Classifying Cell Types with DNA-Encoded Ligand-Receptor Interactions on the Cell Membrane

Orthogonal Host-Guest Interactions Enable Programming of Protocell Membranes for Cellular High-Order Assembly and Enhanced Immunogenicity

The complement system's distinguishing feature is its cell-specific surface ligands. However, the limited scalability and complexity of incorporating surface-customizable ligands into membrane-bound cell-like microassemblages have hindered their widespread adoption in synthetic biology and bioengineering. Here, we present a method for the batch construction of polysaccharide-based microcapsules (polysaccharidosomes, P-somes) with intrinsic functional host membranes capable of docking guest ligands via facile host-guest interactions. β-Cyclodextrin (β-CD) conjugated to the microcapsule membrane building block serves as the host entity for guest adamantane-linked functional molecules Cyanine5 (Cy5) and Pam3CSK4 (PAM). Interactive docking of either an aggregation agent, Cy5, or a Toll-like receptor agonist, Pam3CSK4, on P-somes followed by incubation with macrophages resulted in aggregation and immune activation of macrophages, respectively. The specificity of host-guest interactions allows for the expedited incorporation of additional functionalities into microassemblages. This can be instrumental in engineering cell-like membrane surfaces that replicate genuine cell-cell interactions, offering a unified platform for the development of micrometer-sized programmable therapeutic protocells.

Functionalized Multichannel Fluorescence-Encoded Nanosystem on Erythrocyte-Coated Nanoparticles for Precise Cancer Subtype Discrimination

Rapid and precise cancer subtype discrimination is essential for personalized oncology. Conventional diagnostic methods often lack sufficient accuracy and speed. Here, we introduce a multichannel fluorescence-encoded nanosystem based on erythrocyte-coated polydopamine nanoparticles (PDA@EM), functionalized with multiple resurfaced fluorescent proteins. The fluorescence of these proteins is initially quenched by PDA@EM and restored upon cell addition. This multichannel fluorescence-encoded nanosystem enables highly sensitive "turn-on" fluorescence profiling of cancer cells within 30 min, achieving 100% accuracy in distinguishing various proteins and classifying a wide range of cancer cell lines, including subtypes of oral squamous cell carcinoma (OSCC). Notably, it offers rapid, label-free diagnostics of OSCC malignancy from clinical samples postsurgery. This capability was validated through histopathological and proteomic analyses, which identified protein signatures associated with tumor progression and immune suppression. Overall, our multichannel nanosensor represents an advanced molecular diagnostics platform, paving the way for personalized cancer treatment in clinical oncology.

Programmable DNA Scaffolds Enable Orthogonal Engineering of Cell Membrane-Based Nanovesicles for Therapeutic Development

Cell membrane-based nanovesicles (CMNVs) play pivotal roles in biomolecular transportation in living organisms and appear as attractive bioinformed nanomaterials for theranostic applications. However, the current surface-engineering technologies are limited in flexibility and orthogonality, making it challenging to simultaneously display multiple different ligands on the CMNV surface in a precisely controlled manner. Here, we developed a DNA scaffold-programmed approach to orthogonally engineer CMNVs with versatile ligands. The designed DNA scaffolds can rapidly anchor onto the CMNV surface, and their unique sequences and hybridized properties enable independent control of the loading of multiple different types of biomolecules on the CMNVs. As a result, the orthogonal engineering of CMNVs with a renal targeted peptide and a therapeutic protein at controlled ratios demonstrated an enhanced renal targeting and repair potential in vivo. This study highlights that a DNA scaffold-programmed platform can provide a potent means for orthogonal and flexible surface engineering of CMNVs for diverse therapeutic purposes.

DNA-based nanostructures for RNA delivery

RNA-based therapeutics have emerged as a promising approach for the treatment of various diseases, including cancer, genetic disorders, and infectious diseases. However, the delivery of RNA molecules into target cells has been a major challenge due to their susceptibility to degradation and inefficient cellular uptake. To overcome these hurdles, DNA-based nano technology offers an unprecedented opportunity as a potential delivery platform for RNA therapeutics. Due to its excellent characteristics such as programmability and biocompatibility, these DNA-based nanostructures, composed of DNA molecules assembled into precise and programmable structures, have garnered significant attention as ideal building materials for protecting and delivering RNA payloads to the desired cellular destinations. In this review, we highlight the current progress in the design and application of three DNA-based nanostructures: DNA origami, lipid-nanoparticle (LNP) technology related to frame guided assembly (FGA), and DNA hydrogel for the delivery of RNA molecules. Their biomedical applications are briefly discussed and the challenges and future perspectives in this field are also highlighted.

Data-driven classification of individual cells by their non-Markovian motion

We present a method to differentiate organisms solely by their motion based on the generalized Langevin equation (GLE) and use it to distinguish two different swimming modes of strongly confined unicellular microalgae Chlamydomonas reinhardtii. The GLE is a general model for active or passive motion of organisms and particles that can be derived from a time-dependent general many-body Hamiltonian and in particular includes non-Markovian effects (i.e., the trajectory memory of its past). We extract all GLE parameters from individual cell trajectories and perform an unbiased cluster analysis to group them into different classes. For the specific cell population employed in the experiments, the GLE-based assignment into the two different swimming modes works perfectly, as checked by control experiments. The classification and sorting of single cells and organisms is important in different areas; our method, which is based on motion trajectories, offers wide-ranging applications in biology and medicine.

Directing the Encapsulation of Single Cells with DNA Framework Nucleator-Based Hydrogel Growth

Encapsulating individual mammalian cells with biomimetic materials holds potential in ex vivo cell culture and engineering. However, current methodologies often present tradeoffs between homogeneity, stability, and cell compatibility. Here, inspired by bacteria that use proteins stably anchored on their outer membranes to nucleate biofilm growth, we develop a single-cell encapsulation strategy by using a DNA framework structure as a nucleator (DFN) to initiate the growth of DNA hydrogels under cell-friendly conditions. We find that among the tested structures, the tetrahedral DFN can evenly and stably reside on cell membranes, effectively initiating hybridization chain reactions which generate homogeneously dense yet flexible single-cell encapsulation for diverse cell lines. The encapsulation persists for up to 72 hours in a serum-containing cell culture environment, representing a ~70-fold improvement compared to encapsulations mediated by single-stranded DNA nucleators. The metabolism and proliferation of the encapsulated cells are suppressed, but can be restored to the original efficiencies upon release, suggesting the superior cell compatibility of the encapsulation. We also find that compared to naked cells, the encapsulated cells exhibit a lower autophagy level after undergoing mechanical stress, suggesting the protective effect of the DNA encapsulation. This method may provide a new tool for ex vivo cell engineering.

Advancing cell surface modification in mammalian cells with synthetic molecules

Biological cells, being the fundamental entities of life, are widely acknowledged as intricate living machines. The manipulation of cell surfaces has emerged as a progressively significant domain of investigation and advancement in recent times. Particularly, the alteration of cell surfaces using meticulously crafted and thoroughly characterized synthesized molecules has proven to be an efficacious means of introducing innovative functionalities or manipulating cells. Within this realm, a diverse array of elegant and robust strategies have been recently devised, including the bioorthogonal strategy, which enables selective modification. This review offers a comprehensive survey of recent advancements in the modification of mammalian cell surfaces through the use of synthetic molecules. It explores a range of strategies, encompassing chemical covalent modifications, physical alterations, and bioorthogonal approaches. The review concludes by addressing the present challenges and potential future opportunities in this rapidly expanding field.

DNA-Programmed Stem Cell Niches via Orthogonal Extracellular Vesicle-Cell Communications

Extracellular vesicles (EVs) are natural carriers for intercellular transfer of bioactive molecules, which are harnessed for wide biomedical applications. However, a facile yet general approach to engineering interspecies EV-cell communications is still lacking. Here, the use of DNA to encode the heterogeneous interfaces of EVs and cells in a manner free of covalent or genetic modifications is reported, which enables orthogonal EV-cell interkingdom interactions in complex environments. Cholesterol-modified DNA strands and tetrahedral DNA frameworks are employed with complementary sequences to serve as artificial ligands and receptors docking on EVs and living cells, respectively, which can mediate specific yet efficient cellular internalization of EVs via Watson-Crick base pairing. It is shown that based on this system, human cells can adopt EVs derived from the mouse, watermelon, and Escherichia coli. By implementing several EV-cell circuits, it shows that this DNA-programmed system allows orthogonal EV-cell communications in complex environments. This study further demonstrates efficient delivery of EVs with bioactive contents derived from feeder cells toward monkey female germline stem cells (FGSCs), which enables self-renewal and stemness maintenance of the FGSCs without feeder cells. This system may provide a universal platform to customize intercellular exchanges of materials and signals across species and kingdoms.

Digital-scRRBS: A Cost-Effective, Highly Sensitive, and Automated Single-Cell Methylome Analysis Platform via Digital Microfluidics

Single-cell DNA methylation sequencing is highly effective for identifying cell subpopulations and constructing epigenetic regulatory networks. Existing methylome analyses require extensive starting materials and are costly, complex, and susceptible to contamination, thereby impeding the development of single-cell methylome technology. In this work, we report digital microfluidics-based single-cell reduced representation bisulfite sequencing (digital-scRRBS), the first microfluidics-based single-cell methylome library construction platform, which is an automatic, effective, reproducible, and reagent-efficient technique to dissect the single-cell methylome. Using our digital microfluidic chip, we isolated single cells in 15 s and successfully constructed single-cell methylation sequencing libraries with a unique genome mapping rate of up to 53.6%, covering up to 2.26 million CpG sites. Digital-scRRBS demonstrates a high capacity for distinguishing cell identity and tracking DNA methylation during drug administration. Digital-scRRBS expands the applicability of single-cell methylation methods as a versatile tool for epigenetic analysis of rare cells and populations with high levels of heterogeneity.

Multiplex lateral flow test strip for detection of carbapenemase genes using barcoded tetrahedral DNA capture probe-based biosensing interface

Carbapenem-resistant Enterobacterales pose significant global health challenges due to their rapid spread and ability to hydrolyse various beta-lactam antibiotics. Rapid tests for these carbapenemase genes are crucial to ensure appropriate prescription administration and infection control. In this study, we developed a rapid visual nanodiagnostic platform for multiplexed detection of carbapenemase genes using a lateral flow strip. The nanodiagnostic strip was designed with separate barcoded DNA tetrahedrons for the blaKPC and blaNDM genes. These tetrahedrons were distributed on a nitrocellulose membrane at two different test lines as capture probes. When tested against a panel of carbapenemase genes, the tetrahedral probes captured single-stranded amplicons of asymmetric PCR via strand hybridisation. The amplicons acted as bridging elements, binding the DNA-modified gold nanoparticles to the test line of the strip, resulting in clear visual readouts specific to the blaKPC and blaNDM genes. By employing barcoded tetrahedrons and asymmetric PCR in conjunction with the lateral flow strip, a single diagnostic test enabled the detection of multiple carbapenemase genes. The test yielded results as low as 0.12 fM for blaKPC and 0.05 fM for blaNDM within 75 min. Furthermore, the strip effectively identified specific carbapenemase genes in clinical isolates using real-time PCR, antibody-based lateral flow systems for carbapenemase detection, and carbapenemase phenotype experiments. Thus, the strip develop has a high potential for testing blaKPC and blaNDM genes in practice.

Programming the self-assembly of amphiphilic DNA frameworks for sequential boolean logic functions

Herein we examined the utilization of the orthogonal noncovalent interaction to program the self-assembly of amphiphilic DNA frameworks (am-FNAs). By finely controlling reaction parameters such as ionic strength, the length of amphiphilic DNA, and mechanical agitation, we constructed a series of amphiphilic DNA-based primary logic gates (NOT, AND, OR and INH) and a secondary logic gate (NOT-OR).

Digging into the biophysical features of cell membranes with lipid-DNA conjugates

Lipid-DNA conjugates have emerged as highly useful tools to modify the cell membranes. These conjugates generally consist of a lipid anchor for membrane modification and a functional DNA nanostructure for membrane analysis or regulation. There are several unique properties of these lipid-DNA conjugates, especially including their programmability, fast and efficient membrane insertion, and precise sequence-specific assembly. These unique properties have enabled a broad range of biophysical applications on live cell membranes. In this review, we will mainly focus on recent tremendous progress, especially during the past three years, in regulating the biophysical features of these lipid-DNA conjugates and their key applications in studying cell membrane biophysics. Some insights into the current challenges and future directions of this interdisciplinary field have also been provided.

Catalytic hairpin assembled polymeric tetrahedral DNA frameworks for MicroRNA imaging in live cells

Dynamic DNA nanodevices-based assembly is currently well developed for a broad range of analytical applications. However, some problems persist, such as false positives, nuclease digestions, and exclusive interferences with single signal in complex cellular environment. Herein, we have established a method for imaging cellular miR-155, where it induced assembly of two tetrahedral DNA frameworks (TDFs), TDF-1 and TDF-2, both of which had four fluorescence modified hairpins (Cy3 for TDF-1 and Cy5 for TDF-2, respectively) at each angle, into polymeric tetrahedral DNA frameworks (PTDFs). The formation of PTDFs was greatly dependent on miR-155 overexpressed in breast cancer cells since miR-155 drove catalytic hairpin assembly (CHA) reaction by opening the hairpins at the vertices of TDF-1 to hybridize with TDF-2. Upon the completion of hybridization, the miR-155 was released, starting the next cycle of the CHA reaction. Measurements of atomic force microscopy (AFM) and Förster resonance energy transfer (FRET) showed that the formation of PTDFs occurred owing to the multivalent assembly of TDF-1 and TDF-2. By utilizing the formation of PTDFs, miR-155 was detected in a linear range from 0.5 nM to 30 nM with a 0.35 nM limit of determination, enabling the successful imaging of endogenous miR-155 in live cells through the FRET signal from Cy3 to Cy5. These studies demonstrated that this method significantly strengthened the resistance nuclease to digestion and stable ability with exclusive interference.

Recent Progress and Perspectives on Cell Surface Modification

The cell membrane is a biological interface consisting of phospholipid bilayer, saccharides and proteins that maintains a stable metabolic intracellular environment as well as regulating and controlling the exchange of substances inside and outside the cell. Cell membranes provide a highly complex biological surface carrying a variety of essential surfaces ligands and receptors for cells to receive various stimuli of external signals, thereby inducing corresponding cell responses regulating the life activities of the cell. These surface receptors can be manipulated via cell surface modification to regulate cellular functions and behaviors Thus, cell surface modification has attracted considerable attention due to its significance in cell fate control, cell engineering and cell therapy. In this minireview, we describe the recent developments and advances of cell surface modification, and summarize the main modification methods with corresponding functions and applications. Finally, the prospect for the future development of the modification of the living cell membrane is discussed.

Programming cell communications with pH-responsive DNA nanodevices

DNA nanoswitches on cell surfaces could respond to changes of pH under physiological conditions by switching from a three-chain structure to a double-chain structure, thus connecting another set of cells modified with complementary single-stranded DNA. This pH-triggered cell communication offers a promising approach for cell-based therapy under a tumor microenvironment.

Engineering a Second-Order DNA Logic-Gated Nanorobot to Sense and Release on Live Cell Membranes for Multiplexed Diagnosis and Synergistic Therapy

Tumor biomarker-based theranostics have achieved broad interest and success in recent years. However, single biomarker-based recognition can cause false-positive feedback, including the on-target off-tumor phenomenon, in the absence of tumor-specific antigen. Multibiomarker-based recognition molecules often elicit nonspecific and undesired internalization when they bind to "bystander" cells. We report a universal DNA tetrahedral scaffold (DTS) that anchors on the cell membrane to load multiple aptamers and therapeutics for precise and effective theranostics. This DNA logic-gated nanorobot (DLGN) not only facilitates precise discrimination among five cell lines, but also triggers synergistic killing of effector aptamer-tethered synergistic drugs (EASDs) to target cancer cells. Logic-gated recognition integrated into aptamer-functionalized molecular machines will prompt fast tumor profiling, in situ capture and isolation, and safe delivery of precise medicine.

DNA nanostructure-based nucleic acid probes: construction and biological applications

In recent years, DNA has been widely noted as a kind of material that can be used to construct building blocks for biosensing, in vivo imaging, drug development, and disease therapy because of its advantages of good biocompatibility and programmable properties. However, traditional DNA-based sensing processes are mostly achieved by random diffusion of free DNA probes, which were restricted by limited dynamics and relatively low efficiency. Moreover, in the application of biosystems, single-stranded DNA probes face challenges such as being difficult to internalize into cells and being easily decomposed in the cellular microenvironment. To overcome the above limitations, DNA nanostructure-based probes have attracted intense attention. This kind of probe showed a series of advantages compared to the conventional ones, including increased biostability, enhanced cell internalization efficiency, accelerated reaction rate, and amplified signal output, and thus improved in vitro and in vivo applications. Therefore, reviewing and summarizing the important roles of DNA nanostructures in improving biosensor design is very necessary for the development of DNA nanotechnology and its applications in biology and pharmacology. In this perspective, DNA nanostructure-based probes are reviewed and summarized from several aspects: probe classification according to the dimensions of DNA nanostructures (one, two, and three-dimensional nanostructures), the common connection modes between nucleic acid probes and DNA nanostructures, and the most important advantages of DNA self-assembled nanostructures in the applications of biosensing, imaging analysis, cell assembly, cell capture, and theranostics. Finally, the challenges and prospects for the future development of DNA nanostructure-based nucleic acid probes are also discussed.

Recent Advances of DNA Nanostructure-Based Cell Membrane Engineering

Materials that can regulate the composition and structure of the cell membrane to fabricate engineered cells with defined functions are in high demand. Compared with other biomolecules, DNA has unique advantages in cell membrane engineering due to its excellent programmability and biocompatibility. Especially, the near-atomic scale precision of DNA nanostructures facilitates the investigation of structure-property relations on the cell membrane. In this review, first the state of the art of functional DNA nanostructures is summarized, and then the overview of the use of DNA nanostructures to engineer the cell membrane is presented. Subsequently, applications of DNA nanostructures in modifying cell membrane morphology, controlling ions transport, and synthesizing high precise liposomes are highlighted. Finally, the challenges and outlook on using DNA nanostructures for cell membrane engineering are discussed.

DNA nanotechnology-empowered nanoscopic imaging of biomolecules

DNA nanotechnology has led to the rise of DNA nanostructures, which possess programmable shapes and are capable of organizing different functional molecules and materials. A variety of DNA nanostructure-based imaging probes have been developed.