Flexible Assembly of an Enzyme Cascade on a DNA Triangle Prism Nanostructure for the Controlled Biomimetic Generation of Nitric Oxide

Spatial organization of multiple enzymes at specific positions for a controlled reaction cascade has attracted wide attention in recent years. Here, we report the construction of a biomimetic enzyme cascade organized on DNA triangle prism (TP) nanostructures to enable the efficient catalytic production of nitric oxide (NO) on a single microbead. Two enzymes, glucose oxidase (GOx) and horseradish peroxidase (HRP), were assembled at adjacent locations on a DNA TP nanostructure by using DNA‐binding protein adaptors with small interenzyme distances. In the cascade, the first enzyme, GOx, converts glucose into gluconic acid in the presence of oxygen. The produced H₂O₂ intermediate is rapidly transported to the second enzyme, HRP, which oxides hydroxyurea into NO and other nitroxyl species. The pH near the surface of the negatively charged DNA nanostructures is believed to be lower than that in the bulk solution; this creates an optimal pH environment for the anchored enzymes, which results in higher yields of the NO product. Furthermore, the multienzyme system was immobilized on a microbead mediated by a DNA adaptor, and this enabled the efficient catalytic generation of gas molecules in the microreactor. Therefore, this work provides an alternative route for the biomimetic generation of NO through enzyme cascades. In particular, the dynamic binding capability of the DNA sequence enabled the positions of the protein enzyme and the DNA nanostructure to be reversed, which allowed the cascade catalysis to be modulated.     

Protein Interactions in the T7 DNA Replisome Facilitate DNA Damage Bypass

The DNA replisome inevitably encounters DNA damage during DNA replication. The T7 DNA replisome contains a DNA polymerase (gp5), the processivity factor thioredoxin (trx), a helicase‐primase (gp4), and a ssDNA‐binding protein (gp2.5). T7 protein interactions mediate this DNA replication. However, whether the protein interactions could promote DNA damage bypass is still little addressed. In this study, we investigated strand‐displacement DNA synthesis past 8‐oxoG or O⁶‐MeG lesions at the synthetic DNA fork by the T7 DNA replisome. DNA damage does not obviously affect the binding affinities between helicase, polymerase, and DNA fork. Relative to unmodified G, both 8‐oxoG and O⁶‐MeG—as well as GC‐rich template sequence clusters—inhibit strand‐displacement DNA synthesis and produce partial extension products. Relative to the gp4 ΔC‐tail, gp4 promotes DNA damage bypass. The presence of gp2.5 also promotes it. Thus, the interactions of polymerase with helicase and ssDNA‐binding protein facilitate DNA damage bypass. Accessory proteins in other complicated DNA replisomes also facilitate bypassing DNA damage in similar manner. This work provides new mechanistic information relating to DNA damage bypass by the DNA replisome.     

One‐Pot Cascade Reactions using Fructose‐6‐phosphate Aldolase: Efficient Synthesis of D‐Arabinose 5‐Phosphate,D‐Fructose 6‐Phosphate and Analogues

One‐pot multienzymatic reactions have been performed for the synthesis of 1‐deoxy‐D ‐fructose 6‐phosphate, 1,2‐dideoxy‐D ‐arabino‐hept‐3‐ulose 7‐phosphate, D ‐fructose 6‐phosphate and D ‐arabinose 5‐phosphate. The whole synthetic strategy is based on an aldol addition reaction catalysed by fructose‐6‐phosphate aldolase (FSA) as a key step of a three or four enzymes‐catalysed cascade reaction. The four known donors for FSA – dihydroxyacetone (DHA), hydroxyacetone (HA), 1‐hydroxy‐2‐butanone (HB) and glycolaldehyde (GA) – were used with D ‐glyceraldehyde 3‐phosphate as acceptor substrate. The target phosphorylated sugars were obtained in good to excellent yields and high purity.     

Structure and Replication of yDNA: A Novel Genetic Set Widened by Benzo‐Homologation

In a functioning genetic system, the information‐encoding molecule must form a regular self‐complementary complex (for example, the base‐paired double helix of DNA) and it must be able to encode information and pass it on to new generations. Here we study a benzo‐widened DNA‐like molecule (yDNA) as a candidate for an alternative genetic set, and we explicitly test these two structural and functional requirements. The solution structure of a 10 bp yDNA duplex is measured by using 2D‐NMR methods for a simple sequence composed of T–yA/yA–T pairs. The data confirm an antiparallel, right‐handed, hydrogen‐bonded helix resembling B‐DNA but with a wider diameter and enlarged base‐pair size. In addition to this, the abilities of two different polymerase enzymes (Klenow fragment of DNA pol I (Kf) and the repair enzyme Dpo4) to synthesize and extend the yDNA pairs T–yA, A–yT, and G–yC are measured by steady‐state kinetics studies. Not surprisingly, insertion of complementary bases opposite yDNA bases is inefficient due to the larger base‐pair size. We find that correct pairing occurs in several cases by both enzymes, but that common and relatively efficient mispairing involving T–yT and T–yC pairs interferes with fully correct formation and extension of pairs by these polymerases. Interestingly, the data show that extension of the large pairs is considerably more efficient with the flexible repair enzyme (Dpo4) than with the more rigid Kf enzyme. The results shed light on the properties of yDNA as a candidate for an alternative genetic information‐encoding molecule and as a tool for application in basic science and biomedicine.     

Genomic structure,cloning and expression of two phospholipase D isoenzymes from white cabbage

Phospholipase D (PLD) from cabbage is interesting as biocatalyst in phospholipid transformation. To provide the basis for genetic engineering of the enzyme, gene cloning and sequencing were carried out. We have recently identified two isoenzymes, PLD1 and PLD2, on the basis of their cDNAs, here we describe their genomic structure consisting of 3404 and 3614 bp, respectively. Based on their sequence, PLD1 and PLD2 can be assigned to the α‐type of plant PLDs, they contain two HKD motifs and the C2 domain with a phosphatidylinositol 4,5‐bisphosphate (PIP₂) binding motif. Starting from pld1 cDNA, expression studies were carried out. Whereas expression using constructs with StrepTactin or Glutathion S‐transferase tags was not successful, soluble active enzyme was produced from constructs without tag. pld2 was expressed accordingly. Both enzymes were purified by Ca²⁺‐mediated hydrophobic interaction chromatography to high purity. N‐terminal sequencing of PLD1 and PLD2 revealed that the Met‐free N‐termini of both enzymes correspond to sequences derived from the coding region of the pld1 and pld2 genes, respectively. Both recombinant enzymes showed highest hydrolytic activities at pH 5.5 to 5.6, independent of Ca²⁺ concentration (10—100 mM). The optimum Ca²⁺ concentration was 45 mM for PLD1 and PLD2. Both enzymes showed comparable activities in hydrolysis and transphosphatidylation of phospholipids.     

In Vitro Double Oxidation of n‐Heptane with Direct Cofactor Regeneration

A novel concept for the direct oxidation of cycloalkanes to the corresponding cyclic ketones in a one‐pot synthesis in water with molecular oxygen as sole oxidizing agent was reported recently. Based on this concept we have developed a new strategy for the double oxidation of n‐heptane to enable a biocatalytic resolution for the direct synthesis of heptanone and (R)‐heptanols in a one‐pot reaction. The bicatalytic cascade employs an NADH driven P450 BM3 monooxygenase variant (WT^NADH, 19A12^NADH or CM1^NADH) and an (S)‐enantioselective alcohol dehydrogenase (RE‐ADH). In the initial step n‐heptane is hydroxylated under consumption of NADH to produce (R/S)‐heptanol. In the second oxidation step the (S)‐heptanol enantiomers are transformed to the corresponding ketones, reducing and thereby regenerating the cofactor. Characterization of initial hydroxylation step revealed high turnover frequencies (TOF) of up to 600 min⁻¹, as well as high coupling efficiencies using NADH as cofactor (up to 44%). In the cascade reaction a nearly 2‐fold improved product formation was achieved, compared to the single hydroxylation reaction. The total product concentration reached 1.1 mM, corresponding to a total turnover number (TTN) of 2500. Implementation of an additional cofactor regeneration system (D ‐glucose/glucose dehydrogenase) enabled a further enhancement in product formation with a total product concentration of 1.8 mM and a TTN of 3500.     

Effect of Ionic Strength on the Thermal Stability of DNA Origami Nanostructures

The stability of DNA origami nanostructures in aqueous media is closely tied to the presence of cations that screen electrostatic inter-helix repulsion. Here, the thermal melting behavior of different DNA origami nanostructures is investigated in dependence on Mg²⁺ concentration and compared to calculated ensemble melting temperatures of the staple strands used in DNA origami folding. Strong deviations of the measured DNA origami melting temperatures from the calculated ones are observed, in particular at high ionic strength where the melting temperature saturates and becomes independent of ionic strength. The degree of deviation between the measured and calculated melting temperatures further depends on the superstructure and in particular the mechanical properties of the DNA origami nanostructures. This indicates that thermal stability of a given DNA origami design at high ionic strength is governed predominantly not by electrostatic inter-helix repulsion but mostly by mechanical strain.     

Loop‐Grafted Old Yellow Enzymes in the Bienzymatic Cascade Reduction of Allylic Alcohols

The enzymatic reduction of C=C bonds in allylic alcohols with Old Yellow Enzymes represents a challenging task, due to insufficient activation through the hydroxy group. In our work, we coupled an alcohol dehydrogenase with three wild‐type ene reductases—namely nicotinamide‐dependent cyclohex‐2‐en‐1‐one reductase (NCR) from Zymomonas mobilis, OYE1 from Saccharomyces pastorianus and morphinone reductase (MR) from Pseudomonas putida M10—and four rationally designed β/α loop variants of NCR in the bienzymatic cascade hydrogenation of allylic alcohols. Remarkably, the wild type of NCR was not able to catalyse the cascade reaction whereas MR and OYE1 demonstrated high to excellent activities. Through the rational loop grafting of two intrinsic β/α surface loop regions near the entrance of the active site of NCR with the corresponding loops from OYE1 or MR we successfully transferred the cascade reduction activity from one family member to another. Further we observed that loop grafting revealed certain influences on the interaction with the nicotinamide cofactor.     

Chemoenzymatic One‐Pot Synthesis of γ‐Butyrolactones

The synthesis of enantio‐ and diastereomerically pure γ‐butyrolactones is described using a one‐pot, two‐enzyme cascade. Ethyl 2‐methyl‐4‐oxopent‐2‐enoate ( 2 ) was reduced selectively first in a 1,4‐reduction using the old yellow enzyme (OYE1) [EC 1.6.99.1] and consecutively in a 1,2‐reduction by an alcohol dehydrogenase [EC 1.1.1.2].     

Two‐Stage Oxidation of Glucose by an Enzymatic Bioanode

The present study reports the design of a novel bioanode to deeply oxidize glucose in an enzymatic biofuel cell (EFC). This enzymatic glucose cell utilizes three co‐immobilized enzymes: NAD‐dependent glucose dehydrogenase (GDH), NAD(P)⁺‐dependent gluconate‐5‐dehydrogenase (Ga5DH), and diaphorase (DI). Glucose is oxidized to gluconate by NAD‐dependent GDH, gaining two electrons per glucose; the gluconate obtained as a by‐product is oxidized at the C5 carbon to 5‐keto‐gluconate by Ga5DH. Operation of our bioanode enabled the oxidation of glucose in two stages, resulting in the gain of four electrons. The three‐enzyme EFC provides a maximum power density of 10.51 ± 1.72 μW cm^–2, which is about 1.6 times higher than the maximum power density of an EFC using a bioanode based on the co‐immobilization of two enzymes (GDH and DI). Our results hold promise for increasing the current density of EFCs, and for application in glucose biosensor.     

How We Make DNA Origami

DNA origami has attracted substantial attention since its invention ten years ago, due to the seemingly infinite possibilities that it affords for creating customized nanoscale objects. Although the basic concept of DNA origami is easy to understand, using custom DNA origami in practical applications requires detailed know‐how for designing and producing the particles with sufficient quality and for preparing them at appropriate concentrations with the necessary degree of purity in custom environments. Such know‐how is not readily available for newcomers to the field, thus slowing down the rate at which new applications outside the field of DNA nanotechnology may emerge. To foster faster progress, we share in this article the experience in making and preparing DNA origami that we have accumulated over recent years. We discuss design solutions for creating advanced structural motifs including corners and various types of hinges that expand the design space for the more rigid multilayer DNA origami and provide guidelines for preventing undesired aggregation and on how to induce specific oligomerization of multiple DNA origami building blocks. In addition, we provide detailed protocols and discuss the expected results for five key methods that allow efficient and damage‐free preparation of DNA origami. These methods are agarose‐gel purification, filtration through molecular cut‐off membranes, PEG precipitation, size‐exclusion chromatography, and ultracentrifugation‐based sedimentation. The guide for creating advanced design motifs and the detailed protocols with their experimental characterization that we describe here should lower the barrier for researchers to accomplish the full DNA origami production workflow.     

Salting-Out of DNA Origami Nanostructures by Ammonium Sulfate

DNA origami technology enables the folding of DNA strands into complex nanoscale shapes whose properties and interactions with molecular species often deviate significantly from that of genomic DNA. Here, we investigate the salting-out of different DNA origami shapes by the kosmotropic salt ammonium sulfate that is routinely employed in protein precipitation. We find that centrifugation in the presence of 3 M ammonium sulfate results in notable precipitation of DNA origami nanostructures but not of double-stranded genomic DNA. The precipitated DNA origami nanostructures can be resuspended in ammonium sulfate-free buffer without apparent formation of aggregates or loss of structural integrity. Even though quasi-1D six-helix bundle DNA origami are slightly less susceptible toward salting-out than more compact DNA origami triangles and 24-helix bundles, precipitation and recovery yields appear to be mostly independent of DNA origami shape and superstructure. Exploiting the specificity of ammonium sulfate salting-out for DNA origami nanostructures, we further apply this method to separate DNA origami triangles from genomic DNA fragments in a complex mixture. Our results thus demonstrate the possibility of concentrating and purifying DNA origami nanostructures by ammonium sulfate-induced salting-out.     

One‐Pot Chemoenzymatic Cascade for Labeling of the Epigenetic Marker 5‐Hydroxymethylcytosine

The epigenetic DNA modification 5‐hydroxymethylcytosine (5‐hmC) is important for the regulation of gene expression during development and in tumorigenesis. 5‐hmC can be selectively glycosylated by T4 β‐glucosyltransferase (β‐GT); introduction of an azide on the attached sugar provides a chemical handle for isolation or fluorescent tagging of 5‐hmC residues by click chemistry. This approach has not been broadly adopted because of the challenging synthesis and limited commercial availability of the glycosylation substrate, 6‐deoxy‐6‐azido‐α‐D ‐glucopyranoside. We report the enzyme‐assisted synthesis of this precursor by the uridylyltransferase from Pasteurella multocida (PmGlmU). We were able to directly label 5‐hmC in genomic DNA by an enzymatic cascade involving successive action of PmGlmU and β‐GT. This is a facile and cost‐effective one‐pot chemoenzymatic methodology for 5‐hmC analysis.     

Evolution of a Transition State: Role of Lys100 in the Active Site of Isocitrate Dehydrogenase

An active site lysine essential to catalysis in isocitrate dehydrogenase (IDH) is absent from related enzymes. As all family members catalyze the same oxidative β‐decarboxylation at the (2R)‐malate core common to their substrates, it seems odd that an amino acid essential to one is not found in all. Ordinarily, hydride transfer to a nicotinamide C4 neutralizes the positive charge at N1 directly. In IDH, the negatively charged C4‐carboxylate of isocitrate stabilizes the ground state positive charge on the adjacent nicotinamide N1, opposing hydride transfer. The critical lysine is poised to stabilize—and perhaps even protonate—an oxyanion formed on the nicotinamide 3‐carboxamide, thereby enabling the hydride to be transferred while the positive charge at N1 is maintained. IDH might catalyze the same overall reaction as other family members, but dehydrogenation proceeds through a distinct, though related, transition state. Partial activation of lysine mutants by K⁺ and NH₄⁺ represents a throwback to the primordial state of the first promiscuous substrate family member.     

1,2,4‐Triazine‐Modified 2′‐Deoxyuridine Triphosphate for Efficient Bioorthogonal Fluorescent Labeling of DNA

In order to establish the Diels–Alder reaction with inverse electron demand for postsynthetic DNA modification, a 1,2,4‐triazine‐modified 2′‐deoxyuridine triphosphate was synthesized. The bioorthogonally reactive 1,2,4‐triazine group was attached at the 5‐position of 2′‐deoxyuridine by a flexible alkyl linker to facilitate its acceptance by DNA polymerases. The screening of four DNA polymerases showed successful primer extensions, using a mixture of dATP, dGTP, dCTP, and the modified 2′‐deoxyuridine triphosphate, by using KOD XL or Vent polymerase. The triazine moiety was stable under the conditions of primer extension, which was evidenced by labeling with a BCN‐modified rhodamine at room temperature in yields of up to 82 %. Two or three modified bases could be incorporated in quantitative yields when the modification sites were separated by three base pairs. These results establish the 1,2,4‐triazene group as a bioorthogonally reactive moiety in DNA, thereby replacing the problematic 1,2,4,5‐tetrazine for postsynthetic labeling by the Diels–Alder reaction with inverse electron demand.     

Structure-Dependent Electrical Conductance of DNA Origami Nanowires

Exploring the structural and electrical properties of DNA origami nanowires is an important endeavor for the advancement of DNA nanotechnology and DNA nanoelectronics. Highly conductive DNA origami nanowires are a desirable target for creating low-cost self-assembled nanoelectronic devices and circuits. In this work, the structure-dependent electrical conductance of DNA origami nanowires is investigated. A silicon nitride (Si₃N₄) on silicon semiconductor chip with gold electrodes was used for collecting electrical conductance measurements of DNA origami nanowires, which are found to be an order of magnitude less electrically resistive on Si₃N₄ substrates treated with a monolayer of hexamethyldisilazane (HMDS) (∼10¹³ ohms) than on native Si₃N₄ substrates without HMDS (∼10¹⁴ ohms). Atomic force microscopy (AFM) measurements of the height of DNA origami nanowires on mica and Si₃N₄ substrates reveal that DNA origami nanowires are ∼1.6 nm taller on HMDS-treated substrates than on the untreated ones indicating that the DNA origami nanowires undergo increased structural deformation when deposited onto untreated substrates, causing a decrease in electrical conductivity. This study highlights the importance of understanding and controlling the interface conditions that affect the structure of DNA and thereby affect the electrical conductance of DNA origami nanowires.     

Conformational Analysis of the Mannosidase Inhibitor Kifunensine: A Quantum Mechanical and Structural Approach

The varied yet family‐specific conformational pathways used by individual glycoside hydrolases (GHs) offer a tantalising prospect for the design of tightly binding and specific enzyme inhibitors. A cardinal example of a GH‐family‐specific inhibitor, and one that finds widespread practical use, is the natural product kifunensine, which is a low‐nanomolar inhibitor that is selective for GH family 47 inverting α‐mannosidases. Here we show, through quantum‐mechanical approaches, that kifunensine is restrained to a “ring‐flipped” ¹C₄ conformation with another accessible, but higher‐energy, region around the ^1,4B conformation. The conformations of kifunensine in complex with a range of GH47 enzymes—including an atomic‐level resolution (1 Å) structure of kifunensine with Caulobacter sp. CkGH47 reported herein and with GH family 38 and 92 α‐mannosidases—were mapped onto the kifunensine free‐energy landscape. These studies revealed that kifunensine has the ability to mimic the product state of GH47 enzymes but cannot mimic any conformational states relevant to the reaction coordinate of mannosidases from other families.     

An Isocytidine Derivative with a 2‐Amino‐6‐methylpyridine Unit for Selective Recognition of the CG Interrupting Site in an Antiparallel Triplex DNA

Sequence‐specific recognition of duplex DNA mediated by triple helix formation offers a potential basis for oligonucleotide therapy and biotechnology. However, triplex formation is limited mostly to homopurine strands, due to poor stabilization at CG or TA base pairs in the target duplex DNA sequences. Several non‐natural nucleosides have been designed for the recognition of CG or TA base pairs within an antiparallel triplex DNA. Nevertheless, problems including low selectivity and high dependence on the neighboring bases remain unsolved. We thus synthesized N²‐arylmethyl isodC derivatives and incorporated them into triplex‐forming oligonucleotides (TFOs) for the selective recognition of the CG base pair within antiparallel triplex DNA. It was shown that an isodC derivative bearing a 2‐amino‐6‐methylpyridine moiety (AP‐isodC) recognizes the CG base pair with high selectivity in antiparallel triplex DNA irrespective of the flanking base pairs.     

Nucleic‐Acid‐Templated Enzyme Cascades

Cellular metabolism involves complex sequences of organized enzymatic reactions, known as metabolic pathways, that convert substrates into readily usable materials. In nature, these enzymatic complexes are organized in a well‐defined manner so that the cascade reactions are more rapid and efficient than they would be if the enzymes were randomly distributed in the cytosol. Development of artificial enzyme cascades that resemble nature's organization of sequentially assembled enzymes is of current interest due to its potential applications, from diagnostics to the production of high‐value chemicals. Nucleic acids and their nanostructures have been used to organize enzyme cascades and have been shown to enhance the efficiencies and rates of sequential reactions. Here we summarize the recent progress in the development of artificial enzyme cascades and sequential reactions by arranging enzymes on various DNA/RNA templates and discuss the future directions of this research endeavour.     

Use of novel hydrogels based on modified cellulosics and methacrylamide for separation of metal ions from water systems

Interpenetrating networks (IPNs) based on extracted cellulose and its derivatives such as hydroxypropyl cellulose (HPC), cyanoethylcellulose, hydroxyethylcellulose, hydrazinodeoxycellulose, cellulosephosphate with methacrylamide (MAAm), and N,N‐methylene bisacrylamide were synthesized at reaction conditions evaluated for optimum network yield as a function of irradiation dose, concentrations of monomer and crosslinker, and amount of water. These networks were used in sorption of Fe²⁺, Cu²⁺, and Cr⁶⁺ ions. The networks were further functionlized by means of partial hydrolysis with 0.5N NaOH and metal ion sorption studies were carried out. Appreciable amount of all the three ions was sorbed and partial functionalization of the hydrogels results in selectivity in ion sorption with enhanced affinity for Fe²⁺ ions and total rejection of Cr⁶⁺ ions. These results are of interest for the development of low‐cost technologies based on smart hydrogels. © 2002 Wiley Periodicals, Inc. J Appl Polym Sci 86: 667–671, 2002