizes the state-of-the-art achievements in cell encapsulation, cell culture, and tissue engineering with DNA hydrogels. Ultimately, the challenges and prospects for cellular applications of DNA hydrogels are delivered.

DNA Templated Silver Nanoclusters for Bioanalytical Applications: A Review

Due to their unique programmability, biocompatibility, photostability and high fluorescent quantum yield, DNA templated silver nanoclusters (DNA Ag NCs) have attracted increasing attention for bioanalytical application. This review summarizes the recent developments in fluorescence properties of DNA templated Ag NCs, as well as their applications in bioanalysis. Finally, we herein discuss some current challenges in bioanalytical applications, to promote developments of DNA Ag NCs in biochemical analysis.

Construction of branched DNA-based nanostructures for diagnosis, therapeutics and protein engineering

Branched DNA with multibranch-like anisotropic topology serves as a promising and powerful building block in constructing multifunctional-integrated nanomaterials in a programmable and controllable manner. Recently, a series of branched DNA-based functional nanomaterials were developed by elaborate molecular design. In this review, we focused on the construction of branched DNA-based nanostructures for biological and biomedical applications. First, the molecular design and synthesis method of branched DNA monomer were briefly described. Then, the construction strategies of branched DNA-based nanostructures were categorially discussed, including target-triggered polymerization, enzymatic extension and hybrid assembly. Finally, the biological and biomedical applications including diagnosis, therapeutics and protein engineering were summarized. We envision that the review will contribute to the further development of branched DNA-based nanomaterials with great application potential in the field of biomedicine, thus building a new bridge between material chemistry and biomedicine.

Dibenzocyclooctyne-Branched Primer Assembled Gene Nanovector and Its Potential Applications in Genome Editing

The CRISPR/Cas9 system has been widely used as an efficient genome editing toolkit for gene therapy. The delivery of vectors encoding the full CRISPR/Cas9 components including Cas9 gene and gRNA expression element into cells is the crucial step to effective genome editing. However, the cargo gene sequence for genome editing is usually large, which reduces the cargo encapsulation efficiency and affects the vector size. To obtain a nanovector with high cargo gene loading capacity and biocompatible size, we report the construction of a gene nanovector from branch-PCR with a dibenzocyclooctyne (DBCO)-branched primer and establish the correlation mapping between gene length and nanovector size. The results show that the size of nanovectors can be tuned according to the gene length. According to the findings, we constructed nanovectors carrying the full CRISPR/Cas9 components in 100-200 nm and validated their application in genome editing. The results show that this kind of nanovector exhibits higher serum stability than plasmids and can reach comparable genome editing efficiency with plasmids. Hence, this type of gene nanovector obtained through branch-PCR can carry large gene cargos and maintain a biocompatible nanoscale size, which we envisage will expand its medical applications in gene therapy.

Chemically Modified DNA Nanostructures for Drug Delivery

Based on predictable, complementary base pairing, DNA can be artificially pre-designed into versatile DNA nanostructures of well-defined shapes and sizes. With excellent addressability and biocompatibility, DNA nanostructures have been widely employed in biomedical research, such as bio-sensing, bio-imaging, and drug delivery. With the development of the chemical biology of nucleic acid, chemically modified nucleic acids are also gradually developed to construct multifunctional DNA nanostructures. In this review, we summarize the recent progress in the construction and functionalization of chemically modified DNA nanostructures. Their applications in the delivery of chemotherapeutic drugs and nucleic acid drugs are highlighted. Furthermore, the remaining challenges and future prospects in drug delivery by chemically modified DNA nanostructures are discussed.

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With excellent addressability and biocompatibility, DNA nanostructures are promising candidates for bio-sensing, bio-imaging, and drug delivery

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The recent progress in chemical modifications of DNA nanostructures is summarized

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Chemically modified DNA nanostructures for efficient delivery of chemotherapeutic drugs and nucleic acid drugs are highlighted

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Challenges and prospects of future development toward chemically modified DNA nanostructures for drug delivery are discussed

Smart Nucleic Acid Hydrogels with High Stimuli-Responsiveness in Biomedical Fields

Due to their hydrophilic, biocompatible and adjustability properties, hydrogels have received a lot of attention. The introduction of nucleic acids has made hydrogels highly stimuli-responsiveness and they have become a new generation of intelligent biomaterials. In this review, the development and utilization of smart nucleic acid hydrogels (NAHs) with a high stimulation responsiveness were elaborated systematically. We discussed NAHs with a high stimuli-responsiveness, including pure NAHs and hybrid NAHs. In particular, four stimulation factors of NAHs were described in details, including pH, ions, small molecular substances, and temperature. The research progress of nucleic acid hydrogels in biomedical applications in recent years is comprehensively discussed. Finally, the opportunities and challenges facing the future development of nucleic acid hydrogels are also discussed.

Hierarchical Assembly of Super-DNA Origami Based on a Flexible and Covalent-Bound Branched DNA Structure

DNA origami technique provides a programmable way to construct nanostructures with arbitrary shapes. The dimension of assembled DNA origami, however, is usually limited by the length of the scaffold strand. Herein, we report a general strategy to efficiently organize multiple DNA origami tiles to form super-DNA origami using a flexible and covalent-bound branched DNA structure. In our design, the branched DNA structures (B_n: with a certain number of 2-6 branches) are synthesized by a copper-free click reaction. Equilateral triangular DNA origamis with different numbers of capture strands (T_n: T₁, T₂, and T₃) are constructed as the coassembly tiles. After hybridization with the branched DNA structures, the super-DNA origami (up to 13 tiles) can be efficiently ordered in the predesigned patterns. Compared with traditional DNA junctions (J_n: J₂-J₆, as control groups) assembled by base pairing between several DNA strands, a higher yield and more compact structures are obtained using our strategy. The highly ordered and discrete DNA origamis can further precisely organize gold nanoparticles into different patterns. This rationally developed DNA origami ordering strategy based on the flexible and covalent-bound branched DNA structure presents a new avenue for the construction of sophisticated DNA architectures with larger molecular weights.

Visible-Light-Mediated Modification and Manipulation of Biomacromolecules

Chemically modified biomacromolecules-i.e., proteins, nucleic acids, glycans, and lipids-have become crucial tools in chemical biology. They are extensively used not only to elucidate cellular processes but also in industrial applications, particularly in the context of biopharmaceuticals. In order to enable maximum scope for optimization, it is pivotal to have a diverse array of biomacromolecule modification methods at one's disposal. Chemistry has driven many significant advances in this area, and especially recently, numerous novel visible-light-induced photochemical approaches have emerged. In these reactions, light serves as an external source of energy, enabling access to highly reactive intermediates under exceedingly mild conditions and with exquisite spatiotemporal control. While UV-induced transformations on biomacromolecules date back decades, visible light has the unmistakable advantage of being considerably more biocompatible, and a spectrum of visible-light-driven methods is now available, chiefly for proteins and nucleic acids. This review will discuss modifications of native functional groups (FGs), including functionalization, labeling, and cross-linking techniques as well as the utility of oxidative degradation mediated by photochemically generated reactive oxygen species. Furthermore, transformations at non-native, bioorthogonal FGs on biomacromolecules will be addressed, including photoclick chemistry and DNA-encoded library synthesis as well as methods that allow manipulation of the activity of a biomacromolecule.

Smart and Functionalized Development of Nucleic Acid-Based Hydrogels: Assembly Strategies, Recent Advances, and Challenges

Nucleic acid-based hydrogels that integrate intrinsic biological properties of nucleic acids and mechanical behavior of their advanced assemblies are appealing bioanalysis and biomedical studies for the development of new-generation smart biomaterials. It is inseparable from development and incorporation of novel structural and functional units. This review highlights different functional units of nucleic acids, polymers, and novel nanomaterials in the order of structures, properties, and functions, and their assembly strategies for the fabrication of nucleic acid-based hydrogels. Also, recent advances in the design of multifunctional and stimuli-responsive nucleic acid-based hydrogels in bioanalysis and biomedical science are discussed, focusing on the applications of customized hydrogels for emerging directions, including 3D cell cultivation and 3D bioprinting. Finally, the key challenge and future perspectives are outlined.

Stimuli Responsive, Programmable DNA Nanodevices for Biomedical Applications

Of the multiple areas of applications of DNA nanotechnology, stimuli-responsive nanodevices have emerged as an elite branch of research owing to the advantages of molecular programmability of DNA structures and stimuli-responsiveness of motifs and DNA itself. These classes of devices present multiples areas to explore for basic and applied science using dynamic DNA nanotechnology. Herein, we take the stake in the recent progress of this fast-growing sub-area of DNA nanotechnology. We discuss different stimuli, motifs, scaffolds, and mechanisms of stimuli-responsive behaviours of DNA nanodevices with appropriate examples. Similarly, we present a multitude of biological applications that have been explored using DNA nanodevices, such as biosensing, in vivo pH-mapping, drug delivery, and therapy. We conclude by discussing the challenges and opportunities as well as future prospects of this emerging research area within DNA nanotechnology.

Temperature-responsive supramolecular hydrogels

Hydrogels comprise a class of soft materials which are extremely useful in a number of contexts, for example as matrix-mimetic biomaterials for applications in regenerative medicine and drug delivery. One particular subclass of hydrogels consists of materials prepared through non-covalent physical crosslinking afforded by supramolecular recognition motifs. The dynamic, reversible, and equilibrium-governed features of these molecular-scale motifs often transcend length-scales to endow the resulting hydrogels with these same properties on the bulk scale. In efforts to engineer hydrogels of all types with more precise or application-specific uses, inclusion of stimuli-responsive sol-gel transformations has been broadly explored. In the context of biomedical uses, temperature is an interesting stimulus which has been the focus of numerous hydrogel designs, supramolecular or otherwise. Most supramolecular motifs are inherently temperature-sensitive, with elevated temperatures commonly disfavoring motif formation and/or accelerating its dissociation. In addition, supramolecular motifs have also been incorporated for physical crosslinking in conjunction with polymeric or macromeric building blocks which themselves exhibit temperature-responsive changes to their properties. Through molecular-scale engineering of supramolecular recognition, and selection of a particular motif or polymeric/macromeric backbone, it is thus possible to devise a number of supramolecular hydrogel materials to empower a variety of future biomedical applications.

Morphological Manipulation of DNA Gel Microbeads with Biomolecular Stimuli

Hydrogels are essential in many fields ranging from tissue engineering and drug delivery to food sciences or cosmetics. Hydrogels that respond to specific biomolecular stimuli such as DNA, mRNA, miRNA and small molecules are highly desirable from the perspective of medical applications, however interfacing classical hydrogels with nucleic acids is still challenging. Here were demonstrate the generation of microbeads of DNA hydrogels with droplet microfluidic, and their morphological actuation with DNA strands. Using strand displacement and the specificity of DNA base pairing, we selectively dissolved gel beads, and reversibly changed their size on-the-fly with controlled swelling and shrinking. Lastly, we performed a complex computing primitive-A Winner-Takes-All competition between two populations of gel beads. Overall, these results show that strand responsive DNA gels have tantalizing potentials to enhance and expand traditional hydrogels, in particular for applications in sequencing and drug delivery.

Tailoring DNA Self-assembly to Build Hydrogels

DNA hydrogels are crosslinked polymeric networks in which DNA is used as the backbone or the crosslinker. These hydrogels are novel biofunctional materials that possess the biological character of DNA and the framed structure of hydrogels. Compared with other kinds of hydrogels, DNA hydrogels exhibit not only high mechanical strength and controllable morphologies but also good recognition ability, designable responsiveness, and programmability. The DNA used in this type of hydrogel acts as a building block for self-assembly or as a responsive element due to its sequence recognition ability and switchable structural transitions, respectively. In this review, we describe recent developments in the field of DNA hydrogels and discuss the role played by DNA in these hydrogels. Various synthetic strategies for and a range of applications of DNA hydrogels are detailed.

DNA Hydrogels and Microgels for Biosensing and Biomedical Applications

DNA hydrogels, which take advantage of the unique properties of functional DNA motifs, such as specific molecular recognition, programmable and high-precision assembly, multifunctionality, and excellent biocompatibility, have attracted increasing research interest in the past two decades in diverse fields, especially in biosensing and biomedical applications. The responsiveness of smart DNA hydrogels to external stimuli by changing their swelling volume, crosslinking density, and optical or mechanical properties has facilitated the development of DNA-hydrogel-based in vitro biosensing systems and actuators. Furthermore, reducing the sizes of DNA hydrogels to the micro- and nanoscale leads to better responsiveness and delivery capacity, thereby making them excellent candidates for rapid detection, in vivo real-time sensing, and drug release applications. Here, the recent progress in the development of smart DNA hydrogels and DNA microgels for biosensing and biomedical applications is summarized, and the current challenges as well as future prospects are also discussed.

Gene Circuit Compartment on Nanointerface Facilitatating Cascade Gene Expression

Cellular genes that are functionally related to each other are usually confined in specialized subcellular compartments for efficient biochemical reactions. Construction of spatially controlled biosynthetic systems will facilitate the study of biological design principles. Herein, we fabricated a gene circuit compartment by coanchoring two function-related genes on surface of gold nanoparticles and investigated the compartment effect on cascade gene expression in a cell-free system. The gene circuit consisted of a T7 RNA polymerase (T7 RNAP) expression cassette as regulatory gene and a fluorescent protein expression cassette as regulated reporter gene. Both the expression cassettes were attached on a Y-shaped DNA nanostructure whose other two branches were mercapto-modified in order to steadily anchor the gene expression cassettes on the surface of gold nanoparticles. Experimental results demonstrated that both the yield and initial expression rate of the fluorescent reporter protein in the gene circuit compartment system were enhanced compared with those in free gene circuit system. Mechanism investigation revealed that the gene circuit compartment on nanoparticle made the regulatory gene and regulated reporter gene spatially proximal at nanoscale, thus effectively improving the transfer efficiency of the regulatory proteins (T7 RNAP) from regulatory genes to the regulated reporter genes in the compartments, and consequently, the biochemical reaction efficiency was significantly increased. This work not only provided a simplified model for rational molecular programming of genes circuit compartments on nanointerface but also presented implications for the cellular structure-function relationship.

Branched DNA Architectures Produced by PCR-Based Assembly as Gene Compartments for Cell-Free Gene-Expression Reactions

The physical distance between genes plays important roles in controlling gene expression reactions in vivo. Herein, we report the design and synthesis of a branched gene architecture in which three transcription units are integrated into one framework through assembly based on the polymerase chain reaction (PCR), together with the exploitation of these constructs as "gene compartments" for cell-free gene expression reactions, probing the impact of this physical environment on gene transcription and translation. We find that the branched gene system enhances gene expression yields, in particular at low concentrations of DNA and RNA polymerase (RNAP); furthermore, in a crowded microenvironment that mimics the intracellular microenvironment, gene expression from branched genes maintains a relatively high level. We propose that the branched gene assembly forms a membrane-free gene compartment that resembles the nucleoid of prokaryotes and enables RNAP to shuttle more efficiently between neighboring transcription units, thus enhancing gene expression efficiency. Our branched DNA architecture provides a valuable platform for studying the influence of "cellular" physical environments on biochemical reactions in simplified cell-free systems.

Ultrasensitive Detection of Circulating Tumor DNA of Lung Cancer via an Enzymatically Amplified SERS-Based Frequency Shift Assay

Circulating tumor DNA (ctDNA) is a promising noninvasive biomarker for the early diagnosis of cancers. However, it is challenging for accurate and sensitive detection of pico-to-femtomolar serum concentration of ctDNA, especially in the presence of its analogues that produce strong background noise. Herein, a DNA-rN1-DNA-mediated surface-enhanced Raman scattering frequency shift assay is developed, which enables sensitive detection of ctDNA with one single base pair mutation (KARS G12D mutation) from the normal ones (KARS G12D normal) of lung cancer. This sensing platform features in both the designed hairpin DNA-rN1-DNA probe for specific ctDNA recognition and the employed RNase HII enzyme that specifically hydrolyzes the DNA-rN1-DNA/ctDNA hybrid and thus allows ctDNA recycling in the system to realize signal amplification. The detection system shows sub-femtomolar-level sensitivity in the phosphate-buffered saline solution and is demonstrated to function well in both fetal bovine serum and human physiological media. In particular, the sensitive assay of ctDNA in serum samples from lung cancer patients is achieved, suggesting its high potential applications in clinical settings for early diagnosis and prognosis of lung cancer.

Ultrasensitive Detection of Serum MicroRNA Using Branched DNA-Based SERS Platform Combining Simultaneous Detection of α-Fetoprotein for Early Diagnosis of Liver Cancer

We provided an ultrasensitive sensing strategy for microRNA detection by first employing branched DNA. With the aid of microcontact printing, we realized the multiplex sensing of different kinds of liver cancer biomarkers: microRNA and protein simultaneously. Delicately designed branched DNA included multiple complementary sticky ends as probe to microRNA capture and the double-stranded rigid branched core to increase the active sticky-ends distance and expose more DNA probes for sensitivity. The branched DNA enables 2 orders of magnitude increase in sensitivity for microRNA detection over single-stranded DNA. The limit of detection reaches as low as 10 attomolar (S/N = 3) for miR-223 and 10^-12 M for α-fetoprotein. In addition, this system shows high selectivity and appropriate reproducibility (the relative standard deviation is less than 20%) in physiological media. Serum samples are tested and the results of α-fetoprotein are in good agreement with the current gold-standard method, electrochemiluminescence immunoassay analyzer. The results suggest the reliability of this approach in physiological media and show high potential in the sensing of low abundant microRNA in serum, especially for early diagnosis of primary liver cancers.

Microfluidic-Assisted Fabrication of Clay Microgels for Cell-Free Protein Synthesis

Cell-free protein synthesis (CFPS) is a robust platform for the simple, rapid, and cost-effective in vitro production of proteins, as well as an important tool for cell-free synthetic biology research. Here, a microfluidic clay microgel system is reported, which creates compartmentalized microenvironments for CFPS capable of high-yield and repeated protein synthesis, as well as an artificial cell-like structure. As an advantageous platform for CFPS, a modular manner to prepare clay microgels with rationally designed functions is demonstrated: (i) gene/clay microgels enhance protein expression, (ii) gene/clay/magnetic nanoparticle microgels enable a repeated protein production system, and (iii) gene/clay microgels in microfluidic droplets serve as a cell-like structure. Beyond CFPS, considering the compatibility of clay microgels with hydrophilic functional materials, our clay microgels will provide a more general platform for preparing a variety of functional materials such as encapsulating drugs and cells, enabling more biomedical applications.

Stemmed DNA nanostructure for the selective delivery of therapeutics

DNA has emerged as a biocompatible biomaterial that may be considered for various applications. Here, we report tumor cell-specific aptamer-modified DNA nanostructures for the specific recognition and delivery of therapeutic chemicals to cancer cells. Protein tyrosine kinase (PTK)7-specific DNA aptamer sequences were linked to 15 consecutive guanines. The resulting aptamer-modified product, AptG15, self-assembled into a Y-shaped structure. The presence of a G-quadruplex at AptG15 was confirmed by circular dichroism and Raman spectroscopy. The utility of AptG15 as a nanocarrier of therapeutics was tested by loading the photosensitizer, methylene blue (MB), to the G-quadruplex as a model drug. The generated MB-loaded AptG15 (MB/AptG15) showed specific and enhanced uptake to CCRF-CEM cells, which overexpress PTK7, compared with Ramos cells, which lack PTK7, or CCRF-CEM cells treated with a PTK7-specific siRNA. The therapeutic activity of MB/AptG15 was tested by triggering its photodynamic effects. Upon 660 nm light irradiation, MB/AptG15 showed greater reactive oxygen species generation and anticancer activity in PTK7-overexpressing cells compared to cells treated with MB alone, those treated with AptG15, and other comparison groups. AptG15 stemmed DNA nanostructures have significant potential for the cell-type-specific delivery of therapeutics, and possibly for the molecular imaging of target cells.

Synthesis of Branched DNA Scaffolded Super-Nanoclusters with Enhanced Antibacterial Performance

Metal nanoclusters (NCs) possess unique optical properties, and exhibit a wide variety of potential applications. DNA with robust molecular programmability is demonstrated as an ideal scaffold to regulate the formation of NCs, offering a rational approach to precisely tune the spatial structures of NCs. Herein, the first use of branched DNA as scaffold to regulate the formation of silver nanoclusters (super-AgNC) is reported, in which the spatial structures are precisely designed and constructed. Super-AgNC with tunable shapes and arm-lengths including Y-, X-, and (Y-X)- shaped super-AgNC is achieved. The molecular structures and optical properties of super-AgNCs are systemically studied. As a proof of application, remarkably, super-AgNCs exhibit superior antibacterial performance. In addition, super-AgNCs show excellent biocompatibility with three types of tissue cells including 293T (human embryonic kidney cells), SMCs (vascular smooth muscle cells), and GLC-82 (lung adenocarcinoma cells). These performances enable the super-AgNCs adaptable in a variety of applications such as biosensing, bioimaging, and antibacterial agents.

Non-invasive detection of gastric cancer relevant d-amino acids with luminescent DNA/silver nanoclusters

Chirality plays essential roles in life systems such that l-amino acids (LAAs) are predominantly found as the building units of protein for organisms. The presence of the d-enantiomer (DAA) has been found to be specifically relevant to gastric cancer. We herein construct a luminescent DNA/silver nanocluster based biosensing system to achieve rapid and specific detection of DAAs. As a proof of application, we detected DAAs in saliva samples from patients with gastric cancer, and the test results exhibited excellent specificity. Our detection system has the following major advantages: (i) the detection is rapid, being completed in less than 1 hour; (ii) the limit of detection falls in the effective range of DAA concentrations of gastric cancer at an early stage, indicating that our method is potentially suitable for early diagnosis of gastric cancer; (iii) the non-invasive sampling manner provides an adaptable system for point-of-care testing (POCT); and (iv) the system does not require any massive instruments or expensive reagents, which enables POCT as well.

DNA Hydrogel with Aptamer-Toehold-Based Recognition, Cloaking, and Decloaking of Circulating Tumor Cells for Live Cell Analysis

Circulating tumor cells (CTCs) contain molecular information on the primary tumor and can be used for predictive cancer diagnostics. Capturing rare live CTCs and their quantification in whole blood remain technically challenging. Here we report an aptamer-trigger clamped hybridization chain reaction (atcHCR) method for in situ identification and subsequent cloaking/decloaking of CTCs by porous DNA hydrogels. These decloaked CTCs were then used for live cell analysis. In our design, a DNA staple strand with aptamer-toehold biblocks specifically recognizes epithelial cell adhesion molecule (EpCAM) on the CTC surface that triggers subsequent atcHCR via toehold-initiated branch migration. Porous DNA hydrogel based-cloaking of single/cluster of CTCs allows capturing of living CTCs directly with minimal cell damage. The ability to identify a low number of CTCs in whole blood by DNA hydrogel cloaking would allow high sensitivity and specificity for diagnosis in clinically relevant settings. More significantly, decloaking of CTCs using controlled and defined chemical stimuli can release living CTCs without damages for subsequent culture and live cell analysis. We expect this liquid biopsy tool to open new powerful and effective routes for cancer diagnostics and therapeutics.

Synthesis of Poly Linear shRNA Expression Cassettes Through Branch-PCR

A facile and universal strategy to construct the poly linear small hairpin RNA (shRNA) expression cassettes with multiple shRNA transcription templates through polymerase chain reaction with flexible branched primers (branch-PCR) is described in this protocol. Double-stranded RNA (dsRNA) is not stable enough for the study of RNA interference (RNAi) delivery in mammalian cells. Therefore, the more stable shRNA transcription template is employed to produce the endogenous transcribed dsRNA. Then, the covalent crosslinked linear shRNA expression cassettes are constructed through the branch-PCR for the long-lasting RNAi effect in this protocol. The branched primer pair is efficiently synthesized through classic click chemistry. In one step of PCR, the much more stable poly linear shRNA expression cassettes can be produced in large scale. This strategy of efficient synthesis of the poly linear gene expression cassettes can also be applied in the field for other target gene delivery. © 2016 by John Wiley & Sons, Inc.

DNA Microgels as a Platform for Cell-Free Protein Expression and Display

Protein expression and selection is an essential process in the modification of biological products. Expressed proteins are selected based on desired traits (phenotypes) from diverse gene libraries (genotypes), whose size may be limited due to the difficulties inherent in diverse cell preparation. In addition, not all genes can be expressed in cells, and linking genotype with phenotype further presents a great challenge in protein engineering. We present a DNA gel-based platform that demonstrates the versatility of two DNA microgel formats to address fundamental challenges of protein engineering, including high protein yield, isolation of gene sets, and protein display. We utilize microgels to show successful protein production and capture of a model protein, green fluorescent protein (GFP), which is further used to demonstrate a successful gene enrichment through fluorescence-activated cell sorting (FACS) of a mixed population of microgels containing the GFP gene. Through psoralen cross-linking of the hydrogels, we have synthesized DNA microgels capable of surviving denaturing conditions while still possessing the ability to produce protein. Lastly, we demonstrate a method of producing extremely high local gene concentrations of up to 32 000 gene repeats in hydrogels 1 to 2 μm in diameter. These DNA gels can serve as a novel cell-free platform for integrated protein expression and display, which can be applied toward more powerful, scalable protein engineering and cell-free synthetic biology with no physiological boundaries and limitations.

Branch-PCR Constructed Stable shRNA Transcription Nanoparticles Have Long-Lasting RNAi Effect

RNA interference (RNAi) is a cellular process for gene silencing. Because of poor serum stability, transferring dsRNA directly into the target cells is a challenge. We report a facile and universal strategy to construct short hairpin RNA (shRNA) transcription nanoparticles with multiple shRNA transcription templates by PCR with flexible branched primers (branch-PCR). Compared with conventional linear shRNA transcription templates, these shRNA transcription nanoparticles show excellent stability against digestion by exonuclease III. Importantly, we found that our highly stable shRNA transcription nanoparticles can also be transcribed and thus induce efficient and long-lasting RNAi with picomolar activity in living mammalian cells. These chemically well-defined branch-PCR-generated stable shRNA transcription nanoparticles might facilitate RNAi delivery with a long-lasting RNAi effects.

Functional nucleic acid-based hydrogels for bioanalytical and biomedical applications

Hydrogels are crosslinked hydrophilic polymers that can absorb a large amount of water. By their hydrophilic, biocompatible and highly tunable nature, hydrogels can be tailored for applications in bioanalysis and biomedicine. Of particular interest are DNA-based hydrogels owing to the unique features of nucleic acids. Since the discovery of the DNA double helical structure, interest in DNA has expanded beyond its genetic role to applications in nanotechnology and materials science. In particular, DNA-based hydrogels present such remarkable features as stability, flexibility, precise programmability, stimuli-responsive DNA conformations, facile synthesis and modification. Moreover, functional nucleic acids (FNAs) have allowed the construction of hydrogels based on aptamers, DNAzymes, i-motif nanostructures, siRNAs and CpG oligodeoxynucleotides to provide additional molecular recognition, catalytic activities and therapeutic potential, making them key players in biological analysis and biomedical applications. To date, a variety of applications have been demonstrated with FNA-based hydrogels, including biosensing, environmental analysis, controlled drug release, cell adhesion and targeted cancer therapy. In this review, we focus on advances in the development of FNA-based hydrogels, which have fully incorporated both the unique features of FNAs and DNA-based hydrogels. We first introduce different strategies for constructing DNA-based hydrogels. Subsequently, various types of FNAs and the most recent developments of FNA-based hydrogels for bioanalytical and biomedical applications are described with some selected examples. Finally, the review provides an insight into the remaining challenges and future perspectives of FNA-based hydrogels.

Efficient construction of stable gene nanoparticles through polymerase chain reaction with flexible branched primers for gene delivery

Flexible branched primers were designed to construct stable gene nanoparticles with multiple target gene copies through polymerase chain reaction, which can be used as an efficient transcription template in eukaryotic cells for gene delivery.

Flexibility of C3h -Symmetrical Linkers in Tris-oligonucleotide-Based Tetrahedral Scaffolds

Flexibility of tris-oligonucleotides is determined by the length of their connecting hydrocarbon chains. Tris-oligonucleotides are branched DNA building blocks with three oligonucleotide arms attached to a C3h -symmetrical linker core at these chains. Four tris-oligonucleotides hybridise into a tetrahedral nanocage by sequence-determined self-assembly. The influence of methylene, ethylene and propylene chains was studied by synthesising sets of tris-oligonucleotides and analysing the relative stability of the hybridisation products against digestion by mung bean nuclease by using gel electrophoresis. Linkers with ethylene chains showed sufficient flexibility, whereas methylene-chain linkers were too rigid. Tris-oligonucleotides based on the latter still formed tetrahedral scaffolds in intermixing experiments with linkers of higher flexibility. Thus, a new generation of versatile isocyanurate-based linkers was established.

Critical Effect of Base Pairing of Target Pyrimidine on the Interstrand Photo-Cross-Linking of DNA via 3-Cyanovinylcarbazole Nucleoside

To evaluate the effect of base pairing of the target pyrimidine on the interstrand photo-cross-linking reaction of DNA via 3-cyanovinylcarbazole nucleoside ((CNV)K), a complementary base of target pyrimidine was substituted with noncanonical purine bases or 1,3-propandiol (S). As the decrease of the hydrogen bonds in the base pairing of target C accelerated the photo-cross-linking reaction markedly (3.6- to 7.7-fold), it can be concluded that the number of hydrogen bonds in the base pairing, i.e., the stability of base pairing, of the target pyrimidine plays a critical role in the interstrand photo-cross-linking reaction. In the case of G to S substitution, the highest photoreactivity toward C was observed, whose photoreaction rate constant (k = 2.0 s(-1)) is comparable to that of (CNV)K toward T paired with A (k = 3.5 s(-1)). This is the most reactive photo-cross-linking reaction toward C in the sequence specific interstrand photo-cross-linking. This might facilitate the design of the photo-cross-linkable oligodeoxyribonucleotides for various target sequences.

"Post-it" type connected DNA created with a reversible covalent cross-link

We report the development of a new heterobase that is held together through reversible bonding. The so-formed cross-link adds strong stabilization to the DNA duplex. Despite this, the cross-link opens and closes through reversible imine bonding. Moreover, even enzymatic incorporation of the cross-link is possible. The new principle can be used to stabilize DNA duplexes and nanostructures that otherwise require high salt concentrations, which may hinder biological applications.

Diffusion-based microfluidic PCR for "one-pot" analysis of cells

Genetic analysis starting with cell samples often requires multi-step processing including cell lysis, DNA isolation/purification, and polymerase chain reaction (PCR) based assays. When conducted on a microfluidic platform, the compatibility among various steps often demands a complicated procedure and a complex device structure. Here we present a microfluidic device that permits a "one-pot" strategy for multi-step PCR analysis starting from cells. Taking advantage of the diffusivity difference, we replace the smaller molecules in the reaction chamber by diffusion while retaining DNA molecules inside. This simple scheme effectively removes reagents from the previous step to avoid interference and thus permits multi-step processing in the same reaction chamber. Our approach shows high efficiency for PCR and potential for a wide range of genetic analysis including assays based on single cells.