DNA as a versatile chemical component for catalysis, encoding, and stereocontrol

Merging DNA Repair with Bioorthogonal Conjugation Enables Accessible and Versatile Asymmetric DNA Catalysis

Optimizing catalysts through high-throughput screening for asymmetric catalysis is challenging due to the difficulty associated with assembling a library of catalyst analogues in a timely fashion. Here, we repurpose DNA excision repair and integrate it with bioorthogonal conjugation to construct a diverse array of DNA hybrid catalysts for highly accessible and high-throughput asymmetric DNA catalysis, enabling a dramatically expedited catalyst optimization process, superior reactivity and selectivity, as well as the first atroposelective DNA catalysis. The bioorthogonality of this conjugation strategy ensures exceptional tolerance toward diverse functional groups, thereby facilitating the facile construction of 44 DNA hybrid catalysts bearing various unprotected functional groups. This unique feature holds the potential to enable catalytic modalities in asymmetric DNA catalysis that were previously deemed unattainable.

The Programmable Catalytic Core of 8-17 DNAzymes

8-17 DNAzymes (8-17, 17E, Mg5, and 17EV1) are in vitro-selected catalytic DNA molecules that are capable of cleaving complementary RNAs. The conserved residues in their similar catalytic cores, together with the metal ions, were suggested to contribute to the catalytic reaction. Based on the contribution of the less conserved residues in the bulge loop residues (W12, A15, A15.0) and the internal stem, new catalytic cores of 8-17 DNAzymes were programmed. The internal stem CTC-GAG seems to be more favorable for the DNAzymes than CCG-GGC, while an extra W12.0 led to a significant loss of activity of DNAzymes, which is contrary to the positive effect of A15.0, by which a new active DNAzyme 17EM was derived. It conducts a faster reaction than 17E. It is most active in the presence of Pb2+, with the metal ion preference of Pb2+ >> Zn2+ > Mn2+ > Ca2+ ≈ Mg2+. In the Pb2+ and Zn2+-mediated reactions of 17EM and 17E, the same Na+- and pH dependence were also observed as what was observed for 17E and other 8-17 DNAzymes. Therefore, 17EM is another member of the 8-17 DNAzymes, and it could be applied as a potential biosensor for RNA and metal ions.

Hidden imaging in thin polymer films with embedded fluorescent peptide nanodots

Fluorescent (FL) encrypting nanostructures, such as quantum dots, carbon dots, organic dyes, lanthanide nanocrystals, DNA, and more, are effective tools for advanced applications in high-resolution hidden imaging. These applications include tracking, labeling, security printing, and anti-counterfeiting drug technology. In this work, what we believe to be a new FL encoding nanostructures has been proposed, which consists of recently discovered nanometer-scale peptide dots. When refolded into a beta-sheet peptide secondary structure, these biocompatible nanoparticles exhibit a strong and tunable FL effect. The biophotonic FL covers the entire visible spectrum, making the peptide dots next-generation nanoscale light sources with a quantum yield of 30%. Our studies demonstrate that these FL bio-nanodots also exhibit a significant irreversible photo-bleaching effect associated with the light-induced destruction of noncovalent intermolecular hydrogen bonds of the peptide dots' highly stable beta-sheet secondary structure. We present what we believe is a new approach for achieving high-resolution long-term optical memory by tailoring various hidden images in the developed thin polyvinyl alcohol (PVA) polymer films with an embedded dense array of FL peptide nanodots. The technology enables recording photo-bleached patterns, barcodes, and high-resolution images.

DNAzyme-based faithful probing and pulldown to identify candidate biomarkers of low abundance

Biomarker discovery is essential for the understanding, diagnosis, targeted therapy and prognosis assessment of malignant diseases. However, it remains a huge challenge due to the lack of sensitive methods to identify disease-specific rare molecules. Here we present MORAC, molecular recognition based on affinity and catalysis, which enables the effective identification of candidate biomarkers with low abundance. MORAC relies on a class of DNAzymes, each cleaving a sole RNA linkage embedded in their DNA chain upon specifically sensing a complex system with no prior knowledge of the system's molecular content. We show that signal amplification from catalysis ensures the DNAzymes high sensitivity (for target probing); meanwhile, a simple RNA-to-DNA mutation can shut down their RNA cleavage ability and turn them into a pure affinity tool (for target pulldown). Using MORAC, we identify previously unknown, low-abundance candidate biomarkers with clear clinical value, including apolipoprotein L6 in breast cancer and seryl-tRNA synthetase 1 in polyps preceding colon cancer.

Construction of a highly efficient DNA nanotube sensor with peroxide-like activity

The G-quadruplex/heme complexes are special DNA-based artificial metalloenzymes with peroxidase-like activity and are widely used in biosensing and biocatalysis. However, their peroxidase-like activity is not satisfactory. Due to the high programmability and good stability of DNA, DNA as a scaffold material is promising for enhancing the activity of artificial metalloenzymes. In this work, an effective DNA nanotube-based peroxidase was constructed using a self-assembly strategy. To improve the activity of G-quadruplex/heme complexes, a new method for the construction of G-quadruplex/heme complex arrays was proposed in a simple and inexpensive way. By designing the toes of DNA nanotubes as G-quadruplexes, G-quadruplex arrays could be formed on pure DNA nanotubes, and then the G-quadruplex arrays bind to heme to form a nanotube-supported DNAzyme termed as DNTzyme. Agarose gel electrophoresis, circular dichroism, and fluorescence microscopy were used to characterize DNTzyme. What is more, because the loading of DNAzyme on DNA nanotubes can increase their biological stability, a hydrogen peroxide detection sensor was constructed using the enhanced enzymatic activity and excellent stability of DNTzyme. The sensor could accurately and efficiently detect peroxide and show enhanced fluorescence with a detection limit of 49 nM for H2O2 and 1.4 μM for TBHP, and a color development time of about 5 min. This sensor is expected to have applications in bio-detection, biocatalysis, and drug delivery.

Rapid identification of bacteria by the pattern of redox reactions rate using 2',7'-dichlorodihydrofluorescein diacetate

Bacterial infection is a life-threatening situation, and its rapid diagnosis is essential for treatment. Apart from medical applications, rapid identification of bacteria is vital in the food industry or the public health system. There are various bacterial identification techniques, including molecular-based methods, immunological approaches, and biosensor-based procedures. The most commonly used methods are culture-based methods, which are time-consuming. The objective of this study is to find a fingerprint of bacteria to identify them. Three strains of bacteria were selected, and seven different concentrations of each bacterium were prepared. The bacteria were then treated with two different molar concentrations of the fluorescent fluorophore, dichlorodihydrofluorescein diacetate for 30 minutes. Then, using the fluorescence mode of a multimode reader, the fluorescence emission of each bacterium is scanned twice during 60 minutes. Plotting the difference between two scans versus the bacteria concentration results in a unique fluorescence pattern for each bacterium. Observation of the redox state of bacteria, during 90 minutes, results in a fluorescence pattern that is clearly a fingerprint of different bacteria. This pattern is independent of fluorophore concentration. Mean Squares Errors (MSE) between the fluorescence patterns of similar bacteria is less than that of different bacteria, which shows the method can properly identify the bacteria. In this study, a new label-free method is developed to detect and identify different species of bacteria by measuring the redox activity and using the fluorescence fluorophore, dichlorodihydrofluorescein diacetate. This robust and low-cost method can properly identify the bacteria, uses only one excitation and emission wavelength, and can be simply implemented with current multimode plate readers.

An RNA-Cleaving DNAzyme That Requires an Organic Solvent to Function

Engineering functional nucleic acids that are active under unusual conditions will not only reveal their hidden abilities but also lay the groundwork for pursuing them for unique applications. Although many DNAzymes have been derived to catalyze diverse chemical reactions in aqueous solutions, no prior study has been set up to purposely derive DNAzymes that require an organic solvent to function. Herein, we utilized in vitro selection to isolate RNA-cleaving DNAzymes from a random-sequence DNA pool that were "compelled" to accept 35 % dimethyl sulfoxide (DMSO) as a cosolvent, via counter selection in a purely aqueous solution followed by positive selection in the same solution containing 35 % DMSO. This experiment led to the discovery of a new DNAzyme that requires 35 % DMSO for its catalytic activity and exhibits drastically reduced activity without DMSO. This DNAzyme also requires divalent metal ions for catalysis, and its activity is enhanced by monovalent ions. A minimized, more efficient DNAzyme was also derived. This work demonstrates that highly functional, organic solvent-dependent DNAzymes can be isolated from random-sequence DNA libraries via forced in vitro selection, thus expanding the capability and potential utility of catalytic DNA.

Chiral Materials: Progress, Applications, and Prospects

Chirality is a universal phenomenon in molecular and biological systems, denoting an asymmetric configurational property where an object cannot be superimposed onto its mirror image by any kind of translation or rotation, which is ubiquitous on the scale from neutrinos to spiral galaxies. Chirality plays a very important role in the life system. Many biological molecules in the life body show chirality, such as the "codebook" of the earth's biological diversity-DNA, nucleic acid, etc. Intriguingly, living organisms hierarchically consist of homochiral building blocks, for example, l-amino acids and d-sugars with unknown reason. When molecules with chirality interact with these chiral factors, only one conformation favors the positive development of life, that is, the chiral host environment can only selectively interact with chiral molecules of one of the conformations. The differences in chiral interactions are often manifested by chiral recognition, mutual matching, and interactions with chiral molecules, which means that the stereoselectivity of chiral molecules can produce changes in pharmacodynamics and pathology. Here, the latest investigations are summarized including the construction and applications of chiral materials based on natural small molecules as chiral source, natural biomacromolecules as chiral sources, and the material synthesized by design as a chiral source.

Microcavity- and Microlaser-Based Optical Barcoding: A Review of Encoding Techniques and Applications

Optical microbarcodes have recently received a great deal of interest because of their suitability for a wide range of applications, such as multiplexed assays, cell tagging and tracking, anticounterfeiting, and product labeling. Spectral barcodes are especially promising because they are robust and have a simple readout. In addition, microcavity- and microlaser-based barcodes have very narrow spectra and therefore have the potential to generate millions of unique barcodes. This review begins with a discussion of the different types of barcodes and then focuses specifically on microcavity-based barcodes. While almost any kind of optical microcavity can be used for barcoding, currently whispering-gallery microcavities (in the form of spheres and disks), nanowire lasers, Fabry-Pérot lasers, random lasers, and distributed feedback lasers are the most frequently employed for this purpose. In microcavity-based barcodes, the information is encoded in various ways in the properties of the emitted light, most frequently in the spectrum. The barcode is dependent on the properties of the microcavity, such as the size, shape, and the gain materials. Various applications of these barcodes, including cell tracking, anticounterfeiting, and product labeling are described. Finally, the future prospects for microcavity- and microlaser-based barcodes are discussed.

Mutual leveraging of proximity effects and click chemistry in chemical biology

Nature has the remarkable ability to realize reactions under physiological conditions that normally would require high temperature and other forcing conditions. In doing so, often proximity effects such as simultaneous binding of two reactants in the same pocket and/or strategic positioning of catalytic functional groups are used as ways to achieve otherwise kinetically challenging reactions. Though true biomimicry is challenging, there have been many beautiful examples of how to leverage proximity effects in realizing reactions that otherwise would not readily happen under near-physiological conditions. Along this line, click chemistry is often used to endow proximity effects, and proximity effects are also used to further leverage the facile and bioorthogonal nature of click chemistry. This review brings otherwise seemingly unrelated topics in chemical biology and drug discovery under one unifying theme of mutual leveraging of proximity effects and click chemistry and aims to critically analyze the biomimicry use of such leveraging effects as powerful approaches in chemical biology and drug discovery. We hope that this review demonstrates the power of employing mutual leveraging proximity effects and click chemistry and inspires the development of new strategies that will address unmet needs in chemistry and biology.

Template-Directed Incorporation of Functional Molecules into DNA

We report a versatile method for the incorporation of functional molecules into oligonucleotides carrying reactive groups by using a template-directed postsynthetic approach in the solution phase. For this purpose, we prepared oligonucleotides carrying an amino group on the backbone by using an acylic threoninol scaffold. The resulting oligonucleotides could be used to introduce almost any molecule carrying aldehyde, which can be, among other things, a metal-binding ligand or a fluorophore. In our study, we incorporated aldehyde-bearing phenanthroline, a metal-binding ligand, into oligonucleotides by template-directed reversible conjugation. We observed that the use of an abasic sugar site instead of a natural nucleobase in the template strand increased the yield of conjugation and induced selective incorporation of the phenanthroline. This method could lead progress in the development of probes for the recognition of abasic regions in duplex DNA. Moreover, template-directed formation of metal ligand-oligonucleotide conjugates might have potential applications in hybrid biocatalysis for enantioselective transformations.

Recent advances in PCR-free nucleic acid detection for SARS-COV-2

As the outbreak of Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory disease coronavirus 2 (SARS-COV-2), fast, accurate, and economic detection of viral infection has become crucial for stopping the spread. Polymerase chain reaction (PCR) of viral nucleic acids has been the gold standard method for SARS-COV-2 detection, which, however, generally requires sophisticated facilities and laboratory space, and is time consuming. This review presents recent advances in PCR-free nucleic acid detection methods for SARS-CoV-2, including emerging methods of isothermal amplification, nucleic acid enzymes, electrochemistry and CRISPR.

Non-binary Encoded Nucleic Acid Barcodes Directly Readable by a Nanopore

A large collection of unique molecular barcodes is useful in the simultaneous sensing or screening of molecular analytes. Though the sequence of DNA has been widely applied to encode for molecular barcodes, decoding of these barcodes is normally assisted by sequencing. We here demonstrate a barcode system based solely on self-assembly of synthetic nucleic acids and direct nanopore decoding. Each molecular barcode is composed of "n" distinct information nodes in a non-binary manner and can be sequentially scanned and decoded by a Mycobacterium smegmatis porin A (MspA) nanopore. Nanopore events containing step-shaped features were consistently reported. 14 unique information nodes were developed which in principle could encode for 14ⁿ unique molecular barcodes in a barcode containing "n" information nodes. These barcode probes were adapted to detect different antibody proteins or cancer-related microRNAs, suggesting their immediate application in a wide variety of sensing applications.

Novel Biorecognition Elements against Pathogens in the Design of State-of-the-Art Diagnostics

Infectious agents, especially bacteria and viruses, account for a vast number of hospitalisations and mortality worldwide. Providing effective and timely diagnostics for the multiplicity of infectious diseases is challenging. Conventional diagnostic solutions, although technologically advanced, are highly complex and often inaccessible in resource-limited settings. An alternative strategy involves convenient rapid diagnostics which can be easily administered at the point-of-care (POC) and at low cost without sacrificing reliability. Biosensors and other rapid POC diagnostic tools which require biorecognition elements to precisely identify the causative pathogen are being developed. The effectiveness of these devices is highly dependent on their biorecognition capabilities. Naturally occurring biorecognition elements include antibodies, bacteriophages and enzymes. Recently, modified molecules such as DNAzymes, peptide nucleic acids and molecules which suffer a selective screening like aptamers and peptides are gaining interest for their biorecognition capabilities and other advantages over purely natural ones, such as robustness and lower production costs. Antimicrobials with a broad-spectrum activity against pathogens, such as antibiotics, are also used in dual diagnostic and therapeutic strategies. Other successful pathogen identification strategies use chemical ligands, molecularly imprinted polymers and Clustered Regularly Interspaced Short Palindromic Repeats-associated nuclease. Herein, the latest developments regarding biorecognition elements and strategies to use them in the design of new biosensors for pathogens detection are reviewed.

Rapid and Specific Imaging of Extracellular Signaling Molecule Adenosine Triphosphate with a Self-Phosphorylating DNAzyme

Adenosine 5'-triphosphate (ATP) is a central extracellular signaling agent involved in various physiological and pathological processes. However, precise measurements of the temporal and spatial components of ATP dynamics are lacking due primarily to the limitations of available methods for ATP detection. Here, we report on the first effort to design a self-phosphorylating DNAzyme (SPDz) sensor for fluorescence imaging of ATP. In response to ATP, SPDz sensors exhibit subsecond response kinetics, extremely high specificity, and micromolar affinities. In particular, we demonstrate cell-surface-anchored SPDz sensors for fluorescence imaging of both stress-induced endogenous ATP release in astrocytes and mechanical stimulation-evoked ATP release at the single-cell level. We also validated their utility for visualizing the rapid dynamic properties of ATP signaling upon electrical stimulation in astrocytes. Thus, SPDz sensors are robust tools for monitoring ATP signaling underlying diverse cellular processes.

Functional Nucleic Acids Under Unusual Conditions

Functional nucleic acids (FNAs), including naturally occurring ribozymes and riboswitches as well as artificially created DNAzymes and aptamers, have been popular molecular toolboxes for diverse applications. Given the high chemical stability of nucleic acids and their ability to fold into diverse sequence-dependent structures, FNAs are suggested to be highly functional under unusual reaction conditions. This review will examine the progress of research on FNAs under conditions of low pH, high temperature, freezing conditions, and the inclusion of organic solvents and denaturants that are known to disrupt nucleic acid structures. The FNA species to be discussed include ribozymes, riboswitches, G-quadruplex-based peroxidase mimicking DNAzymes, RNA-cleaving DNAzymes, and aptamers. Research within this space has not only revealed the hidden talents of FNAs but has also laid important groundwork for pursuing these intriguing functional macromolecules for unique applications.

Characterization and Optimization of a Deoxyribozyme with a Short Left Binding Arm

Deoxyribozymes capable of catalyzing sequence-specific RNA cleavage have broad applications in biotechnology. In vitro selected RNA-cleaving deoxyribozymes normally contain two substrate-binding arms and a central catalytic core region. Here, we describe the systematic characterization and optimization of an RNA-cleaving deoxyribozyme with an unusually short left binding arm, and its special sequence requirement for its optimal catalytic activity.

A highly sensitive and adjustable colorimetric assay of hydrogen sulfide by signal amplification based on G-quadruplex-Cu2+ peroxidase mimetics

This work reports the first example of a colorimetric H2S sensor constructed through G-quadruplex-Cu2+ (G4-Cu2+) peroxidase mimetics employing Cu2+ ions and G-rich DNA with signal amplification. In the hydrogen peroxide (H2O2)-mediated oxidation of 3,3',5,5'-tetramethylbenzidine (TMB), the catalytic capacity of Cu2+ can be greatly improved in the presence of 22AG DNA, where 22AG DNA acts as a signal amplifier. However, G4-Cu2+ peroxidase mimetics lose their catalytic abilities after reacting with H2S. This is employed to develop a colorimetric assay of H2S without complex synthesis and instrumentation, with a linear range from 0.01 μM to 150 μM and a detection limit of 7.5 nM. The sensitivity of the sensor can also be adjusted by changing the concentration of Cu2+. Moreover, the developed sensor is successfully applied for the quantitative determination of H2S in human serum samples.

Post-synthetic transamination at position N4 of cytosine in oligonucleotides assembled with routinely used phosphoramidites

The commercially available and cheap nucleotide phosphoramidites are routinely used for the oligonucleotide (ODN) assembly. T, isobutyryl-dG (iBudG), benzoyl-dA (BzdA), acetyl-dC (AcdC) and benzoyl-dC (BzdC) derivatives are sufficient to produce orthogonally protected ODNs. Clean and efficient (ca. 30%-70% yield) post-synthetic amination of an ODN assembled with such phosphoramidites was selectively achieved at the N4 position of a singly introduced BzdC. Such a method represents a novel and cheap strategy for the user-friendly post-modification of oligonucleotides at the internal position.

Smart Bilayer Polyacrylamide/DNA Hybrid Hydrogel Film Actuators Exhibiting Programmable Responsive and Reversible Macroscopic Shape Deformations

As a crucial instinct for the survival of organisms, adaptive smart deformation has been well shown via profusely astounding examples within biological morphogenesis in nature, which inspired the construction of biomimetic shape-morphing materials with controlled actuating behaviors. Herein, the construction of nature-inspired bilayer hydrogel film actuators, composed of a polyacrylamide hydrogel passive layer and a polyacrylamide-DNA hybrid hydrogel active layer, which exhibited programmable stimuli-responsive and reversible macroscopic shape deformations directed by the sequence of DNA crosslinking units in the active layer, is reported. As a proof-of-concept, the introduction of DNA i-motif based crosslinking structures into the active layer, which can undergo pH-stimulated formation and dissociation of crosslinking between polymers and therefore change the crosslinking density of the active layer, lead to the redistribution of the internal stresses within the bilayer structure, and result in the pH-stimulated shape deformations. By programming the sequence of DNA units in the active layer, a Ag⁺ /Cysteamine-stimulated bilayer DNA hybrid hydrogel film actuator is further constructed and exhibits excellent actuation behaviors. Thanks to the micrometer-scale thickness of the films, these actuators exhibit a high degree of macroscopic and reversible shape deformations at high speed, which may find use in future smart biosensing and biomedical applications.

Modular quadruplex-duplex hybrids as biomolecular scaffolds for asymmetric Michael addition reactions

Asymmetric synthesis based on DNA scaffolds has been actively exploited because of the advantages of DNA such as diverse tertiary structures, chemical stability, and easy handling. Since duplex DNA-based hybrid catalysts have demonstrated this remarkable capability, efforts have been made to investigate new biomolecular scaffolds. Herein, we report modular quadruplex-duplex (QD) hybrid DNA catalysts containing bipyridine ligands and hydrogen donor moieties. The conformation, thermal stability, and metal-binding ability of modified QD hybrid DNA were characterized using spectroscopy. The QD hybrid-based DNA catalysts were successfully applied to asymmetric Michael addition reactions (86% conversion and 76% ee). This study describes a new type of DNA hybrid catalyst produced by the construction of a cooperative active site with a Lewis acid and a H-bond donor.

Covalently Functionalized DNA Duplexes and Quadruplexes as Hybrid Catalysts in an Enantioselective Friedel-Crafts Reaction

The precise site-specific positioning of metal-ligand complexes on various DNA structures through covalent linkages has gained importance in the development of hybrid catalysts for aqueous-phase homogeneous catalysis. Covalently modified double-stranded and G-quadruplex DNA-based hybrid catalysts have been investigated separately. To understand the role of different DNA secondary structures in enantioselective Friedel-Crafts alkylation, a well-known G-quadruplex-forming sequence was covalently modified at different positions. The catalytic performance of this modified DNA strand was studied in the presence and absence of a complementary DNA sequence, resulting in the formation of two different secondary structures, namely duplex and G-quadruplex. Indeed, the secondary structures had a tremendous effect on both the yield and stereoselectivity of the catalyzed reaction. In addition, the position of the modification, the topology of the DNA, the nature of the ligand, and the length of the linker between ligand and DNA were found to modulate the catalytic performance of the hybrid catalysts. Using the optimal linker length, the quadruplexes formed the (-)-enantiomer with up to 65% ee, while the duplex yielded the (+)-enantiomer with up to 62% ee. This study unveils a new and simple way to control the stereochemical outcome of a Friedel-Crafts reaction.

Context-Sensitive Cleavage of Folded DNAs by Loop-Targeting bPNAs

Herein, we demonstrate context-dependent molecular recognition of DNA by synthetic bPNA iron and copper complexes, using oxidative backbone cleavage as a chemical readout for binding. Oligoethylenimine bPNAs displaying iron·EDTA or copper·phenanthroline sites were found to be efficient chemical nucleases for designed and native structured DNAs with T-rich single-stranded domains. Cleavage reactivity depends strongly on structural context, as strikingly demonstrated with DNA substrates of the form (GGGTTA)_n. This repeat sequence from the human telomere is known to switch between parallel and antiparallel G-quadruplex (G4) topologies with a change from potassium to sodium buffer: notably, bPNA-copper complexes efficiently cleave long repeat sequences into ∼22-nucleotide portions in sodium, but not potassium, buffer. We hypothesize preferential cleavage of the antiparallel topology (Na⁺) over the parallel topology (K⁺) due to the greater accessibility of the TTA loop to bPNA in the antiparallel (Na⁺) form. Similar ion-sensitive telomere shortening upon treatment with bPNA nucleases can be observed in both isolated and intracellular DNA from PC3 cells by quantitative polymerase chain reaction. Live cell treatment was accompanied by accelerated cellular senescence, as expected for significant telomere shortening. Taken together, the loop-targeting approach of bPNA chemical nucleases complements prior intercalation strategies targeting duplex and quadruplex DNA. Structurally sensitive loop targeting enables discrimination between similar target sequences, thus expanding bPNA targeting beyond simple oligo-T sequences. In addition, bPNA nucleases are cell membrane permeable and therefore may be used to target native intracellular substrates. In addition, these data indicate that bPNA scaffolds can be a platform for new synthetic binders to particular nucleic acid structural motifs.

Synthesis of a Mechanically Planar Chiral Rotaxane Ligand for Enantioselective Catalysis

Rotaxanes are interlocked molecules in which a molecular ring is trapped on a dumbbell-shaped axle because of its inability to escape over the bulky end groups, resulting in a so-called mechanical bond. Interlocked molecules have mainly been studied as components of molecular machines, but the crowded, flexible environment created by threading one molecule through another has also been explored in catalysis and sensing. However, so far, the applications of one of the most intriguing properties of interlocked molecules, their ability to display stereogenic units that do not rely on the stereochemistry of their covalent subunits, termed "mechanical chirality," have yet to be properly explored, and prototypical demonstration of the applications of mechanically chiral rotaxanes remain scarce. Here, we describe a mechanically planar chiral rotaxane-based Au complex that mediates a cyclopropanation reaction with stereoselectivities that are comparable with the best conventional covalent catalyst reported for this reaction.

Live-Cell Sensing of Telomerase Activity by Using Hybridization-Sensitive Fluorescent Oligonucleotide Probes

Live-cell sensing of telomerase activity with simple and efficient strategies remains a challenging target. In this work, a strategy for telomerase sensing by using hybridization-sensitive fluorescent oligonucleotide probes is reported. In the presence of telomerase and dNTPs, the designed supporting strand was extended and generated the hairpin structure that catalyzed the next telomerase extending reaction. The special extension mechanism increased the local concentration of another supporting strand and telomerase, which resulted in enhanced telomerase activity. The hybridization-sensitive oligonucleotide probes bound to the hairpin catalyst and generated turn-on fluorescence. This method realized the sensing of telomerase activity in HeLa cell extract with a detection limit below 1.6×10^-6  IU μL^-1 . The real-time in situ observation of telomerase extension was achieved in living HeLa cells. This strategy has been applied to monitor the efficiency of telomerase-targeting anticancer drugs in situ.

Capture and selective release of multiple types of circulating tumor cells using smart DNAzyme probes

The effective capture, release and reanalysis of circulating tumor cells (CTCs) are of great significance to acquire tumor information and promote the progress of tumor therapy. Particularly, the selective release of multiple types of CTCs is critical to further study; however, it is still a great challenge. To meet this challenge, we designed a smart DNAzyme probe-based platform. By combining multiple targeting aptamers and multiple metal ion responsive DNAzymes, efficient capture and selective release of multiple types CTCs were realized. Sgc8c aptamer integrated Cu2+-dependent DNAzyme and TD05 aptamer integrated Mg2+-dependent DNAzyme can capture CCRF-CEM cells and Ramos cells respectively on the substrate. With the addition of Cu2+ or Mg2+, CCRF-CEM cells or Ramos cells will be released from the substrate with specific selectivity. Furthermore, our platform has been successfully demonstrated in the whole blood sample. Therefore, our capture/release platform will benefit research on the molecular analysis of CTCs after release and has great potential for cancer diagnosis and individualized treatment.

A superior G-quadruplex DNAzyme through functionalized modification of the hemin cofactor

Chemical modifications of the hemin structure through introducing new functionalities are proposed to enhance the catalytic efficiency of the hemin/G-quadruplex DNAzyme.

Enhanced reactivity of the pyrimidine peroxyl radical towards the C–H bond in duplex DNA – a theoretical study

The peroxyl radical exhibits a much stronger reactivity towards C1′–H1′ in duplex DNA with respect to single-stranded DNA.

Enzymatic Synthesis of Base-Functionalized Nucleic Acids for Sensing, Cross-linking, and Modulation of Protein-DNA Binding and Transcription

Protein-DNA interactions are important in replication, transcription, repair, as well as epigenetic modifications of DNA, which involve methylation and demethylation of DNA resulting in regulation of gene expression. Understanding of these processes and chemical tools for studying and perhaps even modulating them could be of great relevance and importance not only in chemical biology but also in real diagnostics and treatment of diseases. In the past decade, we have been working on development of synthesis of base-modified 2'-deoxyribo- or ribonucleoside triphosphates (dNTPs or NTPs) and their use in enzymatic synthesis of modified nucleic acids using DNA or RNA polymerases. These synthetic and enzymatic methods are briefly summarized with focus on recent development and outlining of scope, limitations, and further challenges. The main focus of this Account is on applications of base-modified nucleic acids in sensing of protein-DNA interactions, in covalent cross-linking to DNA-binding proteins ,and in modulation of protein-DNA binding and transcription. Several environment-sensitive fluorescent nucleotides were incorporated to DNA probes which responded to protein binding by light-up, changing of color, or lifetime of fluorescence. Using a cyclodextrin-peptide transporter, fluorescent nucleotides can be transported through the cell membrane and incorporated to genomic DNA. Several dNTPs bearing reactive groups (i.e., vinylsulfonamide or chloroacetamide) were used for polymerase synthesis of DNA reactive probes which cross-link to Cys, His, or Lys in peptides or proteins. An attractive challenge is to use DNA modifications and bioorthogonal reactions in the major groove of DNA for modulation and switching of protein-DNA interactions. We have systematically explored the influence of major-groove modifications on recognition and cleavage of DNA by restriction endonucleases and constructed simple chemical switches of DNA cleavage. Systematic study of the influence of major-groove modifications on transcription with bacterial RNA polymerases revealed not only that some modified bases are tolerated, but also that the presence of 5-hydroxymethyluracil or -cytosine can even enhance the transcription (350 or 250% compared to native DNA). Based on these results, we have constructed the first chemical switch of transcription based on photocaging of hydroxymethylpyrimidines in DNA by 2-nitrobenzyl protection (transcription off), photochemical deprotection of the DNA (transcription on), and enzymatic phosphorylation (only for 5-hydroxymethyluracil, transcription off). Although it has been so far demonstrated only in vitro, it is the proof-of-principle first step toward chemical epigenetics.

Arylation Chemistry for Bioconjugation

Bioconjugation chemistry has been used to prepare modified biomolecules with functions beyond what nature intended. Central to these techniques is the development of highly efficient and selective bioconjugation reactions that operate under mild, biomolecule compatible conditions. Methods that form a nucleophile-sp2 carbon bond show promise for creating bioconjugates with new modifications, sometimes resulting in molecules with unparalleled functions. Here we outline and review sulfur, nitrogen, selenium, oxygen, and carbon arylative bioconjugation strategies and their applications to modify peptides, proteins, sugars, and nucleic acids.

G-quadruplexes as versatile scaffolds for catalysis

This review summarizes the beginning, progress, and prospects of non-canonical DNA-based hybrid catalysts focusing on G-quadruplexes as versatile scaffolds for catalysis.

Peroxidase mimicking DNAzymes degrade graphene oxide

DNAzymes made of supramolecular guanine-rich G-quadruplexes and hemin are attracting a lot of interest due to their peroxidase activity mimicking the natural enzyme horseradish peroxidase (HRP). Herein, we demonstrate that DNAzyme consisting of a PS2.M-hemin complex can be an alternative to natural HRP for the oxidation and degradation of graphene oxide (GO). The degradation of GO sheets was carried out by incubating the PS2.M-hemin complex in the presence of hydrogen peroxide for 30 days. The degradation of GO has been confirmed using transmission electron microscopy and 2d Raman mapping. The current study suggests that the peroxidase activity of DNAzymes is similar to HRP and DNAzymes are able to degrade carbon-based nanomaterials.

Fluorescence Spectroscopic Insight into the Supramolecular Interactions in DNA-Based Enantioselective Sulfoxidation

Interactions of copper(II)-bipyridine cofactors and thioanisole substrate with human telomeric G-quadruplex DNA were studied by UV/Vis absorption, circular dichroism, and fluorescence quenching titration. Three copper(II)-bipyridine complexes are equivalently anchored to the G-quadruplex scaffold at all five fluorescently labeled sites. Thioanisole interacts with the DNA architecture at both the second loop and 3' terminus in the absence or presence of copper(II)-bipyridine complexes. These nonspecificities in the weak interactions of Cu^II complexes and thioanisole with G-quadruplex might explain why DNA only affords a modest enantioselectivity in the oxidation of thioanisole. These findings provide insights toward the construction of highly enantioselective DNA-based catalysts.

Facile immobilization of DNA using an enzymatic his-tag mimic

Methods for immobilization of DNA on solid supports are in high demand. Herein, we present a generally applicable enzymatic method for the immobilization of DNA without any prior chemical derivatization. This strategy relies on the homopolymerization of the modified triphosphate dImTP by the TdT. The resulting enzymatic his-tag mimic ensures binding of DNA on Ni-NTA agarose. The usefulness of this method is highlighted by the immobilization of functional nucleic acids without impairing their specific activities.

Programmable DNA switches and their applications

DNA switches are ideally suited for numerous nanotechnological applications, and increasing efforts are being directed toward their engineering. In this review, we discuss how to engineer these switches starting from the selection of a specific DNA-based recognition element, to its adaptation and optimisation into a switch, with applications ranging from sensing to drug delivery, smart materials, molecular transporters, logic gates and others. We provide many examples showcasing their high programmability and recent advances towards their real life applications. We conclude with a short perspective on this exciting emerging field.

Assessing histidine tags for recruiting deoxyribozymes to catalyze peptide and protein modification reactions

We evaluate the ability of hexahistidine (His6) tags on peptide and protein substrates to recruit deoxyribozymes for modifying those substrates. For two different deoxyribozymes, one that creates tyrosine-RNA nucleopeptides and another that phosphorylates tyrosine side chains, we find substantial improvements in yield, kobs, and Km for peptide substrates due to recruiting by His6/Cu(2+). However, the recruiting benefits of the histidine tag are not observed for larger protein substrates, likely because the tested deoxyribozymes either cannot access the target peptide segments or cannot function when these segments are presented in a structured protein context.