The Evolution of DNA-Templated Synthesis as a Tool for Materials Discovery

Sequencing of d/l-DNA and XNA by Templated-Synthesis

Progress in oligonucleotide sequencing has transformed modern biology and medicine. Here we report a fast and efficient enzyme-free primer extension of PNA with reversible chain termination and its application to DNA and XNA sequencing. The approach leverages activated 4-mer PNAs that react in a templated ligation reaction at μM concentrations within minutes. We demonstrate that the fidelity of this enzyme-free primer extension benefits from reactions performed with a mixture of activated PNAs where every 4-mer has its self-complementary 4-mer. The reactions can be performed using the whole repertoire of 4-mers (256 permutations) in a parallelized manner. Using a primer in combination with its -1, -2, and -3 deletion allows for sequencing by MALDI analysis, using the increment in mass for each nucleobase assignment. Given the enzyme-free nature of this sequencing and the achiral nature of PNA, we further demonstrate that the technology can be used to sequence d- or l-DNA as well as LNA and PNA (XNA).

Nucleic Acid Covalent Tags

The selective and site-specific chemical labeling of proteins has emerged as a pivotal research area in chemical biology and cell biology. An effective protein labeling typically meets several criteria, including high specificity, rapid and robust conjugation under physiological conditions, operation at low concentrations with biocompatibility, and minimal perturbation of the protein function and activity. The conjugation of nucleic acids with proteins has garnered significant attention recently due to the rapid advancements in nucleic acid probe technologies, leveraging the programmable nature of nucleic acids alongside the multifaceted functionalities of proteins. It helps to convert protein-specific information into nucleic acid signals, facilitating upstream versatile recognition and downstream signal amplification for the target protein. This review critically evaluates the recent progress in nucleic acid-based protein labeling methodologies, with a specific focus on covalent labeling using aptamer tags, protein fusion tags or the technique of metabolic oligosaccharide engineering. The tags establish covalent linkages with target proteins through various modalities such as small molecules or metabolic glycan engineering. The insights presented in the review highlight promising avenues for the development of highly specific and versatile protein labeling techniques, which is essential for the improvement of protein-targeted detection and imaging across diverse biological contexts.

Protein-Templated Click Ligation Reaction Triggered by Protein-Split Aptamer Interactions

DNA-templated reactions have found wide applications in sensing and drug discovery. However, this strategy has been limited to the use of nucleic acids as templating elements to direct the proximity effect. Herein, we describe a versatile protein-templated split aptamer click ligation reaction (PT-SpA-CLR) in which the protein template-induced covalent proximity ligation of split aptamer elements enables translating protein/aptamer binding events into the output of ligated DNA products. A ligation yield of >80% is observed for three model protein templates, including VEGF165, PDGF-BB, and SARS-CoV-2 S1. The ligation reaction compensates for the weakness of reduced binding affinity resulting from splitting the aptamer, as evidenced by an approximately 2-fold lower dissociation constant than the non-ligated system. This newly developed PT-SpA-CLR strategy is further integrated with colorimetric or fluorescent reporting mechanisms to achieve easy-to-use and low-cost biosensors utilizing ligation to produce a fully active G-quadruplex or an RNA-cleaving DNAzyme to report protein binding. Both assays can achieve specific detection of an intended protein target with a limit of detection at the picomolar level even when challenged in biological samples. The combined PT-SpA-CLR and versatile sensing strategies offer attractive universal platforms for efficient detection of protein biomarkers.

Modeling One-Electron Oxidation Potentials and Hole Delocalization in Double-Stranded DNA by Multilayer and Dynamic Approaches

The number of innovative applications for DNA nowadays is growing quickly. Its use as a nanowire or electrochemical biosensor leads to the need for a deep understanding of the charge-transfer process along the strand, as well as its redox properties. These features are computationally simulated and analyzed in detail throughout this work by combining molecular dynamics, multilayer schemes, and the Marcus theory. One-electron oxidation potential and hole delocalization have been analyzed for six DNA double strands that cover all possible binary combinations of nucleotides. The results have revealed that the one-electron oxidation potential decreases with respect to the single-stranded DNA, giving evidence that the greater rigidity of a double helix induces an increase in the capacity of storing the positive charge generated upon oxidation. In addition, the hole is mainly stored in nucleobases with large reducer character, i.e., purines, especially when those are arranged in a stacked configuration in the same strand. From the computational point of view, the sampling needed to describe biological systems implies a significant computational cost. Here, we show that a small number of representative conformations generated by clustering analysis provides accurate results when compared with those obtained from sampling, reducing considerably the computational cost.

Framework Nucleic Acids-Based VEGF Signaling Activating System for Angiogenesis: A Dual Stimulation Strategy

Angiogenesis is crucial for tissue engineering, wound healing, and regenerative medicine. Nanomaterials constructed based on specific goals can be employed to activate endogenous growth factor-related signaling. In this study, based on the conventional single-stranded DNA self-assembly into tetrahedral framework nucleic acids (tFNAs), the Apt02 nucleic acid aptamer and dimethyloxallyl glycine (DMOG) small molecule are integrated into a complex via a template-based click chemistry reaction and toehold-mediated strand displacement reaction. Thus, being able to simulate the VEGF (vascular endothelial growth factor) function and stabilize HIF (hypoxia-inducible factor), a functional whole is constructed and applied to angiogenesis. Cellular studies demonstrate that the tFNAs-Apt02 complex (TAC) has a conspicuous affinity to human umbilical vein endothelial cells (HUVECs). Further incubation with DMOG yields the tFNAs-Apt02-DMOG complex (TACD), which promotes VEGF secretion, in vitro blood vessel formation, sprouting, and migration of HUVECs. Additionally, TACD enhances angiogenesis by upregulating the VEGF/VEGFR and HIF signaling pathways. Moreover, in a diabetic mouse skin defect repair process, TACD increases blood vessel formation and collagen deposition, therefore accelerating wound healing. The novel strategy simulating VEGF and stabilizing HIF promotes blood-vessel formation in vivo and in vitro and has the potential for broad applications in the vascularization field.

Sub-100 nm carriers by template polymerization for drug delivery applications

Size-controlled drug delivery systems (DDSs) have gained significant attention in the field of pharmaceutical sciences due to their potential to enhance drug efficacy, minimize side effects, and improve patient compliance. This review provides a concise overview of the preparation method, advancements, and applications of size-controlled drug delivery systems focusing on the sub-100 nm size DDSs. The importance of tailoring the size for achieving therapeutic goals is briefly mentioned. We highlight the concept of "template polymerization", a well-established method in covalent polymerization that offers precise control over molecular weight. We demonstrate the utility of this approach in crafting a monolayer of a polymer around biomolecule templates such as DNA, RNA, and protein, achieving the generation of DDSs with sizes ranging from several tens of nanometers. A few representative examples of small-size DDSs that share a conceptual similarity to "template polymerization" are also discussed. This review concludes by briefly discussing the drug release behaviors and the future prospects of "template polymerization" for the development of innovative size-controlled drug delivery systems, which promise to optimize drug delivery precision, efficacy, and safety.

A New Architecture for DNA-Templated Synthesis in Which Abasic Sites Protect Reactants from Degradation

The synthesis of artificial sequence-defined polymers that match and extend the functionality of proteins is an important goal in materials science. One way of achieving this is to program a sequence of chemical reactions between precursor building blocks by means of attached oligonucleotide adapters. However, hydrolysis of the reactive building blocks has so far limited the length and yield of product that can be obtained using DNA-templated reactions. Here, we report an architecture for DNA-templated synthesis in which reactants are tethered at internal abasic sites on opposite strands of a DNA duplex. We show that an abasic site within a DNA duplex can protect a nearby thioester from degradation, significantly increasing the yield of a DNA-templated reaction. This protective effect has the potential to overcome the challenges associated with programmable, sequence-controlled synthesis of long non-natural polymers by extending the lifetime of the reactive building blocks.

High-Throughput Synthesis, Purification, and Application of Alkyne-Functionalized Discrete Oligomers

The development of synthetic oligomers as discrete single molecular entities with accurate control over the number and nature of functional groups along the backbone has enabled a variety of new research opportunities. From fundamental studies of self-assembly in materials science to understanding efficacy and safety profiles in biology and pharmaceuticals, future directions are significantly impacted by the availability of discrete, multifunctional oligomers. However, the preparation of diverse libraries of discrete and stereospecific oligomers remains a significant challenge. We report a novel strategy for accelerating the synthesis and isolation of discrete oligomers in a high-throughput manner based on click chemistry and simplified bead-based purification. The resulting synthetic platform allows libraries of discrete polyether oligomers to be prepared and the impact of variables such as chain length, number, and nature of side chain functionalities and molecular dispersity on antibacterial behavior examined. Significantly, discrete oligomers were shown to exhibit enhanced activity with lower toxicity compared with traditional disperse samples. This work provides a practical and scalable methodology for nonexperts to prepare libraries of multifunctional discrete oligomers and demonstrates the advantages of discrete materials in biological applications.

Bioorthogonal chemistry of polyoxometalates - challenges and prospects

Bioorthogonal chemistry has enabled scientists to carry out controlled chemical processes in high yields in vivo while minimizing hazardous effects. Its extension to the field of polyoxometalates (POMs) could open up new possibilities and new applications in molecular electronics, sensing and catalysis, including inside living cells. However, this comes with many challenges that need to be addressed to effectively implement and exploit bioorthogonal reactions in the chemistry of POMs. In particular, how to protect POMs from the biological environment but make their reactivity selective towards specific bioorthogonal tags (and thereby reduce their toxicity), as well as which bioorthogonal chemistry protocols are suitable for POMs and how reactions can be carried out are questions that we are exploring herein. This perspective conceptualizes and discusses advances in the supramolecular chemistry of POMs, their click chemistry, and POM-based surface engineering to develop innovative bioorthogonal approaches tailored to POMs and to improve POM biological tolerance.

Exchanging and Releasing Information in Synthetic Digital Polymers Using a Strand-Displacement Strategy

Toehold-mediated strand displacement (TMSD) was tested as a tool to edit information in synthetic digital polymers. Uniform DNA-polymer biohybrid macromolecules were first synthesized by automated phosphoramidite chemistry and characterized by HPLC, mass spectrometry, and polyacrylamide gel electrophoresis (PAGE). These precursors were diblock structures containing a synthetic poly(phosphodiester) (PPDE) segment covalently attached to a single-stranded DNA sequence. Three types of biohybrids were prepared herein: a substrate containing an accessible toehold as well as input and output macromolecules. The substrate and the input macromolecules contained noncoded PPDE homopolymers, whereas the output macromolecule contained a digitally encoded segment. After hybridization of the substrate with the output, incubation in the presence of the input led to efficient TMSD and the release of the digital segment. TMSD can therefore be used to erase or rewrite information in self-assembled biohybrid superstructures. Furthermore, it was found in this work that the conjugation of DNA single strands to synthetic segments of chosen lengths greatly facilitates the characterization and PAGE visualization of the TMSD process.

Stimuli-responsive synthetic helical polymers

Synthetic dynamic helical polymers (supramolecular and covalent) and foldamers share the helix as a structural motif. Although the materials are different, these systems also share many structural properties, such as helix induction or conformational communication mechanisms. The introduction of stimuli responsive building blocks or monomer repeating units in these materials triggers conformational or structural changes, due to the presence/absence of the external stimulus, which are transmitted to the helix resulting in different effects, such as assymetry amplification, helix inversion or even changes in the helical scaffold (elongation, J/H helical aggregates). In this review, we show through selected examples how different stimuli (e.g., temperature, solvents, cations, anions, redox, chiral additives, pH or light) can alter the helical structures of dynamic helical polymers (covalent and supramolecular) and foldamers acting on the conformational composition or molecular structure of their components, which is also transmitted to the macromolecular helical structure.

DNA Nanostructures as Catalysts: Double Crossover Tile-Assisted 5' to 5' and 3' to 3' Chemical Ligation of Oligonucleotides

Accessibility of synthetic oligonucleotides and the success of DNA nanotechnology open a possibility to use DNA nanostructures for building sophisticated enzyme-like catalytic centers. Here we used a double DNA crossover (DX) tile nanostructure to enhance the rate, the yield, and the specificity of 5'-5' ligation of two oligonucleotides with arbitrary sequences. The ligation product was isolated via a simple procedure. The same strategy was applied for the synthesis of 3'-3' linked oligonucleotides, thus introducing a synthetic route to DNA and RNA with a switched orientation that is affordable by a low-resource laboratory. To emphasize the utility of the ligation products, we synthesized a circular structure formed from intramolecular complementarity that we named "an impossible DNA wheel" since it cannot be built from regular DNA strands by enzymatic reactions. Therefore, DX-tile nanostructures can open a route to producing useful chemical products that are unattainable via enzymatic synthesis. This is the first example of the use of DNA nanostructures as a catalyst. This study advocates for further exploration of DNA nanotechnology for building enzyme-like reactive systems.

One-Electron Oxidation Potentials and Hole Delocalization in Heterogeneous Single-Stranded DNA

The study of DNA processes is essential to understand not only its intrinsic biological functions but also its role in many innovative applications. The use of DNA as a nanowire or electrochemical biosensor leads to the need for a deep investigation of the charge transfer process along the strand as well as of the redox properties. In this contribution, the one-electron oxidation potential and the charge delocalization of the hole formed after oxidation are computationally investigated for different heterogeneous single-stranded DNA strands. We have established a two-step protocol: (i) molecular dynamics simulations in the frame of quantum mechanics/molecular mechanics (QM/MM) were performed to sample the conformational space; (ii) energetic properties were then obtained within a QM1/QM2/continuum approach in combination with the Marcus theory over an ensemble of selected geometries. The results reveal that the one-electron oxidation potential in the heterogeneous strands can be seen as a linear combination of that property within the homogeneous strands. In addition, the hole delocalization between different nucleobases is, in general, small, supporting the conclusion of a hopping mechanism for charge transport along the strands. However, charge delocalization becomes more important, and so does the tunneling mechanism contribution, when the reducing power of the nucleobases forming the strand is similar. Moreover, charge delocalization is slightly enhanced when there is a correlation between pairs of some of the interbase coordinates of the strand: twist/shift, twist/slide, shift/slide, and rise/tilt. However, the internal structure of the strand is not the predominant factor for hole delocalization but the specific sequence of nucleotides that compose the strand.

Fluorescent Investigation of Proteins Using DNA-Synthetic Ligand Conjugates

The unfathomable role that fluorescence detection plays in the life sciences has prompted the development of countless fluorescent labels, sensors, and analytical techniques that can be used to detect and image proteins or investigate their properties. Motivated by the demand for simple-to-produce, modular, and versatile fluorescent tools to study proteins, many research groups have harnessed the advantages of oligodeoxynucleotides (ODNs) for scaffolding such probes. Tight control over the valency and position of protein binders and fluorescent dyes decorating the polynucleotide chain and the ability to predict molecular architectures through self-assembly, inherent solubility, and stability are, in a nutshell, the important properties of DNA probes. This paper reviews the progress in developing DNA-based, fluorescent sensors or labels that navigate toward their protein targets through small-molecule (SM) or peptide ligands. By describing the design, operating principles, and applications of such systems, we aim to highlight the versatility and modularity of this approach and the ability to use ODN-SM or ODN-peptide conjugates for various applications such as protein modification, labeling, and imaging, as well as for biomarker detection, protein surface characterization, and the investigation of multivalency.

Rapid Chemical Ligation of DNA and Acyclic Threoninol Nucleic Acid (aTNA) for Effective Nonenzymatic Primer Extension

Previously, nonenzymatic primer extension reaction of acyclic l-threoninol nucleic acid (L-aTNA) was achieved in the presence of N-cyanoimidazole (CNIm) and Mn2+; however, the reaction conditions were not optimized and a mechanistic insight was not sufficient. Herein, we report investigation of the kinetics and reaction mechanism of the chemical ligation of L-aTNA to L-aTNA and of DNA to DNA. We found that Cd2+, Ni2+, and Co2+ accelerated ligation of both L-aTNA and DNA and that the rate-determining step was activation of the phosphate group. The activation was enhanced by duplex formation between a phosphorylated L-aTNA fragment and template, resulting in unexpectedly more effective L-aTNA ligation than DNA ligation. Under optimized conditions, an 8-mer L-aTNA primer could be elongated by ligation to L-aTNA trimers to produce a 29-mer full-length oligomer with 60% yield within 2 h at 4 °C. This highly effective chemical ligation system will allow construction of artificial genomes, robust DNA nanostructures, and xeno nucleic acids for use in selection methods. Our findings also shed light on the possible pre-RNA world.

Intramolecular and intermolecular hole delocalization rules the reducer character of isolated nucleobases and homogeneous single-stranded DNA

The use of DNA strands as nanowires or electrochemical biosensors requires a deep understanding of charge transfer processes along the strand, as well as of the redox properties. These properties are computationally assessed in detail throughout this study. By applying molecular dynamics and hybrid QM/continuum and QM/QM/continuum schemes, the vertical ionization energies, adiabatic ionization energies, vertical attachment energies, one-electron oxidation potentials, and delocalization of the hole generated upon oxidation have been determined for nucleobases in their free form and as part of a pure single-stranded DNA. We show that the reducer ability of the isolated nucleobases is explained by the intramolecular delocalization of the positively charged hole, while the enhancement of the reducer character when going from aqueous solution to the strand correlates very well with the intermolecular hole delocalization. Our simulations suggest that the redox properties of DNA strands can be tuned by playing with the balance between intramolecular and intermolecular charge delocalization.

Programmable DNA Interstrand Crosslinking by Alkene-Alkyne [2 + 2] Photocycloaddition

Covalent crosslinking of DNA strands provides a useful tool for medical, biochemical, and DNA nanotechnology applications. Here we present a light-induced interstrand DNA crosslinking reaction using the modified nucleoside 5-phenylethynyl-2'-deoxyuridine (^PhedU). The crosslinking ability of ^PhedU was programmed by base pairing and by metal ion interaction at the Watson-Crick base pairing site. Rotation to intrahelical positions was favored by hydrophobic stacking and enabled an unexpected photochemical alkene-alkyne [2 + 2] cycloaddition within the DNA duplex, resulting in efficient formation of a ^PhedU dimer after short irradiation times of a few seconds. A ^PhedU-dimer-containing DNA was shown to efficiently bind a helicase complex, but the covalent crosslink completely prevented DNA unwinding, suggesting possible applications in biochemistry or structural biology.

Screw sense and screw sensibility: communicating information by conformational switching in helical oligomers

Biological systems have evolved a number of different strategies to communicate information on the molecular scale. Among these, the propagation of conformational change is among the most important, being the means by which G-protein coupled receptors (GPCRs) use extracellular signals to modulate intracellular processes, and the way that opsin proteins translate light signals into nerve impulses. The developing field of foldamer chemistry has allowed chemists to employ conformationally well-defined synthetic structures likewise to mediate information transfer, making use of mechanisms that are not found in biological contexts. In this review, we discuss the use of switchable screw-sense preference as a communication mechanism. We discuss the requirements for functional communication devices, and show how dynamic helical foldamers derived from the achiral monomers such as α-aminoisobutyric acid (Aib) and meso-cyclohexane-1,2-diamine fulfil them by communicating information in the form of switchable screw-sense preference. We describe the various stimuli that can be used to switch screw sense, and explore the way that propagation of the resulting conformational preference in a well-defined helical molecule allows screw sense to control chemical events remote from a source of information. We describe the operation of these conformational switches in the membrane phase, and outline the progress that has been made towards using conformational switching to communicate between the exterior and interior of a phospholipid vesicle.

Protein-Templated Reactions Using DNA-Antibody Conjugates

DNA-templated chemical reactions have found wide applications in drug discovery, programmed multistep synthesis, nucleic acid detection, and targeted drug delivery. The control of these reactions has, however, been limited to nucleic acid hybridization as a means to direct the proximity between reactants. In this work a system capable of translating protein-protein binding events into a DNA-templated reaction which leads to the covalent formation of a product is introduced. Protein-templated reactions by employing two DNA-antibody conjugates that are both able to recognize the same target protein and to colocalize a pair of reactant DNA strands able to undergo a click reaction are achieved. Two individual systems, each responsive to human serum albumin (HSA) and human IgG, are engineered and it is demonstrated that, while no reaction occurs in the absence of proteins, both protein-templated reactions can occur simultaneously in the same solution without any inter-system crosstalk.

Privileged heterocycles for DNA-encoded library design and hit-to-lead optimization

It is well known that heterocyclic compounds play a key role in improving drug activity, target selectivity, physicochemical properties as well as reducing toxicity. In this review, we summarized the representative heterocyclic structures involved in hit compounds which were obtained from DNA-encoded library from 2013 to 2021. In some examples, the state of the art in heterocycle-based DEL synthesis and hit-to-lead optimization are highlighted. We hope that more and more novel heterocycle-based DEL toolboxes and in-depth pharmaceutical research on these lead compounds can be developed to accelerate the discovery of new drugs.

Improved Metal-Free Approach for the Synthesis of Protected Thiol Containing Thymidine Nucleoside Phosphoramidite and Its Application for the Synthesis of Ligatable Oligonucleotide Conjugates

Oligonucleotide conjugates are versatile scaffolds that can be applied in DNA-based screening platforms and ligand display or as therapeutics. Several different chemical approaches are available for functionalizing oligonucleotides, which are often carried out on the 5' or 3' end. Modifying oligonucleotides in the middle of the sequence opens the possibility to ligate the conjugates and create DNA strands bearing multiple different ligands. Our goal was to establish a complete workflow that can be applied for such purposes from monomer synthesis to templated ligation. To achieve this, a monomer is required with an orthogonal functional group that can be incorporated internally into the oligonucleotide sequence. This is followed by conjugation with different molecules and ligation with the help of a complementary template. Here, we show the synthesis and the application of a thiol-modified thymidine nucleoside phosphoramidite to prepare ligatable oligonucleotide conjugates. The conjugations were performed both in solution and on solid phase, resulting in conjugates that can be assembled into multivalent oligonucleotides decorated with tissue-targeting peptides using templated ligation.

The wending rhombus: Self-assembling 3D DNA crystals

In this perspective, we provide a summary of recent developments in self-assembling three-dimensional (3D) DNA crystals. Starting from the inception of this subfield, we describe the various advancements in structure that have led to an increase in the diversity of macromolecular crystal motifs formed through self-assembly, and we further comment on the future directions of the field, which exploit noncanonical base pairing interactions beyond Watson-Crick. We then survey the current applications of self-assembling 3D DNA crystals in reversibly active nanodevices and materials engineering and provide an outlook on the direction researchers are taking these structures. Finally, we compare 3D DNA crystals with DNA origami and suggest how these distinct subfields might work together to enhance biomolecule structure solution, nanotechnological motifs, and their applications.

Assembly of Biologically Functional Structures by Nucleic Acid Templating: Implementation of a Strategy to Overcome Inhibition by Template Excess

Delivery of therapeutic molecules to pathogenic cells is often hampered by unintended toxicity to normal cells. In principle, this problem can be circumvented if the therapeutic effector molecule is split into two inactive components, and only assembled on or within the target cell itself. Such an in situ process can be realized by exploiting target-specific molecules as templates to direct proximity-enhanced assembly. Modified nucleic acids carrying inert precursor fragments can be designed to co-hybridize on a target-specific template nucleic acid, such that the enforced proximity accelerates assembly of a functional molecule for antibody recognition. We demonstrate the in vitro feasibility of this adaptation of nucleic acid-templated synthesis (NATS) using oligonucleotides bearing modified peptides (“haplomers”), for templated assembly of a mimotope recognized by the therapeutic antibody trastuzumab. Enforced proximity promotes mimotope assembly via traceless native chemical ligation. Nevertheless, titration of participating haplomers through template excess is a potential limitation of trimolecular NATS. In order to overcome this problem, we devised a strategy where haplomer hybridization can only occur in the presence of target, without being subject to titration effects. This generalizable NATS modification may find future applications in enabling directed targeting of pathological cells.

Biomacromolecule-Assisted Screening for Reaction Discovery and Catalyst Optimization

Reaction discovery and catalyst screening lie at the heart of synthetic organic chemistry. While there are efforts at de novo catalyst design using computation/artificial intelligence, at its core, synthetic chemistry is an experimental science. This review overviews biomacromolecule-assisted screening methods and the follow-on elaboration of chemistry so discovered. All three types of biomacromolecules discussed─enzymes, antibodies, and nucleic acids─have been used as "sensors" to provide a readout on product chirality exploiting their native chirality. Enzymatic sensing methods yield both UV-spectrophotometric and visible, colorimetric readouts. Antibody sensors provide direct fluorescent readout upon analyte binding in some cases or provide for cat-ELISA (Enzyme-Linked ImmunoSorbent Assay)-type readouts. DNA biomacromolecule-assisted screening allows for templation to facilitate reaction discovery, driving bimolecular reactions into a pseudo-unimolecular format. In addition, the ability to use DNA-encoded libraries permits the barcoding of reactants. All three types of biomacromolecule-based screens afford high sensitivity and selectivity. Among the chemical transformations discovered by enzymatic screening methods are the first Ni(0)-mediated asymmetric allylic amination and a new thiocyanopalladation/carbocyclization transformation in which both C-SCN and C-C bonds are fashioned sequentially. Cat-ELISA screening has identified new classes of sydnone-alkyne cycloadditions, and DNA-encoded screening has been exploited to uncover interesting oxidative Pd-mediated amido-alkyne/alkene coupling reactions.

Chalcones, a Privileged Scaffold: Highly Versatile Molecules in [4+2] Cycloadditions

Chalcones are aromatic ketones found in nature as the central core of many biological compounds. They have a wide range of biological activity and are biogenetic precursors of other important molecules such as flavonoids. Their pharmacological relevance makes them a privileged scaffold, advantageous for seeking alternative therapies in medicinal chemistry. Due to their structural diversity and ease of synthesis, they are often employed as building blocks for chemical transformations. Chalcones have a carbonyl conjugated system with two electrophilic centers that are commonly used for nucleophilic additions, as described in numerous articles. They can also participate in Diels-Alder reactions, which are [4+2] cycloadditions between a diene and a dienophile. This microreview presents a chronological survey of studies on chalcones as dienes and dienophiles in Diels-Alder cycloadditions. Although these reactions occur in nature, isolation of chalcones from plants yields very small quantities. Contrarily, synthesis leads to large quantities at a low cost. Hence, novel methodologies have been developed for [4+2] cycloadditions, with chalcones serving as a 2π or 4π electron system.

Standardized excitable elements for scalable engineering of far-from-equilibrium chemical networks

Engineered far-from-equilibrium synthetic chemical networks that pulse or switch states in response to environmental signals could precisely regulate the kinetics of chemical synthesis or self-assembly. Currently, such networks must be extensively tuned to compensate for the different activities of and unintended reactions between a network's various chemical components. Modular elements with standardized performance could be used to rapidly construct networks with designed functions. Here we develop standardized excitable chemical regulatory elements, termed genelets, and use them to construct complex in vitro transcriptional networks. We develop a protocol for identifying >15 interchangeable genelet elements with uniform performance and minimal crosstalk. These elements can be combined to engineer feedforward and feedback modules whose dynamics match those predicted by a simple kinetic model. Modules can then be rationally integrated and organized into networks that produce tunable temporal pulses and act as multistate switchable memories. Standardized genelet elements, and the workflow to identify more, should make engineering complex far-from-equilibrium chemical dynamics routine.

Opportunities for Expanding Encoded Chemical Diversification and Improving Hit Enrichment in mRNA-Displayed Peptide Libraries

DNA-encoded small-molecule libraries and mRNA displayed peptide libraries both use numerically large pools of oligonucleotide-tagged molecules to identify potential hits for protein targets. They differ dramatically, however, in the 'drug-likeness' of the molecules that each can be used to discover. We give here an overview of the two techniques, comparing some advantages and disadvantages of each, and suggest areas where particularly mRNA display can benefit from adopting advances developed with DNA-encoded small molecule libraries. We outline cases where chemical modification of the peptide library has already been used in mRNA display, and survey opportunities to expand this using examples from DNA-encoded small molecule libraries. We also propose potential opportunities for encoding such reactions within the mRNA/cDNA tag of an mRNA-displayed peptide library to allow a more diversity-oriented approach to library modification. Finally, we outline alternate approaches for enriching target-binding hits from a pooled and tagged library, and close by detailing several examples of how an adjusted mRNA-display based approach could be used to discover new 'drug-like' modified small peptides.

Hybridization-specific chemical reactions to create interstrand crosslinking and threaded structures of nucleic acids

The interstrand crosslinking and threaded structures of nucleic acids have high potential in oligonucleotide therapeutics, chemical biology, and nanotechnology. For example, properly designed crosslinking structures provide high activity and nuclease resistance for anti-miRNAs. The noncovalent labeling and modification by the threaded structures are useful as new chemical biology tools. Photoreversible crosslinking creates smart materials, such as reversible photoresponsive gels and DNA origami objects. This review introduces the creation of interstrand crosslinking and threaded structures, such as catenanes and rotaxanes, based on hybridization-specific chemical reactions and their functions and perspectives.

Tug-of-War between DNA Chelation and Silver Agglomeration in DNA-Silver Cluster Chromophores

Supramolecular chromophores form when a DNA traps silvers that then coalesce into clusters with discrete, molecular electronic states. However, DNA strands are polymeric ligands that disperse silvers and thus curb agglomeration. We study this competition using two chromophores that share three common components: a dimeric DNA scaffold, Ag⁺-nucleobase base pairs, and Ag⁰ chromophores. The DNA host C₄-A₂-iC₄T mimics structural elements in a DNA-cluster crystal structure using a phosphodiester backbone with combined 5' → 3' and 3' → 5' (indicated by "i") directions. The backbone directions must alternate to form the two silver clusters, and this interdependence supports a silver-linked structure. This template creates two chromophores with distinct sizes, charges, and hence spectra: (C₄-A₂-iC₄T)₂/Ag₁₁⁷⁺ with λ_abs/λ_em = 430/520 nm and (C₄-A₂-iC₄T)₂/Ag₁₄⁸⁺ with λ_abs/λ_em = 510/630 nm. The Ag⁺ and Ag⁰ constituents in these partially oxidized clusters are linked with structural elements in C₄-A₂-iC₄T. Ag⁺ alone binds sparsely but strongly to form C₄-A₂-iC₄T/3-4 Ag⁺ and (C₄-A₂-iC₄T)₂/7-8 Ag⁺ complexes, and these stoichiometries suggest that Ag⁺ cross-links pairs of cytosines to form a hairpin with a metallo-C₄/iC₄ duplex and an adenine loop. The Ag⁰ are chemically orthogonal because they can be oxidatively etched without disrupting the underlying Ag⁺-DNA matrix, and their reactivity is attributed to their valence electrons and weaker chelation by the adenines. These studies suggest that Ag⁺ disperses with the cytosines to create an adenine binding pocket for the Ag⁰ cluster chromophores.

Combinatorial technology revitalized by DNA-encoding

Combinatorial chemistry invented nearly 40 years ago was welcomed with enthusiasm in the drug research community. The method offered access to a practically unlimited number of new compounds. The new compounds however are mixtures, and methods had to be developed for the identification of the bioactive components. This was one of the reasons why the method could not providethe expected cornucopia of new drugs. Among the different screening methods, two approaches seem to offer the best results. One of them is based on the intrinsic property of the combinatorial split and pool solid-phase synthesis: One compound forms on each bead of the solid support. Different methods have been developed to encode the beads and identify the structure of compounds formed on them. The most important method applies DNA oligomers for encoding. As a second approach in screening, DNA-encoded combinatorial libraries are synthesized omitting the solid support and the mixtures are screened in solution using affinity binding methods. Libraries containing billions and even trillions of components are synthesized and successfully tested, which led to the identification of a significant number of new leads.

Covalent Positioning of Single DNA Molecules for Nanopatterning

Bottom-up micropatterning or nanopatterning can be viewed as the localization of target molecules to the desired area of a surface. A majority of these processes rely on the physical adsorption of ink-like molecules to the paper-like surface, resulting in unstable immobilization of the target molecules owing to their noncovalent linkage to the surface. Herein, successive single nick-sealing facilitated the covalent immobilization of individual DNA molecules at defined positions on a dendron-coated silicon surface using atomic force microscopy. The covalently-patterned ssDNA was visualized when the streptavidin-coated gold nanoparticles bound to the biotinylated DNA. The successive covalent positioning of the target DNA under ambient conditions may facilitate the bottom-up construction of DNA-based durable nanostructures, nanorobots, or memory system.

Templated approach to well-defined, oxidatively coupled conjugated polymers

Templated oxidative polymerization affords organic soluble, oxidatively doped PEDOT-based polymers with controlled molecular weights and low dispersities (Đ ∼ 1.2) for the first time.

Using antibodies to control DNA-templated chemical reactions

DNA-templated synthesis takes advantage of the programmability of DNA-DNA interactions to accelerate chemical reactions under diluted conditions upon sequence-specific hybridization. While this strategy has proven advantageous for a variety of applications, including sensing and drug discovery, it has been so far limited to the use of nucleic acids as templating elements. Here, we report the rational design of DNA templated synthesis controlled by specific IgG antibodies. Our approach is based on the co-localization of reactants induced by the bivalent binding of a specific IgG antibody to two antigen-conjugated DNA templating strands that triggers a chemical reaction that would be otherwise too slow under diluted conditions. This strategy is versatile, orthogonal and adaptable to different IgG antibodies and can be employed to achieve the targeted synthesis of clinically-relevant molecules in the presence of specific IgG biomarker antibodies.

Visible-light triggered templated ligation on surface using furan-modified PNAs

Oligonucleotide-templated reactions are frequently exploited for target detection in biosensors and for the construction of DNA-based materials and probes in nanotechnology. However, the translation of the specifically used template chemistry from solution to surfaces, with the final aim of achieving highly selective high-throughput systems, has been difficult to reach and therefore, poorly explored. Here, we show the first example of a visible light-triggered templated ligation on a surface, employing furan-modified peptide nucleic acids (PNAs). Tailored photo-oxidation of the pro-reactive furan moiety is ensured by the simultaneous introduction of a weak photosensitizer as well as a nucleophilic moiety in the reacting PNA strand. This allows one to ensure a localized production of singlet oxygen for furan activation, which is not affected by probe dilution or reducing conditions. Simple white light irradiation in combination with target-induced proximity between reactive functionalities upon recognition of a short 22mer DNA or RNA sequence that functions as a template, allows sensitive detection of nucleic acid targets in a 96 well plate format.

Scalable One-Pot-Liquid-Phase Oligonucleotide Synthesis for Model Network Hydrogels

Solid-phase oligonucleotide synthesis (SPOS) based on phosphoramidite chemistry is currently the most widespread technique for DNA and RNA synthesis but suffers from scalability limitations and high reagent consumption. Liquid-phase oligonucleotide synthesis (LPOS) uses soluble polymer supports and has the potential of being scalable. However, at present, LPOS requires 3 separate reaction steps and 4-5 precipitation steps per nucleotide addition. Moreover, long acid exposure times during the deprotection step degrade sequences with high A content (adenine) due to depurination and chain cleavage. In this work, we present the first one-pot liquid-phase DNA synthesis technique which allows the addition of one nucleotide in a one-pot reaction of sequential coupling, oxidation, and deprotection followed by a single precipitation step. Furthermore, we demonstrate how to suppress depurination during the addition of adenine nucleotides. We showcase the potential of this technique to prepare high-purity 4-arm PEG-T20 (T = thymine) and 4-arm PEG-A20 building blocks in multigram scale. Such complementary 4-arm PEG-DNA building blocks reversibly self-assemble into supramolecular model network hydrogels and facilitate the elucidation of bond lifetimes. These model network hydrogels exhibit new levels of mechanical properties (storage modulus, bond lifetimes) in DNA bonds at room temperature (melting at 44 °C) and thus open up pathways to next-generation DNA materials programmable through sequence recognition and available for macroscale applications.

Modified nucleic acids: replication, evolution, and next-generation therapeutics

Modified nucleic acids, also called xeno nucleic acids (XNAs), offer a variety of advantages for biotechnological applications and address some of the limitations of first-generation nucleic acid therapeutics. Indeed, several therapeutics based on modified nucleic acids have recently been approved and many more are under clinical evaluation. XNAs can provide increased biostability and furthermore are now increasingly amenable to in vitro evolution, accelerating lead discovery. Here, we review the most recent discoveries in this dynamic field with a focus on progress in the enzymatic replication and functional exploration of XNAs.

Programming DNA-Based Systems through Effective Molarity Enforced by Biomolecular Confinement

The fundamental concept of effective molarity is observed in a variety of biological processes, such as protein compartmentalization within organelles, membrane localization and signaling paths. To control molecular encountering and promote effective interactions, nature places biomolecules in specific sites inside the cell in order to generate a high, localized concentration different from the bulk concentration. Inspired by this mechanism, scientists have artificially recreated in the lab the same strategy to actuate and control artificial DNA-based functional systems. Here, it is discussed how harnessing effective molarity has led to the development of a number of proximity-induced strategies, with applications ranging from DNA-templated organic chemistry and catalysis, to biosensing and protein-supported DNA assembly.

Sequence-Controlled Synthesis of Advanced Clickable Synthetic Oligonucleotides

Through thiol-ene photopolymerization of presynthesized oligomers, advanced clickable nucleic acids (CNA-2G) are synthesized with sequence-controlled repeating units. As examples, poly(thymine-adenine) (polyTA) CNA-2G and poly(thymine-thymine-cytosine) CNA-2G are synthesized by polymerizing thiol-ene heterofunctional dimers with pendant thymine-adenine nucleobases and trimer with pendant thymine-thymine-cytosine nucleobases. Based on size exclusion chromatography (SEC) analysis, polyTA and polyTTC have number average molecular weights of 2000 and 1800, respectively, which contain 7-8 pendant nucleobases. Based on the different behavior of the CNA-2G monomers and CNA-2G oligomers with two or more pendant nucleobases in photopolymerization, an unusual thiol-ene chain-growth propagation mechanism is observed for the former and a common thiol-ene step-growth propagation mechanism for the latter. The uncommon thiol-ene chain-growth propagation is hypothesized to rely on a six-membered ring mediated intramolecular hydrogen atom transfer process.

Autonomous Discovery in the Chemical Sciences Part II: Outlook

This two-part Review examines how automation has contributed to different aspects of discovery in the chemical sciences. In this second part, we reflect on a selection of exemplary studies. It is increasingly important to articulate what the role of automation and computation has been in the scientific process and how that has or has not accelerated discovery. One can argue that even the best automated systems have yet to "discover" despite being incredibly useful as laboratory assistants. We must carefully consider how they have been and can be applied to future problems of chemical discovery in order to effectively design and interact with future autonomous platforms. The majority of this Review defines a large set of open research directions, including improving our ability to work with complex data, build empirical models, automate both physical and computational experiments for validation, select experiments, and evaluate whether we are making progress towards the ultimate goal of autonomous discovery. Addressing these practical and methodological challenges will greatly advance the extent to which autonomous systems can make meaningful discoveries.

Photoactivated Artificial Molecular Machines that Can Perform Tasks

Research on artificial photoactivated molecular machines has moved in recent years from a basic scientific endeavor toward a more applicative effort. Nowadays, the prospect of reproducing the operation of natural nanomachines with artificial counterparts is no longer a dream but a concrete possibility. The progress toward the construction of molecular-machine-based devices and materials in which light irradiation results in the execution of a task as a result of nanoscale movements is illustrated here. After a brief description of a few basic types of photoactivated molecular machines, significant examples of their exploitation to perform predetermined functions are presented. These include switchable catalysts, nanoactuators that interact with cellular membranes, transporters of small molecular cargos, and active joints capable of mechanically coupling molecular-scale movements. Investigations aimed at harnessing the collective operation of a multitude of molecular machines organized in arrays to perform tasks at the microscale and macroscale in hard and soft materials are also reviewed. Surfaces, gels, liquid crystals, polymers, and self-assembled nanostructures are described wherein the nanoscale movement of embedded molecular machines is amplified, allowing the realization of muscle-like actuators, microfluidic devices, and polymeric materials for light energy transduction and storage.

From Interaction to Function in DNA-Templated Supramolecular Self-Assemblies

DNA-templated self-assembly represents a rich and growing subset of supramolecular chemistry where functional self-assemblies are programmed in a versatile manner using nucleic acids as readily-available and readily-tunable templates. In this review, we summarize the different DNA recognition modes and the basic supramolecular interactions at play in this context. We discuss the recent results that report the DNA-templated self-assembly of small molecules into complex yet precise nanoarrays, going from 1D to 3D architectures. Finally, we show their emerging functions as photonic/electronic nanowires, sensors, gene delivery vectors, and supramolecular catalysts, and their growing applications in a wide range of area from materials to biological sciences.

Deep Eutectic Solvents as Media for the Prebiotic DNA-Templated Synthesis of Peptides

Translation of genetic information into peptide products is one of the fundamental processes of biology. How this occurred prebiotically, in the absence of enzyme catalysts, is an intriguing question. Nucleic acid-templated synthesis (NATS) promotes reactions by bringing building blocks tethered to complementary DNA strands into close proximity and has been shown to enable peptide synthesis without enzymes—it could therefore serve as a model for prebiotic translation of information stored in nucleic acid sequences into functional peptides. The decomposition of highly reactive DNA adapters has so far limited the effectiveness of NATS, but these studies have been performed exclusively in aqueous solution. Deep eutectic solvents (DESs) have been proposed as a feasible solvent for prebiotic replication of nucleic acids, and here are studied as media for prebiotic translation using NATS as a model. DESs are shown to enhance the stability of DNA-conjugated activated esters, the precursors of peptides. However, this enhanced stability was coupled with decreased amine reactivity that hampered the formation of peptide bonds in DESs. These properties are exploited to demonstrate the storage of DNA-conjugated activated esters in a DES followed by transfer into aqueous buffer to activate the NATS of peptides “on demand.” These findings, together with the reported functions of DESs in prebiotic processes, shed light on how DESs could have facilitated the non-enzymatic translation of genetic information into functional peptides on the early Earth.

Building in vitro transcriptional regulatory networks by successively integrating multiple functional circuit modules

The regulation of cellular dynamics and responses to stimuli by genetic regulatory networks suggests how in vitro chemical reaction networks might analogously direct the dynamics of synthetic materials or chemistries. A key step in developing genetic regulatory network analogues capable of this type of sophisticated regulation is the integration of multiple coordinated functions within a single network. Here, we demonstrate how such functional integration can be achieved using in vitro transcriptional genelet circuits that emulate essential features of cellular genetic regulatory networks. By successively incorporating functional genelet modules into a bistable circuit, we construct an integrated regulatory network that dynamically changes its state in response to upstream stimuli and coordinates the timing of downstream signal expression. We use quantitative models to guide module integration and develop strategies to mitigate undesired interactions between network components that arise as the size of the network increases. This approach could enable the construction of in vitro networks capable of multifaceted chemical and material regulation.

Photo- and Redox-Driven Artificial Molecular Motors

Directed motion at the nanoscale is a central attribute of life, and chemically driven motor proteins are nature's choice to accomplish it. Motivated and inspired by such bionanodevices, in the past few decades chemists have developed artificial prototypes of molecular motors, namely, multicomponent synthetic species that exhibit directionally controlled, stimuli-induced movements of their parts. In this context, photonic and redox stimuli represent highly appealing modes of activation, particularly from a technological viewpoint. Here we describe the evolution of the field of photo- and redox-driven artificial molecular motors, and we provide a comprehensive review of the work published in the past 5 years. After an analysis of the general principles that govern controlled and directed movement at the molecular scale, we describe the fundamental photochemical and redox processes that can enable its realization. The main classes of light- and redox-driven molecular motors are illustrated, with a particular focus on recent designs, and a thorough description of the functions performed by these kinds of devices according to literature reports is presented. Limitations, challenges, and future perspectives of the field are critically discussed.

Capping Strategies for Covalent Template-Directed Synthesis of Linear Oligomers Using CuAAC

Covalent templating provides an attractive solution to the controlled synthesis of linear oligomers because a template oligomer can be used to define the precise length and sequence of the product. If the monomer units are attached to the template using kinetically inert covalent bonds it should be possible to operate at high dilution to favor intramolecular over intermolecular reaction. However, for oligomerization reactions using copper-catalyzed azide alkyne cycloaddition (CuAAC) this is not the case. The rate-limiting step is formation of an activated copper complex, so any alkyne that is activated by copper reacts rapidly with the nearest available azide. As a result, every time a chain end alkyne is activated, rapid intermolecular reaction takes place with a different oligomer leading to the formation of higher order products. It proved possible to block these intermolecular reactions by adding an excess of an azide capping agent that intercepts the chain end of the growing oligomer on the template. By adjusting the concentration of the capping agent to compete effectively with the unwanted intermolecular reactions without interfering with the desired intramolecular reactions, it was possible to obtain quantitative yields of copy strands from covalent template-directed oligomerization reactions. Remarkably, the capping agent could also be used to control the stereochemistry of the duplex formed in the templated oligomerization reaction to give exclusively the antiparallel product.