DNA Block Copolymers Research Articles

A Comprehensive Review of Self-Assembly Techniques Used to Fabricate as DNA Origami, Block Copolymers, and Colloidal Nanostructures

Abstract: Self-assembly techniques play a pivotal role in the field of nanotechnology, enabling the spontaneous organization of individual building blocks into ordered nanostructures without external intervention. In DNA origami, the design and synthesis of DNA strands allow for precise folding into complex nanoarchitectures. This technique holds immense promise in nanoelectronics, nanomedicine, and nanophotonics, offering nanoscale precision and versatility in structural design. Block copolymers represent another fascinating self-assembly system, driven by phase separation and microdomain formation. Understanding and controlling the self-assembly behavior of block copolymers enable applications in nanolithography, nanopatterning, and nanofabrication, owing to their ability to generate well-defined nanostructures. Colloidal assembly is a versatile and powerful technique for fabricating ordered nanostructures and materials with precise control over their properties. The process involves the spontaneous arrangement of colloidal particles into well-defined structures at the microscale or larger, driven by interparticle interactions, Brownian motion, and entropic effects. As research and technology continue to progress, colloidal assembly holds promising opportunities for creating novel materials with applications in diverse fields, contributing to advancements in nanotechnology, optics, electronics, and biomedicine. The continuous exploration and development of colloidal assembly techniques will undoubtedly open new avenues for innovation and impact various areas of science and technology in the future. This review article provides a comprehensive overview of various self-assembly techniques used to fabricate nanostructures, focusing on DNA origami, block copolymers, and colloidal assembly. With a focus on DNA origami in particular, its uses in drug administration, biosensing, nanofabrication, and computational storage are introduced. There is also a discussion of the potential and difficulties involved in assembling and using DNA origami.

Studies on the Synergistic Effect of Tandem Semi-Stable Complementary Domains on Sequence-Defined DNA Block Copolymers.

Tandem semi-stable complementary domains play an important role in life, while the role of these domains in the folding process of nucleic acid molecules has not been systematically studied. Here, we designed a clean model system by synthesizing sequence-defined DNA-OEG copolymers composed of ssDNA fragments with palindromic sequences and orthogonal oligo(tetraethylene glycol) (OEG) linkers. By altering the lengths of DNA units (6-12 nt) and OEG linkers (Xn = 0-4) separately, we systematically studied how stabilities of tandem complementary domains and connecting flexibilities affect the assembly topology. Combining experimental methods and coarse-grained molecular simulation analysis, distributions of multiple assembled conformations (mainly monomers, dimers, and clusters) were characterized. Both results indicated that tandem semi-stable complementary domains tend to form homogeneous closed circular dimers instead of larger clusters due to the synergistic enhancement effect, and the distributions of each conformation highly depend on flexibilities.

Engineering Programmable DNA Particles and Capsules Using Catechol-Functionalized DNA Block Copolymers

Engineering Programmable DNA Particles and Capsules Using Catechol-Functionalized DNA Block Copolymers

DNA Sequence and Length Dictate the Assembly of Nucleic Acid Block Copolymers.

The self-assembly of block copolymers is often rationalized by structure and microphase separation; pathways that diverge from this parameter space may provide new mechanisms of polymer assembly. Here, we show that the sequence and length of single-stranded DNA directly influence the self-assembly of sequence-defined DNA block copolymers. While increasing the length of DNA led to predictable changes in self-assembly, changing only the sequence of DNA produced three distinct structures: spherical micelles (spherical nucleic acids, SNAs) from flexible poly(thymine) DNA, fibers from semirigid mixed-sequence DNA, and networked superstructures from rigid poly(adenine) DNA. The secondary structure of poly(adenine) DNA strands drives a temperature-dependent polymerization and assembly mechanism: copolymers stored in an SNA reservoir form fibers after thermal activation, which then aggregate upon cooling to form interwoven networks. DNA is often used as a programming code that aids in nanostructure addressability and function. Here, we show that the inherent physical and chemical properties of single-stranded DNA sequences also make them an ideal material to direct self-assembled morphologies and select for new methods of supramolecular polymerization.

DNA-derived nanostructures selectively capture gram-positive bacteria.

We report the first demonstration of the efficient bacteria targeting properties of DNA-based polymeric micelles with high-density DNA corona. Nanoscale polymer micelles derived from DNA-b-polystyrene (DNA-b-PS) efficiently selected most tested Gram-positive strains over Gram-negative strains; single-strand DNAs were 20-fold less selective. We demonstrate that these targeting properties were derived from the interaction between densely packed DNA strands of the micelle corona and the peptidoglycan layers of Gram-positive bacteria. DNA-b-PS micelles incorporating magnetic nanoparticles (MNPs) can efficiently capture and concentrate Gram-positive bacteria suggesting the simple applications of these DNA block copolymer micelles for concentrating bacteria. Adenine (A), thymine (T), cytosine (C), and guanine (G)-rich nanostructures were fabricated, respectively, for investigating the effect of sequence on Gram-selective bacteria targeting. T-rich micelles showed the most efficient targeting properties. The targeting properties of these DNA nanostructures toward Gram-positive bacteria may have applications as a targeted therapeutic delivery system.

The core composition of DNA block copolymer micelles dictates DNA hybridization properties, nuclease stabilities, and cellular uptake efficiencies.

Here, we report how the nature of the hydrophobic core affects the molecular interactions of DNA block copolymer assemblies. Three different amphiphilic DNA block copolymers, DNA-b-polystyrene (DNA-b-PS), DNA-b-poly(2-vinylpyridine) (DNA-b-P2VP), and DNA-b-poly(methyl acrylate) (DNA-b-PMA) were synthesized and assembled into spherical micelles composed of a hydrophobic polymer core and DNA corona. Interestingly, DNA block copolymer micelles having different hydrophobic cores exhibited markedly different molecular and biological interactions. DNA-b-PS exhibited higher melting temperature, sharper melting transition, higher stability to nuclease-catalyzed DNA degradation, and higher cellular uptake efficiency compared to DNA-b-P2VP and DNA-b-PMA. The investigation of the self-assembly behavior revealed a much higher aggregation number and DNA density for DNA-b-PS micelles, which explains the superior properties of DNA-b-PS. These results demonstrate that the type of the hydrophobic core polymer, which has been largely overlooked, has a profound impact on the molecular and biological interactions of the DNA shell.

Engineering exosome polymer hybrids by atom transfer radical polymerization

Exosomes are emerging as ideal drug delivery vehicles due to their biological origin and ability to transfer cargo between cells. However, rapid clearance of exogenous exosomes from the circulation as well as aggregation of exosomes and shedding of surface proteins during storage limit their clinical translation. Here, we demonstrate highly controlled and reversible functionalization of exosome surfaces with well-defined polymers that modulate the exosome's physiochemical and pharmacokinetic properties. Using cholesterol-modified DNA tethers and complementary DNA block copolymers, exosome surfaces were engineered with different biocompatible polymers. Additionally, polymers were directly grafted from the exosome surface using biocompatible photo-mediated atom transfer radical polymerization (ATRP). These exosome polymer hybrids (EPHs) exhibited enhanced stability under various storage conditions and in the presence of proteolytic enzymes. Tuning of the polymer length and surface loading allowed precise control over exosome surface interactions, cellular uptake, and preserved bioactivity. EPHs show fourfold higher blood circulation time without altering tissue distribution profiles. Our results highlight the potential of precise nanoengineering of exosomes toward developing advanced drug and therapeutic delivery systems using modern ATRP methods.

Organic Spherical Nucleic Acids for the Transport of a NIR‐II‐Emitting Dye Across the Blood–Brain Barrier

AbstractDNA nanotechnology plays an increasingly important role in the biomedical field; however, its application in the design of organic nanomaterials is underexplored. Herein, we report the use of DNA nanotechnology to transport a NIR‐II‐emitting nanofluorophore across the blood–brain barrier (BBB), facilitating non‐invasive imaging of brain tumors. Specifically, the DNA block copolymer, PS‐b‐DNA, is synthesized through a solid‐phase click reaction. We demonstrate that its self‐assembled structure shows exceptional cluster effects, among which BBB‐crossing is the most notable. Therefore, PS‐b‐DNA is utilized as an amphiphilic matrix to fabricate a NIR‐II nanofluorephore, which is applied in in vivo bioimaging. Accordingly, the NIR‐II fluorescence signal of the DNA‐based nanofluorophore localized at a glioblastoma is 3.8‐fold higher than the NIR‐II fluorescence signal of the PEG‐based counterpart. The notably increased imaging resolution will significantly benefit the further diagnosis and therapy of brain tumors.

Organic Spherical Nucleic Acids for the Transport of a NIR-II-Emitting Dye Across the Blood-Brain Barrier.

DNA nanotechnology plays an increasingly important role in the biomedical field; however, its application in the design of organic nanomaterials is underexplored. Herein, we report the use of DNA nanotechnology to transport a NIR-II-emitting nanofluorophore across the blood-brain barrier (BBB), facilitating non-invasive imaging of brain tumors. Specifically, the DNA block copolymer, PS-b-DNA, is synthesized through a solid-phase click reaction. We demonstrate that its self-assembled structure shows exceptional cluster effects, among which BBB-crossing is the most notable. Therefore, PS-b-DNA is utilized as an amphiphilic matrix to fabricate a NIR-II nanofluorephore, which is applied in in vivo bioimaging. Accordingly, the NIR-II fluorescence signal of the DNA-based nanofluorophore localized at a glioblastoma is 3.8-fold higher than the NIR-II fluorescence signal of the PEG-based counterpart. The notably increased imaging resolution will significantly benefit the further diagnosis and therapy of brain tumors.

Peptide-Driven Shape Control of Low-Dimensional DNA Nanostructures.

We report the rational design and fabrication of unusual low-dimensional DNA nanostructures through programmable and sequence-specific peptide interactions. Dual-bioactive block copolymers composed of DNA and amino acid-based polymers (DNA-b-poly(amino acid)) were synthesized by coupling oligonucleotides to phenylalanine (Phe)-based polymers. Unlike prototypical DNA block copolymers, which typically form simple spherical micelles, DNA-b-poly(amino acid) assemble into various low-dimensional structures such as nanofibers, ribbons, and sheets through controllable amino acid interactions. Moreover, DNA-b-poly(amino acid) assemblies can undergo protease-induced fiber-to-sheet shape transformations, where the morphology change is dictated by the type of enzymes and amino acid sequences. The peptide-based self-assembly reported here provides a programmable approach to fabricate dynamic DNA assemblies with diverse and unusual low-dimensional structures.

Utilization of a Multiple Cloning Site as a Versatile Platform for DNA Triblock Copolymer Synthesis.

DNA-containing block copolymers have utility in a wide range of biomedical applications. However, synthesis of these hybrid materials, especially ones with complex chain structures, remains to be a major challenge. Here, we report the use of a combination of restriction enzyme sites and ligation enzymes to synthesize DNA triblock copolymers. In contrast to triblock structures held together by DNA hybridization, the newly synthesized DNA triblocks have all blocks connected by covalent bonds. The improved stability of the triblocks against environmental factors such as urea denaturing is confirmed. Furthermore, we incorporate a multiple cloning site (MCS) into the DNA block copolymers and show that the restriction sites can be cut by their corresponding restriction enzymes, generating diblocks with different sticky ends. By utilizing these sticky ends of specific sequences, the cut diblocks are further ligated to create a variety of triblock copolymers with different DNA center blocks and synthetic polymer end blocks. This study presents a versatile platform based on MCS for the synthesis and regeneration of a range of DNA-containing block copolymers.

Hierarchical Self-Assembly of Cholesterol-DNA Nanorods.

Amphiphilic DNA block copolymers have been utilized in preparing self-assembled amphiphilic structures in aqueous solution. These block copolymers usually contain specifically designed hydrophobic regions, and typically assemble under near-physiological conditions. Here, we report self-assembly of spherical micelles and one-dimensional nanorods under acidic conditions from cholesterol-conjugated DNA strands (Cholesterol-DNA). Further study also revealed that the nanorods were hierarchically assembled from the micelle nanostructures. The morphology of the nanorod assemblies can be tuned by altering solution condition and the design of Cholesterol-DNA. The self-assembly of Cholesterol-DNA nanostructures under acidic conditions and the discovery of the relationship between the nanorods and the micelles can provide new insights for future design of self-assemblies of amphiphilic DNA block copolymers.

A dynamic DNA nanostructure with switchable and size-selective molecular recognition properties.

Herein, we report a dynamic DNA nanostructure exhibiting switchable and size-selective molecular recognition properties. A DNA block copolymer, polystyrene-b-DNA (PS-b-DNA), and a thermo-responsive block copolymer, PS-b-poly(N-isopropylacrylamide) (PS-b-PNIPAM), were simultaneously assembled to form hybrid micelles composed of a PS core and a DNA/PNIPAM corona. PNIPAM strands did not significantly hinder the binding of molecular DNA for a broad range of PNIPAM lengths. On the other hand, they exerted significant steric hindrance for interactions with nanoscale species, which can be reversibly turned off by increasing the temperature above the lower critical solution temperature (LCST) of PNIPAM. Owing to the switchable and size-selective steric hindrance, the hybrid DNA micelles showed thermally controllable enzymatic degradation and cellular uptake. These results demonstrate that the binary self-assembly of two different responsive block copolymers is a promising approach to prepare dynamic nanostructures with controllable biological recognition properties.

Amphiphilic DNA Organic Hybrids: Functional Materials in Nanoscience and Potential Application in Biomedicine.

Due to the addressability and programmability, DNA has been applied not merely in constructing static elegant nanostructures such as two dimensional and three dimensional DNA nanostructures but also in designing dynamic nanodevices. Moreover, DNA could combine with hydrophobic organic molecules to be a new amphiphilic building block and then self-assemble into nanomaterials. Of particular note, a recent state-of-the-art research has turned our attention to the amphiphilic DNA organic hybrids including small molecule modified DNA (lipid-DNA, fluorescent molecule-DNA, etc.), DNA block copolymers, and DNA-dendron hybrids. This review focuses mainly on the development of their self-assembly behavior and their potential application in nanomaterial and biomedicine. The potential challenges regarding of the amphiphilic DNA organic hybrids are also briefly discussed, aiming to advance their practical applications in nanoscience and biomedicine.

Recent progress on DNA block copolymer

DNA has gained great attention because of its unique structure, excellent molecular recognition property, and biological functions. When married with versatile synthetic polymers, the DNA conjugated polymer hybrids, known as DNA block copolymers (DBCs), have been launched and well developed for the syntheses of new materials and nanostructures with different functions in the past several decades. Compared to conventional synthetic block copolymers, using DNA as a building block provides several advantages over other polymer candidates, such as molecular recognition, programmable self-assembly, biocompatibility, and sequence-encoded information. In this review, recent developments in this area will be summarized and meaningful breakthroughs will be highlighted. We will discuss representative examples of recent progress in the syntheses, structure manipulations, and applications of DBCs.

Ultrasensitive Detection of Oligonucleotides: Single-Walled Carbon Nanotube Transistor Assembled by DNA Block Copolymer

Biosensors, which harness the unique specific binding properties of biomaterials such as proteis, are increasingly recognized as a powerful tool for chemical sensing. In this context, the detection of nucleic acids DNA and RNA will take on ever more importance for screening as the fields of genomics and diagnostics advance. The same properties that allow molecular recognition-strong, specific non-covalent interactions-also enable bottom-up assembly of sensing architectures. Here, we take advantage of such interactions for the self-assembly of field-effect transistors from semi-conducting single-walled carbon nanotubes selectively dispersed by DNA-block-copolymers and anchored to the electrodes through DNA hybridization. These transistors can sensitively detect the hybridization of complementary target DNA strands through transduction of the chemical recognition event into electrical doping, achieving an analyte sensitivity of 10 fM. Such ultra-sensitive electrical-based detection removes the need for DNA amplification and offers a new route to nucleic acids diagnostics.

Self-assembly of DNA-based Nanomaterials and Potential Application in Drug Delivery.

DNA can be self-assembled into programmable two-dimensional and three-dimensional nanoarchitectures with arbitrarily predetermined sizes and shapes. Because of the addressable arbitrary size and shape, great capacity of cargo loading, ability to be internalized by cells, the stability of structures under physiological conditions and excellent biocompatibility, the pristine DNA nanostructures are explored as drug vehicles in drug delivery. In addition, DNA block copolymer and DNADendron hybrid, as new building blocks, can be self-assembled into different kinds of ordered structures, e.g., nanofibers, spherical micelles, and vesicles, in aqueous solution. Recent studies have shown that some of these nanostructures could easily enter cells with excellent cell uptake efficiency. Herein, this review will mainly introduce the self-assembly behavior of pristine DNA and DNA hybrid materials including DNA block copolymers and DNA-Dendron hybrids, and their application in drug delivery.

Andreas Herrmann

Angewandte Chemie International EditionVolume 56, Issue 8 p. 1956-1956 Author ProfileFree Access Andreas Herrmann First published: 19 January 2017 https://doi.org/10.1002/anie.201611742AboutSectionsPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat Graphical Abstract “I can never resist sweets. My favorite food is venison ...” This and more about Andreas Herrmann can be found on page 1956. Andreas Herrmann The author presented on this page has recently published his 10th article in Angewandte Chemie in the last 10 years: “High Affinity Recognition of a Selected Amino Acid Epitope within a Protein by Cucurbit[8]uril Complexation”: S. Sonzini, A. Marcozzi, R. J. Gubeli, C. F. van der Walle, P. Ravn, A. Herrmann, O. A. Scherman, Angew. Chem. Int. Ed. 2016, 55, 14000; Angew. Chem. 2016, 128, 14206. The work of A. Herrmann has been featured on the inside cover of Angewandte Chemie: “Light-Triggered Sequence-Specific Cargo Release from DNA Block Copolymer-Lipid Vesicles”: A. Rodríguez-Pulido, A. Kondratchuk, D. K. Prusty, J. Gao, M. Loi, A. Herrmann, Angew. Chem. Int. Ed. 2013, 52, 1008; Angew. Chem. 2013, 125, 1042. Date of birth: October 14, 1970 Position: Professor of Polymer Chemistry & Bioengieneering, Zernike Institute for Advanced Materials, University of Groningen E-mail: a.herrmann@rug.nl Homepage: http://www.rug.nl/research/zernike/polymer-chemistry-and-bioengineering/group-herrmann/polymer-chemistry-_-bioengineering-research ORCID: orcid.org/0000-0002-8886-0894 Education: 1997 Diploma in chemistry, University of Mainz 2001 PhD with Klaus Müllen, Max Planck Institute for Polymer Research, Mainz 2002–2003 Postdoctoral research with Donald Hilvert, ETH Zurich Awards: 2008 Reimund Stadler Prize, Gesellschaft Deutscher Chemiker (GDCh; German Chemical Society); 2009 ERC Starting Grant; 2009 Dr. Hermann Schnell Prize, GDCh; 2010 VICI Grant, Netherlands Organization for Scientific Research; 2013 EYEnovative Prize, Novartis; 2016 ERC Advanced Grant Current research interests: DNA hybrid materials; supercharged polypeptides; nanochemistry; biomacromolecular liquids and liquid crystals; supramolecular protecting groups Hobbies: Surfing, soccer, and skiing I can never resist sweets. My favorite food is venison. My favorite place on earth is the French Atlantic coast because it combines excellent waves and food. I chose chemistry as a career because I could not enter chemical engineering as I could not pursue the necessary practical training because of military service. Retrospectively, that was the best thing that ever happened. If I were not a scientist, I would be a cook developing new flavors with the help of chemistry. My worst nightmare is that all my PhD students and postdoctoral researchers follow my advice. The most exciting thing about my research is that the materials that we are fabricating on the nanometer scale execute functions in the macroscopic world. If I could go forward in time and do any experiment, it would be the fabrication of a cell from exclusively unnatural components that can grow and divide. The downside of my job is having too little time for my wife and three kids. When I'm frustrated, I bike home earlier and faster than usual. My best investment was in smart students. My 5 top papers: References 1“High-Density Noncovalent Functionalization of DNA by Electrostatic Interactions”: W. Chen, J. Y. Gerasimov, P. Zhao, K. Liu, A. Herrmann, J. Am. Chem. Soc. 2015, 137, 12884. (A general method for enveloping DNA with various amines in organic solvents.) 2“Thermotropic liquid crystals from biomacromolecules”: K. Liu et al., PNAS 2014, 111, 18596. (A simple method for liquifying and ordering DNA, RNA, and proteins in the absence of water.) 3“Selective Transformations of Complex Molecules are Enabled by Aptameric Protective Groups”: A. A. Bastian, A. Marcozzi, A. Herrmann, Nat. Chem. 2012, 4, 789. (Allows the regioselective one-step derivatization of natural products.) 4“DNA Block Copolymer Doing It All: From Selection to Self-Assembly of Semiconducting Carbon Nanotubes”: M. Kwak et al., Angew. Chem. Int. Ed. 2011, 50, 3206; Angew. Chem. 2011, 123, 3264. (A DNA polymer hybrid selectively disperses single-walled carbon nanotubes and guides their assembly in devices.) 5“DNA Block Copolymer Micelles—A Combinatorial Tool for Cancer Nanotechnology”: F. E. Alemdaroglu, N. C. Alemdaroglu, P. Langguth, A. Herrmann, Adv. Mat. 2008, 20, 899. (Fast and easy fabrication of drug carrier systems based on nucleic acid self-assembly.) Volume56, Issue8February 13, 2017Pages 1956-1956 ReferencesRelatedInformation

Multimodal Shape Transformation of Dual-Responsive DNA Block Copolymers.

Herein, we report the self-assembly and multimodal shape transformation of dual-responsive DNA di- and triblock copolymers. Dual-responsive DNA diblock copolymer was synthesized by coupling a thermoresponsive polymer, poly(N-isopropylacrylamide (PNIPAM), and an oligonucleotide. DNA-b-PNIPAM possesses thermoresponsive properties of PNIPAM as well as molecular recognition properties of DNA. Thus, they undergo reversible temperature-triggered transition at lower critical solution temperature (LCST) between molecular DNA and polymer micelles with high density DNA corona. The hybridization of DNA-b-PNIPAM and DNA-modified nanoparticles generates functional nanoparticles showing unique temperature-dependent aggregation and disaggregation behaviors due to the dual-responsive nature of DNA-b-PNIPAM. DNA triblock copolymers of DNA-b-PNIPAM-b-PMA were synthesized by introducing a hydrophobic block, poly(methyl acrylate) (PMA), to DNA/PNIPAM block copolymers, which form spherical micelles at room temperature. They are capable of nanoscale shape transformation through the combination of thermal trigger and DNA binding. DNA-b-PNIPAM-b-PMA micelles undergo sphere-to-cylinder shape changes above LCST due to the conformational change of PNIPAM. The shape change is reversible, and fast cylinder-to-sphere transition occurs when the temperature is lowered below LCST. The low temperature spherical morphology can also be accessed while keeping the temperature above LCST by introducing complementary DNA strands with single stranded overhang regions. These results demonstrate the multidimensional shape changing capability of DNA-b-PNIPAM-b-PMA enabled by the dual-responsive property.

DNA Island Formation on Binary Block Copolymer Vesicles.

Here, we report DNA-induced polymer segregation and DNA island formation in binary block copolymer assemblies. A DNA diblock copolymer of polymethyl acrylate-block-DNA (PMA-b-DNA) and a triblock copolymer of poly(butadiene)-block-poly(ethylene oxide)-block-DNA (PBD-b-PEO-b-DNA) were synthesized, and each was coassembled with a prototypical amphiphilic polymer of poly(butadiene)-block-poly(ethylene oxide) (PBD-b-PEO). The binary self-assembly of PMA-b-DNA and PBD-b-PEO resulted in giant polymersomes with DNA uniformly distributed in the hydrophilic PEO shell. When giant polymersomes were connected through specific DNA interactions, DNA block copolymers migrated to the junction area, forming DNA islands within polymersomes. These results indicate that DNA hybridization can induce effective lateral polymer segregation in mixed polymer assemblies. The polymer segregation and local DNA enrichment have important implications in DNA melting properties, as mixed block copolymer assemblies with low DNA block copolymer contents can still exhibit useful DNA melting properties that are characteristic of DNA nanostructures with high DNA density.