Chemistry and biology of DNA repair

Numerous agents of endogenous and exogenous origin damage DNA in our genome. There are several DNA-repair pathways that recognize lesions in DNA and remove them through a number of diverse reaction sequences. Defects in DNA-repair proteins are associated with several human hereditary syndromes, which show a marked predisposition to cancer. Although DNA repair is essential for a healthy cell, DNA-repair enzymes counteract the efficiency of a number of important antitumor agents that exert their cytotoxic effects by damaging DNA. DNA-repair enzymes are therefore also targets for drug design. DNA-repair processes differ greatly in their nature and complexity. Whereas some pathways only require a single enzyme to restore the original DNA sequence, others operate through the coordinated action of 30 or more proteins. Our understanding of the genetic, biochemical, and structural basis of DNA repair and related processes has increased dramatically over the past decade. This review summarizes the latest developments in this field.     

"Non-VSEPR" Structures and Bonding in d(0) Systems

Under certain circumstances, metal complexes with a formal d(0) electronic configuration may exhibit structures that violate the traditional structure models, such as the VSEPR concept or simple ionic pictures. Some examples of such behavior, such as the bent gas-phase structures of some alkaline earth dihalides, or the trigonal prismatic coordination of some early transition metal chalcogenides or pnictides, have been known for a long time. However, the number of molecular examples for "non-VSEPR" structures has increased dramatically during the past decade, in particular in the realm of organometallic chemistry. At the same time, various theoretical models have been discussed, sometimes controversially, to explain the observed, unusual structures. Many d(0) systems are important in homogeneous and heterogeneous catalysis, biocatalysis (e.g. molybdenum or tungsten enzymes), or materials science (e.g. ferroelectric perovskites or zirconia). Moreover, their electronic structure without formally nonbonding d orbitals makes them unique starting points for a general understanding of structure, bonding, and reactivity of transition metal compounds. Here we attempt to provide a comprehensive view, both of the types of deviations of d(0) and related complexes from regular coordination arrangements, and of the theoretical framework that allows their rationalization. Many computational and experimental examples are provided, with an emphasis on homoleptic mononuclear complexes. Then the factors that control the structures are discussed in detail. They are a) metal d orbital participation in sigma bonding, b) polarization of the outermost core shells, c) ligand repulsion, and d) pi bonding. Suggestions are made as to which of the factors are the dominant ones in certain situations. In heteroleptic complexes, the competition of sigma and pi bonding of the various ligands controls the structures in a complicated fashion. Some guidelines are provided that should help to better understand the interrelations. Bent's rule is of only very limited use in these types of systems, because of the paramount influence of pi bonding. Finally, computed and measured structures of multinuclear complexes are discussed, including possible consequences for the properties of bulk solids.     

Structure-switching allosteric deoxyribozymes

DNA aptamers and DNA enzymes (DNAzymes or deoxyribozymes) are single-stranded DNA molecules with ligand-binding and catalytic capabilities, respectively. Allosteric DNA enzymes (aptazymes) are deoxyribozymes whose activity can be regulated by the binding state of an appended aptamer domain and have many potential uses in the fields of drug discovery and diagnostics. In this report, we describe a simple, yet potentially general, DNA aptazyme rational design strategy that requires no structural characterization of the constituent deoxyribozymes and aptamers. It is based on the concept originally developed in our laboratory for the design of structure-switching signaling aptamers that change structural states from a DNA-DNA duplex to a DNA-target complex upon target binding. In our new strategy, an antisense oligonucleotide is used to regulate the enzymatic activity of a linked aptamer-deoxyribozyme by annealing with a stretch of nucleotides on each side of the aptamer-DNAzyme junction. Structural reorganization of the aptamer domain upon target binding relieves the suppressive effect of this regulatory oligonucleotide on the attached DNA enzyme. Consequently, the target-binding event triggers the catalytic action of the aptazyme. We have demonstrated this concept using two RNA-cleaving deoxyribozymes, each adjoined to a DNA aptamer that binds ATP. These allosteric DNA enzymes exhibit the same ligand-binding specificity as the parental DNA aptamer and show up to 30-fold rate enhancement in the presence of ATP. The described methodology provides a convenient approach for rationally designing catalytic DNA-based biosensors.     

DNA与其靶向分子相互作用研究进展

DNA与其靶向分子相互作用的研究不仅对阐述一些抗肿瘤、抗病毒药物及致癌物的作用机理,而且对进一步指导人工核酸酶的合成及DNA高级结构研究等方面的工作都具有重要意义.本文着重评述了近年来不同结构类型的DNA靶向分子与DNA相互作用研究方面的进展.     

Spectroscopic studies of molybdenum and tungsten enzymes

Molybdenum and tungsten are the only second and third-row transition elements with a known function in living systems. Molybdenum fulfills functional roles in enzyme systems in almost all living creatures, from bacteria through plants to invertebrates and mammals, while tungsten takes the place of molybdenum in some prokaryotes, especially the hyperthermophilic archaea. The enzymes contain the metal bound by an unusual sulfur-containing cofactor. Despite possessing common structural elements, the enzymes are remarkable in the range of different chemical reactions that are catalyzed, although almost all are two-electron oxidation–reduction reactions in which an oxygen atom is transferred to or from the molybdenum. The functional roles filled by molybdenum enzymes are equally diverse; for example, they play essential roles in microbial respiration, in the uptake of nitrogen in green plants, in controlling insect eye color, and in human health. Spectroscopic studies, in particular electron paramagnetic resonance and X-ray absorption spectroscopy, have played an essential role in our understanding of the active site structures and catalytic mechanisms of the molybdenum and tungsten enzymes. This review summarizes the role spectroscopy has played in the state of our knowledge of the molybdenum and tungsten enzymes, with particular regard to structural information on the molybdenum sites.     

Crystallographic and bioinformatic studies on restriction endonucleases: inference of evolutionary relationships in the "midnight zone" of homology

Type II restriction endonucleases (ENases) cleave DNA with remarkable sequence specificity. Their discovery in 1970 and studies on molecular genetics and biochemistry carried out over the past four decades laid foundations for recombinant DNA techniques. Today, restriction enzymes are indispensable tools in molecular biology and molecular medicine and a paradigm for proteins that specifically interact with DNA as well as a challenging target for protein engineering. The sequence-structure-function relationships for these proteins are therefore of central interest in biotechnology. However, among numerous ENase sequences, only a few exhibit statistically significant similarity in pairwise comparisons, which was initially interpreted as evidence for the lack of common origin. Nevertheless, X-ray crystallographic studies of seemingly dissimilar type II ENases demonstrated that they share a common structural core and metal-binding/catalytic site, arguing for extreme divergence rather than independent evolution. A similar nuclease domain has been also identified in various enzymes implicated in DNA repair and recombination. Ironically, following the series of crystallographic studies suggesting homology of all type II ENases, bioinformatic studies provided evidence that some restriction enzymes are in fact diverged members of unrelated nuclease superfamilies: Nuc, HNH and GIY-YIG. Hence, the restriction enzymes as a whole, represent a group of functionally similar proteins, which evolved on multiple occasions and subsequently diverged into the "midnight zone" of homology, where common origins within particular groups can be inferred only from structure-guided comparisons. The structure-guided approaches used for this purpose include: identification of functionally important residues using superposition of atomic coordinates, alignment of sequence profiles enhanced by secondary structures, fold recognition, and homology modeling. This review covers recent results of comparative analyses of restriction enzymes from the four currently known superfamilies of nucleases with distinct folds, using crystallographic and bioinformatic methods, with the emphasis on theoretical predictions and their experimental validation by site-directed mutagenesis and biochemical analyses of the mutants.     

Understanding enzyme catalysis by means of supramolecular artificial enzymes

Enzymes are biomacromolecules responsible for the abundant chemical biotransformations that sustain life. Recently, biochemists have discovered that multiple conformations and numerous parallel paths are involved during the processes catalyzed by enzymes. It is plausible that the entire macromolecular scaffold is involved in catalysis via cooperative motions that result in incredible catalytic efficiency. Moreover, some enzymes can very strongly bind the transition state with an association constant of up to 1024 M-1, suggesting that covalent bond formation is a possible process during the conversion of the transition state in enzyme catalysis, in addition to the concatenation of noncovalent interactions. Supramolecular chemistry provides fundamental knowledge about the relationships between the dynamic structures and functions of organized molecules. By tak-ing advantage of supramolecular concepts, numerous supramolecular enzyme mimics with complex and hierarchical structures have been designed and investigated. Through the study of supramolecular enzyme models, a great deal of information to aid our understanding of the mechanism of catalysis by natural enzymes has been acquired. With the development of supramolec-ular artificial enzymes, it is possible to replicate the features of natural enzymes with regards to their constitutional complexity and cooperative motions, and eventually decipher the conformation-based catalytic mystery of natural enzymes.     

DNA Origami Post‐Processing by CRISPR‐Cas12a

Customizable nanostructures built through the DNA‐origami technique hold tremendous promise in nanomaterial fabrication and biotechnology. Despite the cutting‐edge tools for DNA‐origami design and preparation, it remains challenging to separate structural components of an architecture built from—thus held together by—a continuous scaffold strand, which in turn limits the modularity and function of the DNA‐origami devices. To address this challenge, here we present an enzymatic method to clean up and reconfigure DNA‐origami structures. We target single‐stranded (ss) regions of DNA‐origami structures and remove them with CRISPR‐Cas12a, a hyper‐active ssDNA endonuclease without sequence specificity. We demonstrate the utility of this facile, selective post‐processing method on DNA structures with various geometrical and mechanical properties, realizing intricate structures and structural transformations that were previously difficult to engineer. Given the biocompatibility of Cas12a‐like enzymes, this versatile tool may be programmed in the future to operate functional nanodevices in cells.     

Bestimmung von Saccharose,Glucose und Fructose mit trägergebundenen Enzymen

In serial chemical analysis the application of free enzymes is a rather uneconomical method because after each determination expensive enzyme reagents are discarded together with the test mixture, although as biocatalysts they are completely regenerated at the end of the reaction. In vivo, enzymes are often fixed to cell structures and more than up to a thousand times effective as biocatalysts. Hence the idea to apply enzymes fixed to a suitable carrier for repeated in vitro usage promises some success. Recently several groups of analysts succeeded in immobilizing enzymes of the protein metabolism for preparative purposes. We immobilized the enzymes saccharose, hexokinase, phosphohexose-isomerase and glucose-6-phosphate-dehydrogenase at CNBr activated agarose and by means of this affinity absorption-method determined the concentration of sucrose solutions in a closed recycling column system. The reduced form of nicotinamide-dinucleotide-phosphate being the measuring agent of the reaction is regenerated by means of glutathion reductase. The results of our investigation show, that the determination of the three carbohydrates sucrose, glucose and fructose by immobilized enzymes is by far superior to the common batch procedure regarding accuracy, velocity and costs.     

Enzyme mimics based upon supramolecular coordination chemistry

Recent advances in supramolecular coordination chemistry have allowed chemists to synthesize macromolecular complexes that exhibit various properties intrinsic to enzymes. This Review focuses on structures inspired by properties and functions observed in enzymes rather than precise models of enzyme active sites. These structures are synthesized using convergent, modular, and high-yielding coordination-chemistry-based methods, which allow one to tailor the size, shape, and properties of the resulting complexes. Many of the structures discussed exhibit reactivity and specificity reminiscent of natural systems, and some of them have functions that exceed the natural systems which provided the inspiration for initially making them.     

From the X-ray compact structure to the elongated form of the full-length MMP-2 enzyme in solution: a molecular dynamics study

Current understanding on the collagenolytic activity performed by the MMPs assumes some degree of relative motion between the catalytic and the hemopexin-like domains of the enzyme. However, all the crystal structures available for the full-length enzymes display a compact arrangement of the protein domains. Herein, we employ Molecular Dynamics simulations to investigate the structure of the full-length MMP-2 enzyme in aqueous solution. This simulation, together with previous experimental results that have been obtained very recently for the MMP-9 and MMP-12 enzymes, gives strong support to the hypothesis that the interdomain dynamics of the MMP enzymes in solution can result in a manifold of conformations including some structures with a large interdomain separation. The simulation of MMP-2 provides also a detailed molecular picture of the structures involved in the transition from the compact X-ray arrangement to the extended form in solution. Such information could be helpful in future studies of the regulation and/or the collagenolytic activity of these important enzymes.     

酶放大DNA电化学传感器的研究进展

DNA电化学传感器灵敏度高、选择性好、分析时间短和检测成本低,极大地推动了生物传感器的发展. 结合蛋白质酶、功能核酸酶的催化效率高与特异性好,可提高检测灵敏度和选择性. 本文评述了酶放大DNA电化学传感器的研究进展,并分析现存问题,展望发展趋势.     

The Art of Designing DNA Nanostructures with CAD Software

Since the arrival of DNA nanotechnology nearly 40 years ago, the field has progressed from its beginnings of envisioning rather simple DNA structures having a branched, multi-strand architecture into creating beautifully complex structures comprising hundreds or even thousands of unique strands, with the possibility to exactly control the positions down to the molecular level. While the earliest construction methodologies, such as simple Holliday junctions or tiles, could reasonably be designed on pen and paper in a short amount of time, the advent of complex techniques, such as DNA origami or DNA bricks, require software to reduce the time required and propensity for human error within the design process. Where available, readily accessible design software catalyzes our ability to bring techniques to researchers in diverse fields and it has helped to speed the penetration of methods, such as DNA origami, into a wide range of applications from biomedicine to photonics. Here, we review the historical and current state of CAD software to enable a variety of methods that are fundamental to using structural DNA technology. Beginning with the first tools for predicting sequence-based secondary structure of nucleotides, we trace the development and significance of different software packages to the current state-of-the-art, with a particular focus on programs that are open source.     

Terpenoid synthase structures: a so far incomplete view of complex catalysis

Covering: up to February 2012The complexity of terpenoid natural products has drawn significant interest, particularly since their common (poly)isoprenyl origins were discovered. Notably, much of this complexity is derived from the highly variable cyclized and/or rearranged nature of the observed hydrocarbon skeletal structures. Indeed, at least in some cases it is difficult to immediately recognize their derivation from poly-isoprenyl precursors. Nevertheless, these diverse structures are formed by sequential elongation to acyclic precursors, most often with subsequent cyclization and/or rearrangement. Strikingly, the reactions used to assemble and diversify terpenoid backbones share a common carbocationic driven mechanism, although the means by which the initial carbocation is generated does vary. High-resolution crystal structures have been obtained for at least representative examples from each of the various types of enzymes involved in producing terpenoid hydrocarbon backbones. However, while this has certainly led to some insights into the enzymatic structure-function relationships underlying the elongation and simpler cyclization reactions, our understanding of the more complex cyclization and/or rearrangement reactions remains limited. Accordingly, selected examples are discussed here to demonstrate our current understanding, its limits, and potential ways forward.     

The crystal structures of 4-methoxybenzoate bound CYP199A2 and CYP199A4: structural changes on substrate binding and the identification of an anion binding site

The crystal structures of the 4-methoxybenzoate bound forms of cytochrome P450 enzymes CYP199A2 and CYP199A4 from the Rhodopseudomonas palustris strains CGA009 and HaA2 have been solved. The structures of these two enzymes, which share 86% sequence identity, are very similar though some differences are found on the proximal surface. In these structures the enzymes have a closed conformation, in contrast to the substrate-free form of CYP199A2 where an obvious substrate access channel is observed. The switch from an open to a closed conformation arises from pronounced residue side-chain movements and alterations of ion pair and hydrogen bonding interactions at the entrance of the access channel. A chloride ion bound just inside the protein surface caps the entrance to the active site and protects the substrate and the heme from the external solvent. In both structures the substrate is held in place via hydrophobic and hydrogen bond interactions. The methoxy group is located over the heme iron, accounting for the high activity and selectivity of these enzymes for oxidative demethylation of the substrate. Mutagenesis studies on CYP199A4 highlight the involvement of hydrophobic (Phe185) and hydrophilic (Arg92, Ser95 and Arg243) amino acid residues in the binding of para-substituted benzoates by these enzymes.     

A Light-up Logic Platform for Selective Recognition of Parallel G-Quadruplex Structures via Disaggregation-Induced Emission

The design of turn-on dyes with optical signals sensitive to the formation of supramolecular structures provides fascinating and underexplored opportunities for G-quadruplex (G4) DNA detection and characterization. Here, we show a new switching mechanism that relies on the recognition-driven disaggregation (on-signal) of an ultrabright coumarin-quinazoline conjugate. The synthesized probe selectively lights-up parallel G4 DNA structures via the disassembly of its supramolecular state, demonstrating outputs that are easily integrable into a label-free molecular logic system. Finally, our molecule preferentially stains the G4-rich nucleoli of cancer cells.     

Transient DNA-Based Nanostructures Controlled by Redox Inputs

Synthetic DNA has emerged as a powerful self-assembled material for the engineering of nanoscale supramolecular devices and materials. Recently dissipative self-assembly of DNA-based supramolecular structures has emerged as a novel approach providing access to a new class of kinetically controlled DNA materials with unprecedented life-like properties. So far, dissipative control has been achieved using DNA-recognizing enzymes as energy dissipating units. Although highly efficient, enzymes pose limits in terms of long-term stability and inhibition of enzyme activity by waste products. Herein, we provide the first example of kinetically controlled DNA nanostructures in which energy dissipation is achieved through a non-enzymatic chemical reaction. More specifically, inspired by redox signalling, we employ redox cycles of disulfide-bond formation/breakage to kinetically control the assembly and disassembly of tubular DNA nanostructures in a highly controllable and reversible fashion.     

Transient DNA‐Based Nanostructures Controlled by Redox Inputs

Synthetic DNA has emerged as a powerful self‐assembled material for the engineering of nanoscale supramolecular devices and materials. Recently dissipative self‐assembly of DNA‐based supramolecular structures has emerged as a novel approach providing access to a new class of kinetically controlled DNA materials with unprecedented life‐like properties. So far, dissipative control has been achieved using DNA‐recognizing enzymes as energy dissipating units. Although highly efficient, enzymes pose limits in terms of long‐term stability and inhibition of enzyme activity by waste products. Herein, we provide the first example of kinetically controlled DNA nanostructures in which energy dissipation is achieved through a non‐enzymatic chemical reaction. More specifically, inspired by redox signalling, we employ redox cycles of disulfide‐bond formation/breakage to kinetically control the assembly and disassembly of tubular DNA nanostructures in a highly controllable and reversible fashion.     

A Light‐up Logic Platform for Selective Recognition of Parallel G‐Quadruplex Structures via Disaggregation‐Induced Emission

The design of turn‐on dyes with optical signals sensitive to the formation of supramolecular structures provides fascinating and underexplored opportunities for G‐quadruplex (G4) DNA detection and characterization. Here, we show a new switching mechanism that relies on the recognition‐driven disaggregation (on‐signal) of an ultrabright coumarin‐quinazoline conjugate. The synthesized probe selectively lights‐up parallel G4 DNA structures via the disassembly of its supramolecular state, demonstrating outputs that are easily integrable into a label‐free molecular logic system. Finally, our molecule preferentially stains the G4‐rich nucleoli of cancer cells.     

Aminoacyl-tRNA Synthetases: The Division into Two Classes Predicted by the Chemistry of Substrates and Enzymes

In biological systems, almost all chemical reactions are catalyzed by enzymes. In order to understand the mode of action of these biocatalysts, we need to know precise details of their structures, their active sites, and their functional groups. Most important are those parts of the protein molecule that are responsible for precise recognition of the substrates, for the specific interaction between the enzymes and their reactants. Decades can pass between the isolation of an enzyme and the determination of its exact structure by X-ray analysis. For the chemist, however, means are known by which initial information may be gathered relatively quickly: the synthesis of modified substrates and affinity labeling. During the last twenty five years these two methods have been put to the test on aminoacyl-tRNA synthetases. Today, we know enough about the structures of these enzymes to evaluate the success of this “chemistry on macromolecules,” or their substrates. Chemists have had some successes, which provided the structural analysts with valuable preliminary results.