Amphiphilic Block Copolymers PEG-b-PMTCs: Synthesis, Self-Assembly, Degradation Properties and Biocompatibility.

As a hydrophilic cyclic ketene acetal (CKA), 2-methylene-1,3,6-trioxocane (MTC) has recently attracted a lot of attention owing to its ability to promote a quicker (bio)degradation as compared to other heavily studied CKAs. Here, we prepared amphiphilic block copolymers based on poly-MTC with varying chain lengths by radical ring opening polymerization. Self-assemblies of these amphiphiles were performed in PBS buffer to generate nanoparticles with sizes from 40 to 105 nm, which were verified by dynamic light scattering, electron microscopy, and static light scattering (Zimm plots). Subsequently, fluorescence spectroscopy was applied to study the enzymatic degradation of Nile red-loaded nanoparticles. By performing a point-by-point comparison of fluorescence intensity decline patterns between nanoparticles, we demonstrated that lipase from Pseudomonas cepacia was very efficient in degrading the nanoparticles. Hydrolysis degradations under basic conditions were also carried out, and a complete degradation was achieved after 4 h. Additionally, cytotoxicity assays were carried out on HEK293 cells, and the results affirmed cell viabilities over 90% when incubated with up to 1 mg/mL nanoparticles for 24 h. These biodegradable and biocompatible nanoparticles hence hold great potential for future applications such as drug release.

Dynamic matrices with DNA-encoded viscoelasticity for cell and organoid culture.

Three-dimensional cell and organoid cultures rely on the mechanical support of viscoelastic matrices. However, commonly used matrix materials lack control over key cell-instructive properties. Here we report on fully synthetic hydrogels based on DNA libraries that self-assemble with ultrahigh-molecular-weight polymers, forming a dynamic DNA-crosslinked matrix (DyNAtrix). DyNAtrix enables computationally predictable and systematic control over its viscoelasticity, thermodynamic and kinetic parameters by changing DNA sequence information. Adjustable heat activation allows homogeneous embedding of mammalian cells. Intriguingly, stress-relaxation times can be tuned over four orders of magnitude, recapitulating mechanical characteristics of living tissues. DyNAtrix is self-healing, printable, exhibits high stability, cyto- and haemocompatibility, and controllable degradation. DyNAtrix-based cultures of human mesenchymal stromal cells, pluripotent stem cells, canine kidney cysts and human trophoblast organoids show high viability, proliferation and morphogenesis. DyNAtrix thus represents a programmable and versatile precision matrix for advanced approaches to biomechanics, biophysics and tissue engineering.

Single-molecule mechanical fingerprinting with DNA nanoswitch calipers.

Decoding the identity of biomolecules from trace samples is a longstanding goal in the field of biotechnology. Advances in DNA analysis have substantially affected clinical practice and basic research, but corresponding developments for proteins face challenges due to their relative complexity and our inability to amplify them. Despite progress in methods such as mass spectrometry and mass cytometry, single-molecule protein identification remains a highly challenging objective. Towards this end, we combine DNA nanotechnology with single-molecule force spectroscopy to create a mechanically reconfigurable DNA nanoswitch caliper capable of measuring multiple coordinates on single biomolecules with atomic resolution. Using optical tweezers, we demonstrate absolute distance measurements with ångström-level precision for both DNA and peptides, and using multiplexed magnetic tweezers, we demonstrate quantification of relative abundance in mixed samples. Measuring distances between DNA-labelled residues, we perform single-molecule fingerprinting of synthetic and natural peptides, and show discrimination, within a heterogeneous population, between different posttranslational modifications. DNA nanoswitch calipers are a powerful and accessible tool for characterizing distances within nanoscale complexes that will enable new applications in fields such as single-molecule proteomics.

A smart polymer for sequence-selective binding, pulldown, and release of DNA targets.

Selective isolation of DNA is crucial for applications in biology, bionanotechnology, clinical diagnostics and forensics. We herein report a smart methanol-responsive polymer (MeRPy) that can be programmed to bind and separate single- as well as double-stranded DNA targets. Captured targets are quickly isolated and released back into solution by denaturation (sequence-agnostic) or toehold-mediated strand displacement (sequence-selective). The latter mode allows 99.8% efficient removal of unwanted sequences and 79% recovery of highly pure target sequences. We applied MeRPy for the depletion of insulin, glucagon, and transthyretin cDNA from clinical next-generation sequencing (NGS) libraries. This step improved the data quality for low-abundance transcripts in expression profiles of pancreatic tissues. Its low cost, scalability, high stability and ease of use make MeRPy suitable for diverse applications in research and clinical laboratories, including enhancement of NGS libraries, extraction of DNA from biological samples, preparative-scale DNA isolations, and sorting of DNA-labeled non-nucleic acid targets.

Rapid in vitro production of single-stranded DNA.

There is increasing demand for single-stranded DNA (ssDNA) of lengths >200 nucleotides (nt) in synthetic biology, biological imaging and bionanotechnology. Existing methods to produce high-purity long ssDNA face limitations in scalability, complexity of protocol steps and/or yield. We present a rapid, high-yielding and user-friendly method for in vitro production of high-purity ssDNA with lengths up to at least seven kilobases. Polymerase chain reaction (PCR) with a forward primer bearing a methanol-responsive polymer generates a tagged amplicon that enables selective precipitation of the modified strand under denaturing conditions. We demonstrate that ssDNA is recoverable in ∼40-50 min (time after PCR) with >70% yield with respect to the input PCR amplicon, or up to 70 pmol per 100 µl PCR reaction. We demonstrate that the recovered ssDNA can be used for CRISPR/Cas9 homology directed repair in human cells, DNA-origami folding and fluorescent in-situ hybridization.

Noncovalent Aqua Materials Based on Perylene Diimides.

Most robust functional organic materials are currently based on polymers. These materials exhibit high stability, but once formed they are difficult to modify, adapt to their environment, and recycle. Materials based on small molecules that are held together by noncovalent interactions can offer an alternative to conventional polymer materials for applications that require adaptive and stimuli-responsive features. However, it is challenging to engineer macroscopic noncovalent materials that are sufficiently robust for practical applications. This Account summarizes progress made by our group towards the development of noncovalent "aqua materials" based on well-defined organic molecules. These materials are uniquely assembled in aqueous media, where they harness the strength of hydrophobic and π-π interactions between large aromatic groups to achieve robustness. Despite their high stability, these supramolecular systems can dynamically respond to external stimuli. We discuss design principles, fundamental properties, and applications of two classes of aqua materials: (1) supramolecular gels and (2) nanocrystalline arrays. The materials were characterized by a combination of steady-state and time-resolved spectroscopic techniques, electrical measurements, molecular modeling, and high-resolution microscopic imaging, in particular cryogenic transmission electron microscopy (cryo-TEM) and cryogenic scanning electron microscopy (cryo-SEM). All investigated aqua materials are based on one key building block, perylene diimide (PDI). PDI exhibits remarkably stable intermolecular bonds, together with useful chemical and optoelectronic properties. PDI-based amphiphiles carrying poly(ethylene glycol) (PEG) were designed to form linear supramolecular polymers in aqueous media. These one-dimensional arrays of noncovalently linked molecules can entangle and form three-dimensional supramolecular networks, leading to soft gel-like materials. Tuning the strength of interactions between fibers enables dynamic adjustment of viscoelastic properties and functional characteristics. Besides supramolecular gels, we show that simple PDI-based molecules can self-assemble in aqueous medium to form robust organic nanocrystals (ONCs). The mechanical and optoelectronic properties of ONCs are distinctly different from gel-phase materials. ONCs are excellent building blocks for macroscopic free-standing materials that can be used in dry state, unlike hydrogels. Being constructed from small molecules, ONC materials are easy to fabricate and recycle. High thermal robustness, good mechanical properties, and modular design render ONC materials versatile and suitable for a variety of applications. In the future, noncovalent aqua materials can become a sustainable alternative to conventional polymer materials. Examples from our research include stimuli-responsive and recyclable filtration membranes for preparative nanoparticle separation, water purification and catalysis, light-harvesting hydrogels for solar energy conversion, and nanocrystalline films for switchable surface coatings and electronic devices.

Selective Nascent Polymer Catch-and-Release Enables Scalable Isolation of Multi-Kilobase Single-Stranded DNA.

Scalable methods currently are lacking for isolation of long ssDNA, an important material for numerous biotechnological applications. Conventional biomolecule purification strategies achieve target capture using solid supports, which are limited in scale and susceptible to contamination owing to nonspecific adsorption and desorption on the substrate surface. We herein disclose selective nascent polymer catch and release (SNAPCAR), a method that utilizes the reactivity of growing poly(acrylamide-co-acrylate) chains to capture acrylamide-labeled molecules in free solution. The copolymer acts as a stimuli-responsive anchor that can be precipitated on demand to pull down the target from solution. SNAPCAR enabled scalable isolation of multi-kilobase ssDNA with high purity and 50-70 % yield. The ssDNA products were used to fold various DNA origami. SNAPCAR-produced ssDNA will expand the scope of applications in nanotechnology, gene editing, and DNA library construction.

Self-Assembly of Perylenediimide-Single-Strand-DNA Conjugates: Employing Hydrophobic Interactions and DNA Base-Pairing To Create a Diverse Structural Space.

The self-assembly behavior of DNA conjugates possessing a perylenediimide (PDI) head group and an N-oligonucleotide tail has been investigated using a combination of optical spectroscopy and cryogenic transmission electron microscopy (cryo-TEM) imaging. To obtain insight into the interplay between PDI hydrophobic interactions and DNA base-pairing we employed systematic variation in the length and composition of the oligo tails. Conjugates with short (TA)n or (CG)n oligo tails (n≤3) form helical or nonhelical fibers constructed from π-stacked PDI head groups with pendent oligo tails in aqueous solution. Conjugates with longer (TA)n oligo tails also form stacks of PDI head groups, which are further aggregated by base-pairing between their oligo tails, leading to fiber bundling and formation of bilayers. The longer (CG)n conjugates form PDI end-capped duplexes, which further assemble into PDI-stacked arrays of duplexes leading to large scale ordered assemblies. Cryo-TEM imaging reveals that (CG)3 gives rise to both fibers and large assemblies, whereas (CG)5 assembles preferentially into large ordered structures.

Supramolecular Polymers in Aqueous Media.

This review discusses one-dimensional supramolecular polymers that form in aqueous media. First, naturally occurring supramolecular polymers are described, in particular, amyloid fibrils, actin filaments, and microtubules. Their structural, thermodynamic, kinetic, and nanomechanical properties are highlighted, as well as their importance for the advancement of biologically inspired supramolecular polymer materials. Second, five classes of synthetic supramolecular polymers are described: systems based on (1) hydrogen-bond motifs, (2) large π-conjugated surfaces, (3) host-guest interactions, (4) peptides, and (5) DNA. We focus on recent studies that address key challenges in the field, providing mechanistic understanding, rational polymer design, important functionality, robustness, or unusual thermodynamic and kinetic properties.

Dispersing perylene diimide/SWCNT hybrids: structural insights at the molecular level and fabricating advanced materials.

The unique properties of carbon nanotubes (CNT) are advantageous for emerging applications. Yet, the CNT insolubility hampers their potential. Approaches based on covalent and noncovalent methodologies have been tested to realize stable dispersions of CNTs. Noncovalent approaches are of particular interest as they preserve the CNT's structures and properties. We report on hybrids, in which perylene diimide (PDI) amphiphiles are noncovalently immobilized onto single wall carbon nanotubes (SWCNT). The resulting hybrids were dispersed and exfoliated both in water and organic solvents in the presence of two different PDI derivatives, PP2b and PP3a. The dispersions were investigated using cryogenic transmission electron microscopy (cryo-TEM), providing unique structural insights into the exfoliation. A helical arrangement of PP2b assemblies on SWCNTs dominates in aqueous dispersions, while a single layer of PP2b and PP3a was found on SWCNTs in organic dispersions. The dispersions were probed by steady-state and time-resolved spectroscopies, revealing appreciable charge redistribution in the ground state, and an efficient electron transfer from SWCNTs to PDIs in the excited state. We also fabricated hybrid materials from the PP2b/SWCNT dispersions. A supramolecular membrane was prepared from aqueous dispersions and used for size-selective separation of gold nanoparticles. Hybrid buckypaper films were prepared from the organic dispersions. In the latter, high conductivity results from enhanced electronic communication and favorable morphology within the hybrid material. Our findings shed light onto SWCNT/dispersant molecular interactions, and introduce a versatile approach toward universal solution processing of SWCNT-based materials.

Understanding the effect of fluorocarbons in aqueous supramolecular polymerization: ultrastrong noncovalent binding and cooperativity.

Achieving supramolecular polymerization based on strong yet reversible bonds represents a significant challenge. A solution may be offered by perfluoroalkyl groups, which have remarkable hydrophobicity. We tested the idea that a perfluorooctyl chain attached to a perylene diimide amphiphile can dramatically enhance the strength of supramolecular bonding in aqueous environments. Supramolecular structures and polymerization thermodynamics of this fluorinated compound (1-F) were studied in comparison to its non-fluorinated analogue (1-H). Depending on the amount of organic cosolvent, 1-F undergoes cooperative or isodesmic aggregation. The switching between two polymerization mechanisms results from a change in polymer structure, as observed by cryogenic electron microscopy. 1-F showed exceptionally strong noncovalent binding, with the largest directly measured association constant of 1.7 × 10(9) M(-1) in 75:25 water/THF mixture (v/v). In pure water, the association constant of 1-F is estimated to be at least in the order of 10(15) M(-1) (based on extrapolation), 3 orders of magnitude larger than that of 1-H. The difference in aggregation strength between 1-F and 1-H can be explained solely on the basis of the larger surface area of the fluorocarbon group, rather than a unique nature of fluorocarbon hydrophobicity. However, differences in aggregation mechanism and cooperativity exhibited by 1-F appear to result from specific fluorocarbon conformational rigidity.

Separation, immobilization, and biocatalytic utilization of proteins by a supramolecular membrane.

Membrane separation of biomolecules and their application in biocatalysis is becoming increasingly important for biotechnology, demanding the development of new biocompatible materials with novel properties. In the present study, an entirely noncovalent water-based material is used as a membrane for size-selective separation, immobilization, and biocatalytic utilization of proteins. The membrane shows stable performance under physiological conditions, allowing filtration of protein mixtures with a 150 kDa molecular weight cutoff (∼8 nm hydrodynamic diameter cutoff). Due to the biocompatibility of the membrane, filtered proteins stay functionally active and retained proteins can be partially recovered. Upon filtration, large enzymes become immobilized within the membrane. They exhibit stable activity when subjected to a constant flux of substrates for prolonged periods of time, which can be used to carry out heterogeneous biocatalysis. The noncovalent membrane material can be easily disassembled, purified, reassembled, and reused, showing reproducible performance after recycling. The robustness, recyclability, versatility, and biocompatibility of the supramolecular membrane may open new avenues for manipulating biological systems.

Noncovalent water-based materials: robust yet adaptive.

The adaptive properties of noncovalent materials allow easy processing, facile recycling, self-healing, and stimuli responsiveness. However, the poor robustness of noncovalent systems has hampered their use in real-life applications. In this Concept Article we discuss the possibility of creating robust noncovalent arrays by utilizing strong hydrophobic interactions. We describe examples from our work on aqueous assemblies based on aromatic amphiphiles with extended hydrophobic cores. These arrays exhibit fascinating properties, including robustness, multiple stimuli-responsiveness, and pathway-dependent self-assembly. We have shown that this can lead to functional materials (filtration membranes) rivaling covalent systems. We anticipate that water-based noncovalent materials have the potential to replace or complement conventional polymer materials in various fields, and to promote novel applications that require the combination of robustness and adaptivity.

Photoinduced singlet charge transfer in a ruthenium(II) perylene-3,4:9,10-bis(dicarboximide) complex.

Elucidation of photoinduced charge transfer behavior in organic dye/metal hybrids is important for developing photocatalytic systems for solar energy conversion. We report the synthesis and photophysical characterization of a perylene-3,4:9,10-bis(dicarboximide) (PDI)-ruthenium(II) complex, bis-PDI-2,2'-bipyridineRu(II)Cl(2)(CN(t)butyl)(2), which has favorable energetics, ΔG(CS) ≈ -1.0 eV, for singlet electron transfer from the Ru complex to PDI. Time-resolved optical spectroscopy reveals that upon selective photoexcitation of PDI, ultrafast charge transfer (<150 fs) from the Ru complex to (1*)PDI generates the Ru(III)-PDI(-•) ion pair. The resulting vibrationally hot Ru(III)-PDI(-•) ion pair exhibits fast relaxation (τ = 3.9 ps) and charge recombination (τ(CR) = 63 ps). Our experimental and computational (DFT and TDDFT) studies show that energy-preserving photodriven singlet electron transfer can dominate in properly designed organic dye/metal complexes, making them of particular interest for use in artificial photosynthetic systems for solar fuels formation.

A recyclable supramolecular membrane for size-selective separation of nanoparticles.

Most practical materials are held together by covalent bonds, which are irreversible. Materials based on noncovalent interactions can undergo reversible self-assembly, which offers advantages in terms of fabrication, processing and recyclability, but the majority of noncovalent systems are too fragile to be competitive with covalent materials for practical applications, despite significant attempts to develop robust noncovalent arrays. Here, we report nanostructured supramolecular membranes prepared from fibrous assemblies in water. The membranes are robust due to strong hydrophobic interactions, allowing their application in the size-selective separation of both metal and semiconductor nanoparticles. A thin (12 µm) membrane is used for filtration (∼5 nm cutoff), and a thicker (45 µm) membrane allows for size-selective chromatography in the sub-5 nm domain. Unlike conventional membranes, our supramolecular membranes can be disassembled using organic solvent, cleaned, reassembled and reused multiple times.

Supramolecular gel based on a perylene diimide dye: multiple stimuli responsiveness, robustness, and photofunction.

Design of an extensive supramolecular three-dimensional network that is both robust and adaptive represents a significant challenge. The molecular system PP2b based on a perylene diimide chromophore (PDI) decorated with polyethylene glycol groups self-assembles in aqueous media into extended supramolecular fibers that form a robust three-dimensional network resulting in gelation. The self-assembled systems were characterized by cryo-TEM, cryo-SEM, and rheological measurements. The gel possesses exceptional robustness and multiple stimuli-responsiveness. Reversible charging of PP2b allows for switching between the gel state and fluid solution that is accompanied by switching on and off the material's birefringence. Temperature triggered deswelling of the gel leads to the (reversible) expulsion of a large fraction of the aqueous solvent. The dual sensibility toward chemical reduction and temperature with a distinct and interrelated response to each of these stimuli is pertinent to applications in the area of adaptive functional materials. The gel also shows strong absorption of visible light and good exciton mobility (elucidated using femtosecond transient absorption), representing an advantageous light harvesting system.