Generation of multiblock copolymers by PCR: synthesis, visualization and nanomechanical properties

Chemical Synthesis and Poly(ethylene glycol)-Like Conjugation of the Mango-II Fluorogenic RNA Aptamer

A reliable method for the efficient chemical synthesis and poly(ethylene glycol) PEG-like modification of fluorogenic RNA aptamers is reported. The 43-mer version of Mango-II RNA (MangoII-v1), which binds tightly and specifically to the green fluorophore TO1-Biotin (TO1-B), was synthesized by automated phosphoramidite chemistry using 2'-O-[(triisopropylsilyl)oxy]methyl] (2'-O-TOM)-protected ribonucleosides. Solid-phase phosphoramidite chemistry was also used as a single tool to prepare MangoII-v1 modified with a PEG-like oligophosphate synthetic segment (MangoII-v1-P). After cleavage from the resin, deprotection, and purification, the capacity to activate the fluorescence of TO1-B and the degradation behavior of the chemically synthesized RNAs MangoII-v1 and MangoII-v1-P, were deeply investigated in comparison with those of the enzymatically synthesized 48 nucleotides long RNA MangoII. Interestingly, the chemically synthesized MangoII-v1 RNA aptamer demonstrated great activity toward its target, compared to the enzymatically synthesized analogue. Moreover, it was found to be highly stable, retaining its structural integrity and bioactivity, even after seven days of incubation in 20% fetal bovine serum. MangoII-v1-P also showed a high affinity for TO1-B and excellent degradation resistance.

Functional DNA-Polymer Conjugates

DNA nanotechnology has seen large developments over the last 30 years through the combination of solid phase synthesis and the discovery of DNA nanostructures. Solid phase synthesis has facilitated the availability of short DNA sequences and the expansion of the DNA toolbox to increase the chemical functionalities afforded on DNA, which in turn enabled the conception and synthesis of sophisticated and complex 2D and 3D nanostructures. In parallel, polymer science has developed several polymerization approaches to build di- and triblock copolymers bearing hydrophilic, hydrophobic, and amphiphilic properties. By bringing together these two emerging technologies, complementary properties of both materials have been explored; for example, the synthesis of amphiphilic DNA-polymer conjugates has enabled the production of several nanostructures, such as spherical and rod-like micelles. Through both the DNA and polymer parts, stimuli-responsiveness can be instilled. Nanostructures have consequently been developed with responsive structural changes to physical properties, such as pH and temperature, as well as short DNA through competitive complementary binding. These responsive changes have enabled the application of DNA-polymer conjugates in biomedical applications including drug delivery. This review discusses the progress of DNA-polymer conjugates, exploring the synthetic routes and state-of-the-art applications afforded through the combination of nucleic acids and synthetic polymers.

Precisely Defined Aptamer-b-Poly(phosphodiester) Conjugates Prepared by Phosphoramidite Polymer Chemistry

Uniform conjugates combining a DNA aptamer (either anti-MUC1 or ATP aptamer) and a synthetic polymer segment were synthesized by automated phosphoramidite chemistry. This multistep growth polymer chemistry enables the use of both natural (i.e., nucleoside phosphoramidites) and non-natural monomers (e.g., alkyl- and oligo(ethylene glycol)-phosphoramidites). Thus, in the present work, six different aptamer-polymer conjugates were synthesized and characterized by ion-exchange HPLC, circular dichroism spectroscopy, and electrospray mass spectrometry. All these methods evidenced the formation of uniform molecules with precisely controlled chain-length and monomer sequences. Furthermore, aptamer folding was not affected by polymer bioconjugation. The method described herein is straightforward and allows covalent attachment of homopolymers and copolymers to biofunctional DNA aptamers.

Design of Abiological Digital Poly(phosphodiester)s

In biological systems, the storage and transfer of genetic information rely on sequence-controlled nucleic acids such as DNA and RNA. It has been realized for quite some time that this property is not only crucial for life but could also be very useful in human applications. For instance, DNA has been actively investigated as a digital storage medium over the past decade. Indeed, the "hard-disk of life" is an obvious choice and a highly optimized material for storing data. Through decades of nucleic acids research, technological tools for parallel synthesis and sequencing of DNA have been readily available. Consequently, it has already been demonstrated that different types of documents (e.g., texts, images, videos, and industrial data) can be stored in chemically synthesized DNA libraries. However, DNA is subject to biological constraints, and its molecular structure cannot be easily varied to match technological needs. In fact, DNA is not the only macromolecule that enables data storage. In recent years, it has been demonstrated that a wide variety of synthetic polymers can also be used for such a purpose. Indeed, modern polymer synthesis allows the preparation of synthetic macromolecules with precisely controlled monomer sequences. Altogether, about a dozens of synthetic digital polymers have already been described, and many more can be foreseen. Among them, sequence-defined poly(phosphodiester)s are one of the most promising options. These polymers are prepared by stepwise phosphoramidite chemistry like chemically synthesized oligonucleotides. However, they are constructed with non-natural building blocks and therefore share almost no structural characteristics with nucleic acids, except phosphate repeat units. Still, they contain readable digital messages that can be deciphered by nanopore sequencing or mass spectrometry sequencing. In this Account, we describe our recent research efforts in synthesizing and sequencing optimal abiological digital poly(phosphodiester)s. A major advantage of these polymers over DNA is that their molecular structure can easily be varied to tune their properties. During the last 5 years, we have engineered the molecular structure of these polymers to adjust crucial parameters such as the storage density, storage capacity, erasability, and readability. Consequently, high-capacity PPDE chains, containing hundreds of bits per chains, can now be synthesized and efficiently sequenced using a routine mass spectrometer. Furthermore, sequencing data can be automatically decrypted with the help of decoding software. This new type of coded matter can also be edited using practical physical triggers such as light and organized in space by programmed self-assembly. All of these recent improvements are summarized and discussed herein.

Combination of DNA with polymers

The preparation and applications of DNA containing polymers are comprehensively reviewed, and they are in the form of DNA−polymer covalent conjugators, supramolecular assemblies and hydrogels for advanced materials with promising features.

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.

From DNA Nanotechnology to Material Systems Engineering

In the past 35 years, DNA nanotechnology has grown to a highly innovative and vibrant field of research at the interface of chemistry, materials science, biotechnology, and nanotechnology. Herein, a short summary of the state of research in various subdisciplines of DNA nanotechnology, ranging from pure "structural DNA nanotechnology" over protein-DNA assemblies, nanoparticle-based DNA materials, and DNA polymers to DNA surface technology is given. The survey shows that these subdisciplines are growing ever closer together and suggests that this integration is essential in order to initiate the next phase of development. With the increasing implementation of machine-based approaches in microfluidics, robotics, and data-driven science, DNA-material systems will emerge that could be suitable for applications in sensor technology, photonics, as interfaces between technical systems and living organisms, or for biomimetic fabrication processes.

DNA block copolymers: functional materials for nanoscience and biomedicine

We live in a world full of synthetic materials, and the development of new technologies builds on the design and synthesis of new chemical structures, such as polymers. Synthetic macromolecules have changed the world and currently play a major role in all aspects of daily life. Due to their tailorable properties, these materials have fueled the invention of new techniques and goods, from the yogurt cup to the car seat belts. To fulfill the requirements of modern life, polymers and their composites have become increasingly complex. One strategy for altering polymer properties is to combine different polymer segments within one polymer, known as block copolymers. The microphase separation of the individual polymer components and the resulting formation of well defined nanosized domains provide a broad range of new materials with various properties. Block copolymers facilitated the development of innovative concepts in the fields of drug delivery, nanomedicine, organic electronics, and nanoscience. Block copolymers consist exclusively of organic polymers, but researchers are increasingly interested in materials that combine synthetic materials and biomacromolecules. Although many researchers have explored the combination of proteins with organic polymers, far fewer investigations have explored nucleic acid/polymer hybrids, known as DNA block copolymers (DBCs). DNA as a polymer block provides several advantages over other biopolymers. The availability of automated synthesis offers DNA segments with nucleotide precision, which facilitates the fabrication of hybrid materials with monodisperse biopolymer blocks. The directed functionalization of modified single-stranded DNA by Watson-Crick base-pairing is another key feature of DNA block copolymers. Furthermore, the appropriate selection of DNA sequence and organic polymer gives control over the material properties and their self-assembly into supramolecular structures. The introduction of a hydrophobic polymer into DBCs in aqueous solution leads to amphiphilic micellar structures with a hydrophobic polymer core and a DNA corona. In this Account, we discuss selected examples of recent developments in the synthesis, structure manipulation and applications of DBCs. We present achievements in synthesis of DBCs and their amplification based on molecular biology techniques. We also focus on concepts involving supramolecular assemblies and the change of morphological properties by mild stimuli. Finally, we discuss future applications of DBCs. DBC micelles have served as drug-delivery vehicles, as scaffolds for chemical reactions, and as templates for the self-assembly of virus capsids. In nanoelectronics, DNA polymer hybrids can facilitate size selection and directed deposition of single-walled carbon nanotubes in field effect transistor (FET) devices.

Syntheses of organic molecule-DNA hybrid structures

Investigation of robust and efficient pathways to build DNA-organic molecule hybrid structures is fundamentally important to realize controlled placement of single molecules for potential applications, such as single-molecule electronic devices. Herein, we report a systematic investigation of synthetic processes for preparing organic molecule-DNA building blocks and their subsequent elongation to generate precise micrometer-sized structures. Specifically, optimal cross-coupling routes were identified to enable chemical linkages between three different organic molecules, namely, polyethylene glycol (PEG), poly(p-phenylene ethynylene) (PPE), and benzenetricarboxylate, with single-stranded (ss) DNA. The resulting DNA-organic molecule hybrid building blocks were purified and characterized by both denaturing gel electrophoresis and electrospray ionization mass spectrometry (ESI-MS). The building blocks were subsequently elongated through both the DNA hybridization and ligation processes to prepare micrometer-sized double-stranded (ds) DNA-organic molecule hybrid structures. The described synthetic procedures should facilitate future syntheses of various hybrid DNA-based organic molecular structures.

Synthesis of DNA block copolymers with extended nucleic acid segments by enzymatic ligation: cut and paste large hybrid architectures

Ultra-high molecular weight DNA/polymer hybrid materials were prepared employing molecular biology techniques. Nucleic acid restriction and ligation enzymes were used to generate linear DNA di- and triblock copolymers that contain up to thousands of base pairs in the DNA segments.

Amphiphilic DNA block copolymers: nucleic acid-polymer hybrid materials for diagnostics and biomedicine

DNA-polymer conjugates have been recognized as versatile functional materials in many different fields ranging from nanotechnology to diagnostics and biomedicine. They combine the favorable properties of nucleic acids and synthetic polymers. Moreover, joining both structures with covalent bonds to form bioorganic hybrids allows for the tuning of specific properties or even the possibility of evolving completely new functions. One important class of this type of material is amphiphilic DNA block copolymers, which, due to microphase separation, can spontaneously adopt nanosized micelle morphologies with a hydrophobic core and a DNA corona. These DNA nano-objects have been explored as vehicles for targeted gene and drug delivery, and also as programmable nanoreactors for organic reactions. Key to the successful realization of these potential applications is that (1) DNA block copolymer conjugates can be fabricated in a fully automated fashion by employing a DNA synthesizer; (2) hydrophobic compounds can be loaded within their interior; and (3) they can be site-specifically functionalized by a convenient nucleic acid hybridization procedure. This chapter aims to broaden the range of biodiagnostic and biomedical applications of these materials by providing a comprehensive outline of the preparation and characterization of multifunctional DNA-polymer nanoparticles.