Reducing Product Inhibition in Nucleic Acid‐Templated Ligation Reactions: DNA‐Templated Cycligation

Programmable interactions allow nucleic acid molecules to template chemical reactions by increasing the effective molarities of appended reactive groups. DNA/RNA‐triggered reactions can proceed, in principle, with turnover in the template. The amplification provided by the formation of many product molecules per template is a valuable asset when the availability of the DNA or RNA target is limited. However, turnover is usually impeded by reaction products that block access to the template. Product inhibition is most severe in ligation reactions, where products after ligation have dramatically increased template affinities. We introduce a potentially generic approach to reduce product inhibition in nucleic acid‐programmed ligation reactions. A DNA‐triggered ligation–cyclization sequence (“cycligation”) of bifunctional peptide nucleic acid (PNA) conjugates affords cyclic ligation products. Melting experiments revealed that product cyclization is accompanied by a pronounced decrease in template affinity compared to linear ligation products. The reaction system relies upon haloacetylated PNA‐thioesters and isocysteinyl‐PNA‐cysteine conjugates, which were ligated on a DNA template according to a native chemical ligation mechanism. Dissociation of the resulting linear product‐template duplex (induced by, for example, thermal cycling) enabled product cyclization through sulfur‐halide substitution. Both ligation and cyclization are fast reactions (ligation: 86 % yield after 20 min, cyclization: quantitative after 5 min). Under thermocycling conditions, the DNA template was able to trigger the formation of new product molecules when fresh reactants were added. Furthermore, cycligation produced 2–3 times more product than a conventional ligation reaction with substoichiometric template loads (0.25–0.01 equiv). We believe that cyclization of products from DNA‐templated reactions could ultimately afford systems that completely overcome product inhibition.     

7‐Azidomethoxy‐Coumarins as Profluorophores for Templated Nucleic Acid Detection

Templated nucleic acid detection is an emerging bioanalytical method that makes use of the target DNA or RNA strand to initiate a fluorogenic reaction. The Staudinger reduction holds particular promise for templated sensing of nucleic acids because the involved functional groups are highly chemoselective. Here, the azidomethoxy group, which can be removed under Staudinger conditions, is used to cage 7‐hydroxycoumarin fluorophores. Reduction by phosphines and subsequent loss of the azidomethoxy substituent induce a significant bathochromic shift of the major absorbance band in the near UV region. When excited at the appropriate wavelength, this change in the absorbance spectrum translates into a substantial fluorescence turn‐on signal. The described profluorophores are readily conjugated to amino‐modified DNAs and are rapidly uncaged by a triphenylphosphine–DNA probe under the control of a DNA template. In addition, turnover of the probes on the target strand occurs and yields substantial signal amplification.     

Native Chemical Ligation Directed by Photocleavable Peptide Nucleic Acid (PNA) Templates

A novel peptide–peptide ligation strategy is introduced that has the potential to provide peptide libraries of linearly or branched coupled fragments and will be suited to introduce simultaneous protein modifications at different ligation sites. Ligation is assisted by templating peptide nucleic acid (PNA) strands, and therefore, ligation specificity is solely encoded by the PNA sequence. PNA templating, in general, allows for various kinds of covalent ligation reactions. As a proof of principle, a native chemical ligation strategy was elaborated. This PNA‐templated ligation includes easy on‐resin procedures to couple linkers and PNA to the respective peptides, and a traceless photocleavage of the linker/PNA oligomer after the ligation step. A 4,5‐dimethoxy‐2‐nitrobenzaldehyde‐based linker that allowed the photocleavable linkage of two bio‐oligomers was developed.     

Vinyl polymer analogues of nucleic acids

The preparation and properties of vinyl polymers carrying the bases of nucleic acids as substituents are described. These compounds form specific complexes with complementary polynucleotides, a process which prevents the latter from functioning as templates in the synthesis of polymeric nucleic acid or protein. The uptake and fate of these polymers in mammalian cells grown in culture and in animals are described; these polymers exhibit weak but selective antiviral effects in such systems.     

Quadruplex-Templated and Catalyzed Ligation of Nucleic Acids

Template-guided chemical reactions between nucleic acid strands are an important process in biomedical research. However, almost all of these reactions employ an oligonucleotide-templated approach that is based on the double-helix alignment. The moderate stability of the double helix makes this approach unsuitable for many chemical reactions, so alternative nucleic acid alignment mechanisms, demonstrating higher thermal and chemical stability, are desirable. Earlier, we described a noncovalent coupling mechanism between DNA strands through a quadruplex-and-Mg²⁺ connection (QMC). QMC is based on G-quadruplexes and allows unusually stable and specific interactions. Herein, a novel catalytic nucleic acid reaction, based on QMC, is described. This approach uses G-tetrads as a structural and recognition element without employing Watson-Crick complementarity rules at any stage of substrate/catalyst formation or interaction between them. Quadruplex-templated ligation can be achieved through the self-ligation of two nucleic acid strands, or through a quadruplex catalyst, which forms a G-triplex and specifically connects the strands. The process is extraordinarily robust and efficient. For instance, the ligation of carbodiimide-activated substrates can proceed in boiling solutions, and complete ligation is demonstrated within a minute. The quadruplex-templated and catalyzed reactions will create new opportunities for chemical reactions requiring harsh experimental conditions.     

A novel nonsurfactant pathway to hydrothermally stable mesoporous silica materials

A novel way is described to tune the pore diameters of the hydroxy-carboxylic acid templated mesoporous silica materials by adding different amount of aluminum chloride to the synthesis mixture for the sol–gel reactions, and these silica materials obtained have higher hydrothermal stability than those prepared without AlCl₃.     

Molecular dynamics applied to nucleic acids

In this Account, we focus on molecular dynamics (MD) simulations involving fully solvated nucleic acids. Historically, MD simulations were first applied to proteins and several years later to nucleic acids. The first MD simulations of DNA were carried out in vacuo, but nowadays fully solvated systems are common practice. Recently, technical improvements have made it possible to conduct accurate MD simulations of highly charged nucleic acids. The state-of-the-art of MD simulations and a number of applications on various nucleic acid systems are discussed.     

Probing Y-shaped DNA structure with time-resolved FRET

Self-assembly based on nucleic acid systems has become highly attractive for bottom-up fabrication of programmable matter due to the highly selective molecular recognition property of biomolecules. In this context, Y-shaped DNA (Y-DNA) provides an effective building block for forming unique self-assembled large-scale architectures. The dimension and growth of the nano- and microstructures depend significantly on the configurational stability of Y-DNA as a building block. Here we present structural studies of Y-DNA systems using a time-resolved FRET (F?rster resonance energy transfer) technique. A fluorophore (Alexa 488) and an acceptor (DABCYL) were placed at two different ends of Y-DNA, and the lifetime of the fluorophore was measured to probe the relative distance between the donor and acceptor. Our results confirmed different distances between the arms of the Y-DNA and highlighted the overall structural integrity of the Y-DNA system as a leading building block for molecular self-assembly. Temperature dependent lifetime measurements indicated configurational changes in the overall Y-DNA nanoarchitecture above 40 °C.     

Characterisation of mesoporous polymer films deposited using lyotropic liquid crystal templating

Porous polymer films show interesting properties as ion selective membranes. In this work, poly(1,2-diaminobenzene) and polytyramine were deposited from hexagonal liquid crystal templates using two different surfactants. Resulting films were investigated to find evidence of mesoporous structures. While templated poly(1,2-diaminobenzene) has already been described as charge selective in the past, electrochemical experiments in this work demonstrate that another mechanism (most likely, size selectivity) also contributes to its ion selective behaviour. Films were characterised using spectroscopic ellipsometry and impedance spectroscopy. Results provide further evidence for the porosity, thinness, and the presence of ions in the templated poly(1,2-diaminobenzene) films. It is demonstrated that the use of a low-cost surfactant (Brij 56) is sufficient for the templating process. In contrast, polytyramine gave no evidence of being templated by the liquid crystal.     

pH‐Cleavable Nucleoside Lipids: A New Paradigm for Controlling the Stability of Lipid‐Based Delivery Systems

Lipid‐based delivery systems are an established technology with considerable clinical acceptance and several applications in human. Herein, we report the design, synthesis and evaluation of novel orthoester nucleoside lipids (ONLs) for the modulation of liposome stability. The ONLs contain head groups with 3′‐orthoester nucleoside derivatives featuring positive or negative charges. The insertion of the orthoester function in the NL structures allows the formation of pH‐sensitive liposomes. ONL‐based liposomes can be hydrolyzed to provide nontoxic products, including nucleoside derivatives and hexadecanol. To allow the release to be tunable at different hydrolysis rates, the charge of the polar head structure is modulated, and the head group can be released at a biologically relevant pH. Crucially, when ONLs are mixed with natural phosphocholine lipids (PC), the resultant liposome evolves toward the formation of a hexadecanol/PC lamellar system. Biological evaluation shows that stable nucleic acid lipid particles (SNALPs) formulated with ONLs and siRNAs can effectively enter into tumor cells and release their nucleic acid payload in response to an intracellular acidic environment. This results in a much higher antitumor activity than conventional SNALPs. The ability to use pH‐cleavable nucleolipids to control the stability of lipid‐based delivery systems represents a promising approach for the intracellular delivery of drug cargos.     

Amplicon Competition Enables End‐Point Quantitation of Nucleic Acids Following Isothermal Amplification

It is inherently difficult to quantitate nucleic acid analytes with most isothermal amplification assays. We developed loop‐mediated isothermal amplification (LAMP) reactions in which competition between defined numbers of “false” and “true” amplicons leads to order of magnitude quantitation by a single endpoint determination. These thresholded LAMP reactions were successfully used to directly and quantitatively estimate the numbers of nucleic acids in complex biospecimens, including directly from cells and in sewage, with the values obtained closely correlating with qPCR quantitations. Thresholded LAMP reactions are amenable to endpoint readout by cell phone, unlike other methods that require continuous monitoring, and should therefore prove extremely useful in developing one‐pot reactions for point‐of‐care diagnostics without needing sophisticated material or informatics infrastructure.     

Recent advances in nonviral vectors for gene delivery

Gene therapy has long been regarded a promising treatment for many diseases, whether acquired (such as AIDS or cancer) or inherited through a genetic disorder. A drug based on a nucleic acid, however, must be delivered to the interior of the target cell while surviving an array of biological defenses honed by evolution. Successful gene therapy is thus dependent on the development of an efficient delivery vector. Researchers have pursued two major vehicles for gene delivery: viral and nonviral (synthetic) vectors. Although viral vectors currently offer greater efficiency, nonviral vectors, which are typically based on cationic lipids or polymers, are preferred because of safety concerns with viral vectors. So far, nonviral vectors can readily transfect cells in culture, but efficient nanomedicines remain far removed from the clinic. Overcoming the obstacles associated with nonviral vectors to improve the delivery efficiency and therapeutic effect of nucleic acids is thus an active area of current research. The difficulties are manifold, including the strong interaction of cationic delivery vehicles with blood components, uptake by the reticuloendothelial system (RES), toxicity, and managing the targeting ability of the carriers with respect to the cells of interest. Modifying the surface with poly(ethylene glycol), that is, PEGylation, is the predominant method used to reduce the binding of plasma proteins to nonviral vectors and minimize clearance by the RES after intravenous administration. Nanoparticles that are not rapidly cleared from the circulation accumulate in the tumors because of the enhanced permeability and retention effect, and the targeting ligands attached to the distal end of the PEGylated components allow binding to the receptors on the target cell surface. Neutral and anionic liposomes have been also developed for systemic delivery of nucleic acids in experimental animal models. Other approaches include (i) designing and synthesizing novel cationic lipids and polymers, (ii) chemically coupling the nucleic acid to peptides, targeting ligands, polymers, or environmentally sensitive moieties, and (iii) utilizing inorganic nanoparticles in nucleic acid delivery. Recently, the different classes of nonviral vectors appear to be converging, and the ability to combine features of different classes of nonviral vectors in a single strategy has emerged. With the strengths of several approaches working in concert, more hurdles associated with efficient nucleic acid delivery might therefore be overcome. In this Account, we focus on these novel nonviral vectors, which are classified as multifunctional hybrid nucleic acid vectors, novel membrane/core nanoparticles for nucleic acid delivery, and ultrasound-responsive nucleic acid vectors. We highlight systemic delivery studies and consider the future prospects for nucleic acid delivery. A better understanding of the fate of the nanoparticles inside the cell and of the interactions between the parts of hybrid particles should lead to a delivery system suitable for clinical use. We also underscore the value of sustained release of a nucleic acid in this endeavor; making vectors targeted to cells with sustained release in vivo should provide an interesting research challenge.     

Electrosynthesized molecularly imprinted polypyrrole films for enantioselective recognition of l-aspartic acid

The electrosynthesis, overoxidation and characterization of l-aspartic acid (l-Asp) imprinted polypyrrole (PPy) films have been performed by using electrochemical quartz crystal microbalance (EQCM). Following the determination of the optimal electrosynthesis parameters for the formation of a smooth and uniform PPy/l-Asp films, the overoxidized polypyrrole (oPPy) matrix templated with either l- or d-aspartic acid (l-, d-Asp) was evaluated as a potential enantioselective recognition element. Under potentiodynamic conditions and in strongly acidic media a significantly higher sensitivity of the l-Asp acid imprinted overoxidized polypyrrole film (oPPy/l-Asp) for l-Asp than d-Asp was observed. The results suggest the feasibility of preparing molecularly imprinted films by electropolymerization for the enantioselective recognition of amino acids and the suitability of EQCM for both monitoring the selective recognition as well as to electrochemically modulate the binding process.     

Efficient Heterogeneous Dual Catalyst Systems for Alkane Metathesis

A fully heterogeneous and highly efficient dual catalyst system for alkane metathesis (AM) has been developed. The system is comprised of an alumina‐supported iridium pincer catalyst for alkane dehydrogenation/olefin hydrogenation and a second heterogeneous olefin metathesis catalyst. The iridium catalysts bear basic functional groups on the aromatic backbone of the pincer ligand and are strongly adsorbed on Lewis acid sites on alumina. The heterogeneous systems exhibit higher lifetimes and productivities relative to the corresponding homogeneous systems as catalyst/catalyst interactions and bimolecular decomposition reactions are inhibited. Additionally, using a “two‐pot” device, the supported Ir catalysts and metathesis catalysts can be physically separated and run at different temperatures. This system with isolated catalysts shows very high turnover numbers and is selective for the formation of high molecular weight alkanes.     

Use of sublimation for template removal from menthol templated mesoporous organosilica prepared via sol-gel process

Menthol templated vinyl-functionalized organosilica materials were prepared by acid catalyzed hydrolytic sol-gel reactions of tetraethyl orthosilicate and vinyltriethoxysilane. The menthol template was removed by sublimation under vacuum, leading to the formation of a mesoporous organosilica material. This work presents a solventless, low temperature method of extraction of template from mesoporous materials. For the first time, sublimation was demonstrated to be an effective means of template removal to generate a mesoporous material. A comparison of sublimation and solvent extraction as template removal methods is also presented.     

CRISPR Approaches for the Diagnosis of Human Diseases

CRISPR/Cas is a prokaryotic self-defense system, widely known for its use as a gene-editing tool. Because of their high specificity to detect DNA and RNA sequences, different CRISPR systems have been adapted for nucleic acid detection. CRISPR detection technologies differ highly among them, since they are based on four of the six major subtypes of CRISPR systems. In just 5 years, the CRISPR diagnostic field has rapidly expanded, growing from a set of specific molecular biology discoveries to multiple FDA-authorized COVID-19 tests and the establishment of several companies. CRISPR-based detection methods are coupled with pre-existing preamplification and readout technologies, achieving sensitivity and reproducibility comparable to the current gold standard nucleic acid detection methods. Moreover, they are very versatile, can be easily implemented to detect emerging pathogens and new clinically relevant mutations, and offer multiplexing capability. The advantages of the CRISPR-based diagnostic approaches are a short sample-to-answer time and no requirement of laboratory settings; they are also much more affordable than current nucleic acid detection procedures. In this review, we summarize the applications and development trends of the CRISPR/Cas13 system in the identification of particular pathogens and mutations and discuss the challenges and future prospects of CRISPR-based diagnostic platforms in biomedicine.     

PNA‐Encoded Synthesis (PES) of a 10 000‐Member Hetero‐Glycoconjugate Library and Microarray Analysis of Diverse Lectins

Identification of selective and synthetically tractable ligands to glycan‐binding proteins is important in glycoscience. Carbohydrate arrays have had a tremendous impact on profiling glycan‐binding proteins and as analytical tools. We report a highly miniaturized synthetic format to access nucleic‐acid‐encoded hetero‐glycoconjugate libraries with an unprecedented diversity in the combinations of glycans, linkers, and capping groups. Novel information about plant and bacterial lectin specificity was obtained by microarray profiling, and we show that a ligand identified on the array can be converted to a high‐affinity soluble ligand by straightforward chemistry.     

The chemistry of lipid peroxidation metabolites: Crosslinking reactions of malondialdehyde

Malondialdehyde reacts readily with amino acids to form adducts containing vinylogous amidine linkages. Crosslinking reactions between nucleic acid bases, and amino acids induced by malondialdehyde also have been investigated. The physical data obtained for the adducts provide structural information on the possible mode of crosslinking of proteins and nucleic acids induced by this lipid metabolite.     

绿色硝化剂N_2O_5的制备方法及其应用进展

对五氧化二氮(N2O5)的制备、放大生产以及N2O5硝化体系的应用进行了综述。其中N2O5/硝酸体系的硝化能力强,但硝化选择性差,故常用于钝化底物的硝化。N2O5/有机溶剂体系硝化温和,选择性好,主要用于酸敏性和水敏性及含多官能团物质的选择性硝化。N2O5/固体载体体系不仅具有N2O5/有机溶剂体系的硝化特点,而且硝化反应在载体表面进行,避免了大量使用有毒的有机溶剂,操作简单,产物易分离。附参考文献30篇。     

Selective Palladium‐Catalyzed Suzuki–Miyaura Reactions of Polyhalogenated Heteroarenes

The palladium‐catalyzed Suzuki–Miyaura reaction of multiply halogenated, electron‐rich and electron‐deficient heteroarenes is one of the most reliable and environmentally friendly tools for installing a wide range of non‐functionalized and functionalized carbon substituents onto heteroaromatic systems with exquisite chemo‐ and site‐selectivity. For substrates with different halogen groups the chemoselectivity of the Suzuki–Miyaura reactions has been found to be dependent on the reactivity difference between the halogens. However, the hardest achievement of selectivity in Suzuki–Miyaura monocouplings involving polyhalogenated heteroarenes with identical halogen atoms has been shown to be dominated by steric and electronic effects and the presence of directing groups at positions neighbouring the reaction sites. Moreover, in the case of symmetrically substituted dihaloheteroarenes with identical halogen atoms, highly selective monocoupling reactions have often been achieved only after a careful optimization of reaction parameters including the catalyst precursor, base, solvent, and the molar ratio between electrophile and organoboron reagent. This critical review with 341 references covers developments on the chemo‐ and site‐selective Suzuki–Miyaura monocoupling reactions of polyhalogenated heteroarenes with different or identical halogen atoms. It also includes the synthesis of polysubstituted heteroarenes, not easily accessible by other means, via consecutive monocoupling reactions and/or a more synthetically valuable approach involving one‐pot polycoupling reactions.