Comparing proteins and nucleic acids for next-generation biomolecular engineering

Topological Single-stranded DNA Encoding and Programmable Assembly of Molecular Nanostructures for NIR-II Cancer Theranostics

Molecular nanotechnology promises to offer privileged access to developing NIR-II materials with precise structural and functional manipulation for transformable theranostic applications. However, the lack of an affordable, yet general, method makes this goal currently inaccessible. By virtue of the intriguing nucleic acid chemistry, here we present an artificial base-directed topological single-strand DNA encoding design that enables one-step synthesis of valence-controlled NIR-II molecular nanostructures and spatial assembly of these nanostructures to modulate their behaviors in living systems. As proof-of-concept studies, we construct ultrasmall Ag2 S quantum dots and pH-responsive, size-tunable CuS assemblies for in vivo NIR-II fluorescence imaging and deep tumor photothermal therapy. This work paves a new way for creating functionally diversified architectures and broadens the scope of DNA-encoded material engineering.

Application of DNA Nanotweezers in biosensing: Nanoarchitectonics and advanced challenges

Deoxyribonucleic acid (DNA) is a carrier of genetic information. DNA hybridization is characterized by predictability, diversity, and specificity owing to the strict complementary base-pairing assembly mode, which stimulates the use of DNA to build a variety of nanomachines, including DNA tweezers, motors, walkers, and robots. DNA nanomachines have become prevalent for signal amplification and transformation in the field of biosensing, providing a new method for constructing highly sensitive sensing analysis strategies. DNA tweezers have exhibited unique advantages in biosensing applications owing to their simple structures and fast responses. The two-state conformation of DNA tweezers, the open and closed states, enable them to open and close autonomously after stimulation, thus facilitating the quick detection of corresponding signal changes of different targets. This review discusses the recent progress in the application of DNA nanotweezers in the field of biosensing, and the trends in their development for application in the field of biosensing are summarized.

Functional Nanopores Enabled with DNA

Membrane-spanning nanopores are used in label-free single-molecule sensing and next-generation portable nucleic acid sequencing, and as powerful research tools in biology, biophysics, and synthetic biology. Naturally occurring protein and peptide pores, as well as synthetic inorganic nanopores, are used in these applications, with their limitations. The structural and functional repertoire of nanopores can be considerably expanded by functionalising existing pores with DNA strands and by creating an entirely new class of nanopores with DNA nanotechnology. This review outlines progress in this area of functional DNA nanopores and outlines developments to open up new applications.

Creating complex protocells and prototissues using simple DNA building blocks

Building synthetic protocells and prototissues hinges on the formation of biomimetic skeletal frameworks. Recreating the complexity of cytoskeletal and exoskeletal fibers, with their widely varying dimensions, cellular locations and functions, represents a major material hurdle and intellectual challenge which is compounded by the additional demand of using simple building blocks to ease fabrication and control. Here we harness simplicity to create complexity by assembling structural frameworks from subunits that can support membrane-based protocells and prototissues. We show that five oligonucleotides can anneal into nanotubes or fibers whose tunable thicknesses and lengths spans four orders of magnitude. We demonstrate that the assemblies' location inside protocells is controllable to enhance their mechanical, functional and osmolar stability. Furthermore, the macrostructures can coat the outside of protocells to mimic exoskeletons and support the formation of millimeter-scale prototissues. Our strategy could be exploited in the bottom-up design of synthetic cells and tissues, to the generation of smart material devices in medicine.

Designer, Programmable DNA-peptide hybrid materials with emergent properties to probe and modulate biological systems

The chemistry of DNA endows it with certain functional properties that facilitate the generation of self-assembled nanostructures, offering precise control over their geometry and morphology, that can be exploited for advanced biological applications. Despite the structural promise of these materials, their applications are limited owing to lack of functional capability to interact favourably with biological systems, which has been achieved by functional proteins or peptides. Herein, we outline a strategy for functionalizing DNA structures with short-peptides, leading to the formation of DNA-peptide hybrid materials. This proposition offers the opportunity to leverage the unique advantages of each of these bio-molecules, that have far reaching emergent properties in terms of better cellular interactions and uptake, better stability in biological media, an acceptable and programmable immune response and high bioactive molecule loading capacities. We discuss the synthetic strategies for the formation of these materials, namely, solid-phase functionalization and solution-coupling functionalization. We then proceed to highlight selected biological applications of these materials in the domains of cell instruction & molecular recognition, gene delivery, drug delivery and bone & tissue regeneration. We conclude with discussions shedding light on the challenges that these materials pose and offer our insights on future directions of peptide-DNA research for targeted biomedical applications.

DNA-Based Molecular Machines

Artificial molecular machines have found widespread applications ranging from fundamental studies to biomedicine. More recent advances in exploiting unique physical and chemical properties of DNA have led to the development of DNA-based artificial molecular machines. The unprecedented programmability of DNA provides a powerful means to design complex and sophisticated DNA-based molecular machines that can exert mechanical force or motion to realize complex tasks in a controllable, modular fashion. This Perspective highlights the potential and strategies to construct artificial molecular machines using double-stranded DNA, functional nucleic acids, and DNA frameworks, which enable improved control over reaction pathways and motion behaviors. We also outline the challenges and opportunities of using DNA-based molecular machines for biophysics, biosensing, and biocomputing.

Inhibition of Bacteria In Vitro and In Vivo by Self-Assembled DNA-Silver Nanocluster Structures

Antimicrobial nanomaterials hold great promise for bacteria-infected wound healing. However, it remains a challenge to balance antimicrobial efficacy and biocompatibility for these artificial antimicrobials. Here we employed biocompatible genetic molecule DNA as a building material to fabricate antimicrobial materials, including self-assembled Y-shaped DNA-silver nanocluster composite (Y-Ag) and Y-Ag hydrogel (Y-Ag-gel). We demonstrate that macroscopic and microcosmic DNA-Ag composites can effectively inhibit bacterial growth but do not affect cell proliferation in vitro. In particular, Y-Ag spray can speed up the process of wound healing in vivo. Considering the efficacy and advantages of DNA-based materials, our findings provide a promising route to fabricate a novel wound dressing such as spray and hydrogel for therapeutic wound healing.

Highly shape- and size-tunable membrane nanopores made with DNA

Membrane nanopores are key for molecular transport in biology, portable DNA sequencing^1-4, label-free single-molecule analysis^5-14 and nanomedicine⁵. Transport traditionally relies on barrel-like channels of a few nanometres width, but there is considerable scientific and technological interest for much wider structures of tunable shape. Yet, these nanopores do not exist in nature and are challenging to build using existing de novo routes for proteins^10,15-17. Here, we show that rational design with DNA can drastically expand the structural and functional range of membrane nanopores. Our design strategy bundles DNA duplexes into pore subunits that modularly arrange to form tunable pore shapes and lumen widths of up to tens of nanometres. Functional units for recognition or signalling can be optionally attached. By dialling in essential parameters, we demonstrate the utility and potential of the custom-engineered nanopores by electrical direct single-molecule sensing of 10-nm-sized proteins using widely used research and hand-held analysis devices. The designer nanopores illustrate how DNA nanotechnology can deliver functional biomolecular structures to be used in synthetic biology, single-molecule enzymology and biophysical analysis, as well as portable diagnostics and environmental screening.

Strategies to Build Hybrid Protein-DNA Nanostructures

Proteins and DNA exhibit key physical chemical properties that make them advantageous for building nanostructures with outstanding features. Both DNA and protein nanotechnology have growth notably and proved to be fertile disciplines. The combination of both types of nanotechnologies is helpful to overcome the individual weaknesses and limitations of each one, paving the way for the continuing diversification of structural nanotechnologies. Recent studies have implemented a synergistic combination of both biomolecules to assemble unique and sophisticate protein-DNA nanostructures. These hybrid nanostructures are highly programmable and display remarkable features that create new opportunities to build on the nanoscale. This review focuses on the strategies deployed to create hybrid protein-DNA nanostructures. Here, we discuss strategies such as polymerization, spatial directing and organizing, coating, and rigidizing or folding DNA into particular shapes or moving parts. The enrichment of structural DNA nanotechnology by incorporating protein nanotechnology has been clearly demonstrated and still shows a large potential to create useful and advanced materials with cell-like properties or dynamic systems. It can be expected that structural protein-DNA nanotechnology will open new avenues in the fabrication of nanoassemblies with unique functional applications and enrich the toolbox of bionanotechnology.

Pathway-Dependent Co-Assembly of Elastin-Like Polypeptides

In natural systems, temperature-induced assembly of biomolecules can lead to the formation of distinct assembly states, created out of the same set of starting compounds, based on the heating trajectory followed. Until now it has been difficult to achieve similar behavior in synthetic polymer mixtures. Here, a novel pathway-dependent assembly based on stimulus-responsive polymers is shown. When a mixture of mono- and diblock copolymers, based on elastin-like polypeptides, is heated with a critical heating rate co-assembled particles are created that are monodisperse, stable, and have tunable hydrodynamic radii between 20 and 120 nm. Below this critical heating rate, the constituents separately form polymer assemblies. This process is kinetically driven and reversible in thermodynamically closed systems. Using the co-assembly pathway, fluorescent proteins and bioluminescent enzymes are encapsulated with high efficiency. Encapsulated cargo shows unperturbed function even after delivery into cells. The pathway-dependent co-assembly of elastin-like polypeptides is not only of fundamental interest from a materials science perspective, allowing the formation of multiple distinct assemblies from the same starting compounds, which can be interconverted by going back to the molecularly dissolved states. It also enables a versatile way for constructing highly effective vehicles for the cellular delivery of biomolecular cargo.

DNA Nanodevices with Selective Immune Cell Interaction and Function

DNA nanotechnology produces precision nanostructures of defined chemistry. Expanding their use in biomedicine requires designed biomolecular interaction and function. Of topical interest are DNA nanostructures that function as vaccines with potential advantages over nonstructured nucleic acids in terms of serum stability and selective interaction with human immune cells. Here, we describe how compact DNA nanobarrels bind with a 400-fold selectivity via membrane anchors to white blood immune cells over erythrocytes, without affecting cell viability. The selectivity is based on the preference of the cholesterol lipid anchor for the more fluid immune cell membranes compared to the lower membrane fluidity of erythrocytes. Compacting DNA into the nanostructures gives rise to increased serum stability. The DNA barrels furthermore functionally modulate white blood cells by suppressing the immune response to pro-inflammatory endotoxin lipopolysaccharide. This is likely due to electrostatic or steric blocking of toll-like receptors on white blood cells. Our findings on immune cell-specific DNA nanostructures may be applied for vaccine development, immunomodulatory therapy to suppress septic shock, or the targeting of bioactive substances to immune cells.

Design, assembly, and characterization of membrane-spanning DNA nanopores

DNA nanopores are bio-inspired nanostructures that control molecular transport across lipid bilayer membranes. Researchers can readily engineer the structure and function of DNA nanopores to synergistically combine the strengths of DNA nanotechnology and nanopores. The pores can be harnessed in a wide range of areas, including biosensing, single-molecule chemistry, and single-molecule biophysics, as well as in cell biology and synthetic biology. Here, we provide a protocol for the rational design of nanobarrel-like DNA pores and larger DNA origami nanopores for targeted applications. We discuss strategies for the pores' chemical modification with lipid anchors to enable them to be inserted into membranes such as small unilamellar vesicles (SUVs) and planar lipid bilayers. The procedure covers the self-assembly of DNA nanopores via thermal annealing, their characterization using gel electrophoresis, purification, and direct visualization with transmission electron microscopy and atomic force microscopy. We also describe a gel assay to determine pore-membrane binding and discuss how to use single-channel current recordings and dye flux assays to confirm transport through the pores. We expect this protocol to take approximately 1 week to complete for DNA nanobarrel pores and 2-3 weeks for DNA origami pores.

Toehold-Mediated Selective Assembly of Compact Discrete DNA Nanostructures

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

Designer, Programmable 3D DNA Nanodevices to Probe Biological Systems

DNA nanotechnology is a unique field that provides simple yet robust design techniques for self-assembling nanoarchitectures with extremely high potential for biomedical applications. Though the field began to exploit DNA to build various nanoscale structures, it has now taken a different path, diverging from the creation of complex structures to functional DNA nanodevices that explore various biological systems and mechanisms. Here, we present a brief overview of DNA nanotechnology, summarizing the key strategies for construction of various DNA nanodevices, with special focus on three-dimensional (3D) nanocages or polyhedras. We then discuss biological applications of 3D DNA nanocages, particularly tetrahedral DNA cages, in their ability to program and modulate cellular systems, in biosensing, and as tools for targeted therapeutics. We conclude with a final discussion on challenges and perspectives of 3D DNA nanodevices in biomedical applications.

Site-Selective and Rewritable Labeling of DNA through Enzymatic, Reversible, and Click Chemistries

Current methods for bioconjugation rely on the introduction of stable linkers that lack the required versatility to perform sequential functionalizations. However, sequential manipulations are an increasing requirement in chemical biology because they can underpin multiple analyses of the same sample to provide a wider understanding of cell behavior. Here, we present a new method to site-selectively write, remove, and rewrite chemical functionality to a biomolecule, DNA in this case. Our method combines the precision and robustness of methyltransferase-directed labeling with the reversibility of acyl hydrazones and the efficiency of click chemistry. Underpinning the method is a new S-adenosyl-l-methionine derivative to site-selectively label DNA with a bifunctional chemical handle containing an acyl hydrazone-linker and a terminal azide. Functional tags are conjugated via the azide and can be removed (i.e., untagged) when needed at the acyl hydrazone via exchange with hydroxyl amine. The formed hydrazide-labeled DNA is a versatile intermediate that can be either rewritten to reset the original chemical handle or covalently reacted with a permanent tag. This ability to write, tag, untag, and permanently tag DNA is exploited to sequentially introduce two fluorescent dyes on DNA. Finally, we demonstrate the potential of the method by developing a protocol to sort labeled DNA using magnetic beads, with subsequent amplification of the sorted DNA sample for further analysis. The presented method opens new avenues for site-selective bioconjugation and should underpin integrative approaches in chemical biology where sequential functionalizations of the same sample are required.

Extracellular Vesicles Derived From Mesenchymal Stem Cells (MSC) in Regenerative Medicine: Applications in Skin Wound Healing

The cells secrete extracellular vesicles (EV) that may have an endosomal origin, or from evaginations of the plasma membrane. The former are usually called exosomes, with sizes ranging from 50 to 100 nm. These EV contain a lipid bilayer associated to membrane proteins. Molecules such as nucleic acids (DNA, mRNA, miRNA, lncRNA, etc.) and proteins may be stored inside. The EV composition depends on the producer cell type and its physiological conditions. Through them, the cells modify their microenvironment and the behavior of neighboring cells. That is accomplished by transferring factors that modulate different metabolic and signaling pathways. Due to their properties, EV can be applied as a diagnostic and therapeutic tool in medicine. The mesenchymal stromal cells (MSC) have immunomodulatory properties and a high regenerative capacity. These features are linked to their paracrine activity and EV secretion. Therefore, research on exosomes produced by MSC has been intensified for use in cell-free regenerative medicine. In this area, the use of EV for the treatment of chronic skin ulcers (CSU) has been proposed. Such sores occur when normal healing does not resolve properly. That is usually due to excessive prolongation of the inflammatory phase. These ulcers are associated with aging and diseases, such as diabetes, so their prevalence is increasing with the one of such latter disease, mainly in developed countries. This has very important socio-economic repercussions. In this review, we show that the application of MSC-derived EV for the treatment of CSU has positive effects, including accelerating healing and decreasing scar formation. This is because the EV have immunosuppressive and immunomodulatory properties. Likewise, they have the ability to activate the angiogenesis, proliferation, migration, and differentiation of the main cell types involved in skin regeneration. They include endothelial cells, fibroblasts, and keratinocytes. Most of the studies carried out so far are preclinical. Therefore, there is a need to advance more in the knowledge about the conditions of production, isolation, and action mechanisms of EV. Interestingly, their potential application in the treatment of CSU opens the door for the design of new highly effective therapeutic strategies.

Single-Atom Catalysts in Catalytic Biomedicine

The intrinsic deficiencies of nanoparticle-initiated catalysis for biomedical applications promote the fast development of alternative versatile theranostic modalities. The catalytic performance and selectivity are the critical issues that are challenging to be augmented and optimized in biological conditions. Single-atom catalysts (SACs) featuring atomically dispersed single metal atoms have emerged as one of the most explored catalysts in biomedicine recently due to their preeminent catalytic activity and superior selectivity distinct from their nanosized counterparts. Herein, an overview of the pivotal significance of SACs and some underlying critical issues that need to be addressed is provided, with a specific focus on their versatile biomedical applications. Their fabrication strategies, surface engineering, and structural characterizations are discussed briefly. In particular, the catalytic performance of SACs in triggering some representative catalytic reactions for providing the fundamentals of biomedical use is discussed. A sequence of representative paradigms is summarized on the successful construction of SACs for varied biomedical applications (e.g., cancer treatment, wound disinfection, biosensing, and oxidative-stress cytoprotection) with an emphasis on uncovering the intrinsic catalytic mechanisms and understanding the underlying structure-performance relationships. Finally, opportunities and challenges faced in the future development of SACs-triggered catalysis for biomedical use are discussed and outlooked.

Visualizing in Vivo Dynamics of Designer Nanoscaffolds

Enzymes of natural biochemical pathways are routinely subcellularly organized in space and time in order to improve pathway efficacy and control. Designer scaffolding platforms are under development to confer similar benefits upon engineered pathways. Herein, we evaluate bacterial microcompartment shell (pfam0936-domain) proteins as modules for constructing well-defined nanometer scale scaffolds in vivo. We use a suite of visualization techniques to evaluate scaffold assembly and dynamics. We demonstrate recruitment of target cargo molecules onto assembled scaffolds by appending reciprocally interacting adaptor domains. These interactions can be refined by fine-tuning the scaffold expression level. Real-time observation of this system reveals a nucleation-limited step where multiple scaffolds initially form within a cell. Over time, nucleated scaffolds reorganize into a single intracellular assembly, likely due to interscaffold competition for protein subunits. Our results suggest design considerations for using self-assembling proteins as building blocks to construct nanoscaffolds, while also providing a platform to visualize scaffold-cargo dynamics in vivo.

A trade-off for covalent and intercalation binding modes: a case study for Copper (II) ions and singly modified DNA nucleoside

Selective binding to nucleic acids and, more generally, to biopolymers, very often requires at a minimum the presence of specific functionalities and precise spatial arrangement. DNA can fold into defined 3D structures upon binding to metal centers and/or lanthanides. Binding efficiency can be boosted by modified nucleosides incorporated into DNA sequences. In this work the high selectivity of modified nucleosides towards copper (II) ions, when used in the monomeric form, is unexpectedly and drastically reduced upon being covalently attached to the DNA sequence in single-site scenario. Surprisingly, such selectivity is partially retained upon non-covalent (i.e. intercalation) mixture formed by native DNA duplex and a nucleoside in the monomeric form. Exploiting the electron spin properties of such different and rich binding mode scenarios, 1D/2D pulsed EPR experiments have been used and tailored to differentiate among the different modes. An unusual correlation of dispersion of hyperfine couplings and strength of the binding mode(s) is described.

Evolutionary Refinement of DNA Nanostructures Using Coarse-Grained Molecular Dynamics Simulations

In the past decade, DNA nanostructures have made the leap from small assemblies of a handful of oligonucleotides to megadalton objects assembled from hundreds or thousands of component DNA strands. Most DNA designs today are either lattice based with simple and reliable design tools or lattice free with a larger shape space but more challenging design and lower rigidity. In parallel with the development of DNA nanostructures, software packages for the simulation of nucleic acids have seen rapid development allowing for the simulation of the dynamics of full DNA nanostructure assemblies. Here, we implement an unsupervised software based on the coarse-grained molecular dynamics package oxDNA to simulate DNA origami structures and evaluate their rigidity. From this, the software autonomously produces mutant structures by adding or removing base pairs or modifying the positions of internal supports. These mutant structures are iteratively generated and evaluated by simulation to create an in silico evolution toward more rigid DNA nanostructures.

Synthetic protein-conductive membrane nanopores built with DNA

Nanopores are key in portable sequencing and research given their ability to transport elongated DNA or small bioactive molecules through narrow transmembrane channels. Transport of folded proteins could lead to similar scientific and technological benefits. Yet this has not been realised due to the shortage of wide and structurally defined natural pores. Here we report that a synthetic nanopore designed via DNA nanotechnology can accommodate folded proteins. Transport of fluorescent proteins through single pores is kinetically analysed using massively parallel optical readout with transparent silicon-on-insulator cavity chips vs. electrical recordings to reveal an at least 20-fold higher speed for the electrically driven movement. Pores nevertheless allow a high diffusive flux of more than 66 molecules per second that can also be directed beyond equillibria. The pores may be exploited to sense diagnostically relevant proteins with portable analysis technology, to create molecular gates for drug delivery, or to build synthetic cells.

Toward Precise Manipulation of DNA-Protein Hybrid Nanoarchitectures

Nucleic acids and proteins are the two primary building materials of living organisms. Over the past decade, artificial DNA-protein hybrid structures have been pursued for a wide range of applications. DNA nanotechnology, in particular, has dramatically expanded nanoscale molecule engineering and contributed to the spatial arrangement of protein components. Strategies for designing site-specific coupling of DNA oligomers to proteins are needed in order to allow for precise control over stoichiometry and position. Efforts have also been focused on coassembly of protein-DNA complexes by engineering their fundamental molecular recognition interactions. This Concept focuses on the precise manipulation of DNA-protein nanoarchitectures. Particular attention is paid to site-selectivity within DNA-protein conjugates, regulation of protein orientation using DNA scaffolds, and coassembly principles upon unique structural motifs. Current challenges and future directions are also discussed in the design and application of DNA-protein nanoarchitectures.

Structural and Functional Stability of DNA Nanopores in Biological Media

DNA nanopores offer a unique nano-scale foothold at the membrane interface that can help advance the life sciences as biophysical research tools or gate-keepers for drug delivery. Biological applications require sufficient physiological stability and membrane activity for viable biological action. In this report, we determine essential parameters for efficient nanopore folding and membrane binding in biocompatible cell media. The parameters are identified for an archetypal DNA nanopore composed of six interwoven strands carrying cholesterol lipid anchors. Using gel electrophoresis and fluorescence spectroscopy, the nanostructures are found to assemble efficiently in cell media, such as LB and DMEM, and remain structurally stable at physiological temperatures. Furthermore, the pores’ oligomerization state is monitored using fluorescence spectroscopy and confocal microscopy. The pores remain predominately water-soluble over 24 h in all buffer systems, and were able to bind to lipid vesicles after 24 h to confirm membrane activity. However, the addition of fetal bovine serum to DMEM causes a significant reduction in nanopore activity. Serum proteins complex rapidly to the pore, most likely via ionic interactions, to reduce the effective nanopore concentration in solution. Our findings outline crucial conditions for maintaining lipidated DNA nanodevices, structurally and functionally intact in cell media, and pave the way for biological studies in the future.

A Temperature-Gated Nanovalve Self-Assembled from DNA to Control Molecular Transport across Membranes

Nanopores are powerful nanodevices that puncture semifluid membranes to enable transport of molecular matter across biological or synthetic thin layers. Advanced nanopores featuring more complex functions such as ambient sensing and reversible channel opening are of considerable scientific and technological interest but challenging to achieve with classical building materials. Here we exploit the predictable assembly properties of DNA to form a multifunctional nanovalve that senses temperature for controlled channel opening and tunable transport. The barrel-shaped valve is formed from solely seven oligonucleotides and is closed at ambient temperatures. At >40 °C a programmable thermosensitive lid opens the barrel to allow transport of small molecules across the membrane. The multifunctional DNA nanodevice may be used to create logic ionic networks or to achieve controlled drug delivery from vesicles.

Cholesterol Anchors Enable Efficient Binding and Intracellular Uptake of DNA Nanostructures

DNA nanostructures constitute a rapidly advancing tool-set for exploring cell-membrane functions and intracellular sensing or advancing delivery of biomolecular cargo  into cells. Chemical conjugation with lipid anchors can mediate binding of DNA nanostructures to synthetic lipid bilayers, yet how such structures interact with biological membranes and internalize cells has not been shown. Here, an archetypal 6-duplex nanobundle is used to investigate how lipid conjugation influences DNA cell binding and internalization kinetics. Cellular interactions of DNA nanobundles modified with one and three cholesterol anchors were assessed using flow cytometry and confocal microscopy. Nuclease digestion was used to distinguish surface-bound DNA, which is nuclease accessible, from internalized DNA. Three cholesterol anchors were found to enhance cellular association by up to 10-fold when compared with unmodified DNA. The bundles were endocytosed efficiently within 24 h. The results can help design controlled DNA binding and trafficking into cells.

Chemistries for DNA Nanotechnology

The predictable nature of DNA interactions enables the programmable assembly of highly advanced 2D and 3D DNA structures of nanoscale dimensions. The access to ever larger and more complex structures has been achieved through decades of work on developing structural design principles. Concurrently, an increased focus has emerged on the applications of DNA nanostructures. In its nature, DNA is chemically inert and nanostructures based on unmodified DNA mostly lack function. However, functionality can be obtained through chemical modification of DNA nanostructures and the opportunities are endless. In this review, we discuss methodology for chemical functionalization of DNA nanostructures and provide examples of how this is being used to create functional nanodevices and make DNA nanostructures more applicable. We aim to encourage researchers to adopt chemical modifications as part of their work in DNA nanotechnology and inspire chemists to address current challenges and opportunities within the field.

Tuning coiled coil stability with histidine-metal coordination

Coiled coils (CCs) have emerged as versatile building blocks for the synthesis of nanostructures, drug delivery systems and biomimetic hydrogels. Bioengineering metal coordination sites into the terminal ends of a synthetic coiled coil (CC), we generate a nanoscale biological building block with tunable stability. The reversible coordination of Ni2+ thermodynamically stabilizes the CC, as shown with circular dichroism spectroscopy. Using atomic force microscopy-based single-molecule force spectroscopy, it is further shown that Ni2+-binding reinforces the CC mechanically, increasing the barrier height for dissociation. When used as a dynamic crosslink in polyethyleneglycol-based hydrogels, the single-molecule stability of the CC is directly transferred to the bulk material and determines its viscoelastic properties. This reversibly tunable CC, thus, highlights an effective strategy for rationally engineering the single-molecule properties of biomolecular building blocks, which can be translated to the emergent properties of biomimetic materials, as well as other CC containing molecular assemblies.