Novel antibiotics: second generation macrocyclic peptides designed to trap Holliday junctions

Described are the syntheses of 15 macrocyclic peptides designed to trap Holliday junctions (HJs) in bacteria during site-specific and homologous recombination. This leads to inhibiting bacterial growth. These second generation macrocycles were based on the C-2 symmetrical HJ. They were synthesized using a strategy that permits elucidation of the amino acid role in binding HJs. The syntheses of these macrocycles are an important step in the development of a new class of antibiotics.     

Fluorophore‐Conjugated Holliday Junctions for Generating Super‐Bright Antibodies and Antibody Fragments

The site‐specific modification of proteins with fluorophores can render a protein fluorescent without compromising its function. To avoid self‐quenching from multiple fluorophores installed in close proximity, we used Holliday junctions to label proteins site‐specifically. Holliday junctions enable modification with multiple fluorophores at reasonably precise spacing. We designed a Holliday junction with three of its four arms modified with a fluorophore of choice and the remaining arm equipped with a dibenzocyclooctyne substituent to render it reactive with an azide‐modified fluorescent single‐domain antibody fragment or an intact immunoglobulin produced in a sortase‐catalyzed reaction. These fluorescent Holliday junctions improve fluorescence yields for both single‐domain and full‐sized antibodies without deleterious effects on antigen binding.     

Bio-switchable optofluidic lasers based on DNA Holliday junctions

Bio-switchable optofluidic lasers based on DNA Holliday junctions were demonstrated. Nearly 100% wavelength switching was achieved through reversible conformational change of the Holliday junction controlled by magnesium ionic strength.     

HolT Hunter: Software for identifying and characterizing low‐strain DNA holliday triangles

Synthetic DNA nanostructures are most commonly held together via Holliday junctions. These junctions allow for a wide variety of different angles between the double helices they connect. Nevertheless, only constructs with a very limited selection of angles have been built, to date, because of the computational complexity of identifying structures that fit together with low strain at odd angles. I have developed an algorithm that finds over 95% of the possible solutions by breaking the problem down into two portions. First, there is a problem of how smooth rods can form triangles by lying across one another. This problem is easily handled by numerical computation. Second, there is the question of how distorted DNA double helices would need to be to fit onto the rod structure. This strain is calculated directly. The algorithm has been implemented in a Mathematica 8 notebook called Holliday Triangle Hunter. A large database of solutions has been identified. Additional interface software is available to facilitate drawing and viewing models. © 2012 Wiley Periodicals, Inc.     

A Self-Assembled Rhombohedral DNA Crystal Scaffold with Tunable Cavity Sizes and High-Resolution Structural Detail

DNA is an ideal molecule for the construction of 3D crystals with tunable properties owing to its high programmability based on canonical Watson–Crick base pairing, with crystal assembly in all three dimensions facilitated by immobile Holliday junctions and sticky end cohesion. Despite the promise of these systems, only a handful of unique crystal scaffolds have been reported. Herein, we describe a new crystal system with a repeating sequence that mediates the assembly of a 3D scaffold via a series of Holliday junctions linked together with complementary sticky ends. By using an optimized junction sequence, we could determine a high-resolution (2.7 Å) structure containing R3 crystal symmetry, with a slight subsequent improvement (2.6 Å) using a modified sticky-end sequence. The immobile Holliday junction sequence allowed us to produce crystals that provided unprecedented atomic detail. In addition, we expanded the crystal cavities by 50 % by adding an additional helical turn between junctions, and we solved the structure to 4.5 Å resolution by molecular replacement.     

Self‐Assembly of a 3D DNA Crystal Structure with Rationally Designed Six‐Fold Symmetry

Programming self‐assembled designer DNA crystals with various lattices and functions is one of the most important goals for nanofabrication using nucleic acids. The resulting porous materials possess atomic precision for several potential applications that rely on crystalline lattices and cavities. Herein, we present a rationally designed and self‐assembled 3D DNA crystal lattice with hexagonal symmetry. In our design, two 21‐base oligonucleotides are used to form a duplex motif that further assembles into a 3D array. The interactions between the strands are programmed using Watson–Crick base‐pairing. The six‐fold symmetry, as well as the chirality, is directed by the Holliday junctions formed between the duplex motifs. The rationally designed DNA crystal provides a new avenue that could create self‐assembled macromolecular 3D crystalline lattices with atomic precision. In addition, the structure contains a highly organized array of well‐defined cavities that are suitable for future applications with immobilized guests.     

Synthesis of Carbohydrate Based Macrolactones and Their Applications as Receptors for Ion Recognition and Catalysis

Glycomacrolactones exhibit many interesting biological properties, and they are also important in molecular recognitions and for supramolecular chemistry. Therefore, it is important to be able to access glycomacrocycles with different sizes and functionality. A new series of carbohydrate-based macrocycles containing triazole and lactone moieties have been designed and synthesized. The synthesis features an intramolecular nucleophilic substitution reaction for the macrocyclization step. In this article, the effect of some common sulfonate leaving groups is evaluated for macrolactonization. Using tosylate gave good selectivity for monolactonization products with good yields. Fourteen different macrocycles have been synthesized and characterized, of which eleven macrocycles are from cyclization of the C1 to C6 positions of N-acetyl D-glucosamine derivatives and three others from C2 to C6 cyclization of functionalized D-glucosamine derivatives. These novel macrolactones have unique structures and demonstrate interesting anion binding properties, especially for chloride. The macrocycles containing two triazoles form complexes with copper sulfate, and they are effective ligands for copper sulfate mediated azide-alkyne cycloaddition reactions (CuAAC). In addition, several macrocycles show some selectivity for different alkynes.     

Utilization of achiral alkenyl amines for the preparation of high affinity Grb2 SH2 domain-binding macrocycles by ring-closing metathesis

A family of previously reported ring-closing metathesis (RCM)-derived macrocycles that exhibit potent Grb2 SH2 domain-binding affinity is characterized by stereoselectively-introduced upper ring junctions that bear bicyclic aryl substituents. However, the synthetic complexity of these macrocycles presents a potential limit to their therapeutic application. Therefore, the current study was undertaken to simplify these macrocycles through the use of achiral 4-pentenylamides as ring-forming components. A series of macrocycles (5a-f) was prepared bearing both open and cyclic constructs at the upper ring junction. The Grb2 SH2 domain-binding affinities of these macrocycles varied, with higher affinities being obtained with cyclo-substituents. The most potent analogue (5d) contained a cyclohexyl group and exhibited Grb2 SH2 domain-binding affinity (K(D) = 1.3 nM) that was nearly equal to the parent macrocycle (2), which bore a stereoselectively-introduced naphthylmethyl substituent at the upper ring junction (K(D) = 0.9 nM). The results of this study advance design considerations that should facilitate the development of Grb2 SH2 domain-binding antagonists.     

Folding of small origamis

A model that preserves the known thermodynamic properties of double stranded DNA is introduced to study the formation of more complex DNA constructions, such as small origamis or Holliday junctions. We show that the thermodynamic behaviour of these complex DNA constructions is not only given by their sequence but also by their topology.     

葫芦[8]脲的环套环分子组装

以4,4'-联吡啶鎓、 2,6-萘二酚和2,7-萘二酚为基本结构单元, 设计合成了2种带有分子内给受体相互作用的大环化合物, 并采用紫外光谱和核磁共振等手段研究了其与葫芦[8]脲的键合行为. 研究结果表明, 在水溶液中大环的2,6-萘二酚和2,7-萘二酚与4,4'-联吡啶鎓之间存在分子内的电荷转移相互作用, 而葫芦[8]脲可以键合这2种大环化合物, 导致电荷转移吸收峰增强并红移, 表明葫芦[8]脲能增强这种分子内的电荷转移相互作用, 形成稳定的环套环分子组装体. 这种结构是基于葫芦[8]脲的新型拓扑结构.     

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.     

Molecular recognition with DNA nanoswitches: effects of single base mutations on structure

This paper investigates the properties of a simple DNA-based nanodevice capable of detecting single base mutations in unlabeled nucleic acid target sequences. Detection is achieved by a two-stage process combining first complementary-base hybridization of a target and then a conformational change as molecular recognition criteria. A probe molecule is constructed from a single DNA strand designed to adopt a partial cruciform structure with a pair of exposed (unhybridized) strands. Upon target binding, a switchable cruciform construct (similar to a Holliday junction) is formed which can adopt open and closed junction conformations. Switching between these forms occurs by junction folding in the presence of divalent ions. It has been shown from the steady-state fluorescence of judiciously labeled constructs that there are differences between the fluorescence resonance energy transfer (FRET) efficiencies of closed forms, dependent on the target sequence near the branch point, where the arms of the cruciform cross. This difference in FRET efficiency is attributed to structural variations between these folded junctions with their different branch point sequences arising from the single base mutations. This provides a robust means for the discrimination of single nucleotide mismatches in a specific region of the target. In this paper, these structural differences are analyzed by fitting observed time-resolved donor fluorescence decay data to a Gaussian distribution of donor-acceptor separations. This shows the closest mean separation (approximately 40 A) for the perfectly matched case, whereas larger separations (up to 50 A) are found for the single point mutations. These differences therefore indicate a structural basis for the observed FRET differences in the closed configuration which underpins the operation of these devices as biosensors capable of resolving single base mutations.     

Synthesis of novel steroid-peptoid hybrid macrocycles by multiple multicomponent macrocyclizations including bifunctional building blocks (MiBs)

Two new groups of cholane-peptoid hybrid macrocycles were produced by implementing novel combinations of the MiB methodology. Steroid-based hybrid macrolactams including heterocycle and aryl moieties were obtained by utilizing cholanic dicarboxylic acids and diamines in a bidirectional double Ugi-Four-Component (Ugi-4CR) based macrocyclization protocol. Alternatively, N-substituted cyclocholamides were produced from a cholanic pseudo-amino acid by an Ugi-4CR-based cyclooligomerization approach. Both types of macrocycles are steroid-peptoid hybrid macrocycles containing exocyclic peptidic chains. These novel frameworks are a result of the use of bile acids bifunctionalized with carboxylic and amino functionalities as bifunctional building blocks of the Ugi-MiB approach.     

Synthesis, structure, and computational studies of soluble conjugated multidentate macrocycles

[Chemical reaction: See text] Conjugated, shape-persistent macrocycles based on [3 + 3] Schiff-base condensation are of interest for supramolecular materials. In an effort to develop new discotic liquid crystals based on these compounds, a series of macrocycles with peripheral alkoxy groups of varying length have been prepared. The synthesis and mechanism of formation have been probed by isolation of oligomeric intermediates. A single-crystal X-ray diffraction study of one macrocycle revealed a nonplanar, strongly hydrogen-bonded structure. To our surprise, even with very long substituents, the macrocycles were not liquid crystalline. This has been rationalized by ab initio calculations that indicate the macrocycles are undergoing rotation of the dihydroxydiiminobenzene rings that may not allow a stable discotic liquid crystalline phase. These results provide new insight into the formation and properties of these large macrocycles and may provide guidance to developing stable liquid crystalline materials in the future.     

Zirconocene-mediated, high-yielding macrocyclizations of silyl-terminated diynes

A series of silyl-terminated diynes of varying lengths and substitution patterns have been prepared. These diynes undergo zirconocene coupling with selective formation of trimeric macrocycles from linear alkynes, while nonlinear diynes give cyclodimeric products. The length of the linear diynes can be increased for the preparation of macrocycles with large nanoscale cavities. Reaction of the zirconium-containing macrocycles with acid results in the synthesis of metal-free cyclophanes. All of these macrocycles were prepared in multigram quantities, in the absence of high-dilution conditions, to give products in > 75% yield that are easily purified as crystalline solids.     

Surface Confined Synthesis of Hydroxy Functionalized Two-Dimensional Polymer: The Effect of the Position of Hydroxy Groups

We report on the on-surface synthesis of a series of two-dimensional polymers (2DPs) and macrocycles containing hydroxyl groups on a highly oriented pyrolytic graphite surface. The formed 2DPs and macrocycles were visualized through scanning tunneling microscopy. By varying the solvent and reaction temperature, structural evolution from oligomers to well-ordered 2DPs or discrete macrocycles was directly followed. In addition, we discovered that the reaction outcome can be steered from extended 2DPs to discrete macrocycles or catenular structures by exchanging the position of the hydroxyl and aldehyde group. These results indicate that the relative positions of hydroxyl and aldehyde groups on the biphenyl ring play a determining role in the control and selection of the final products of the surface-confined Schiff base coupling reaction.     

Macrocyclic Eu3+ chelates show selective luminescence responses to anions

A series of lanthanide-containing macrocycles, Eu2-Eu5, exhibited unique luminescent responses in the presence of strong hydrogen-bond-accepting anions (F-, CH3COO-, and H2PO4-) in dimethyl sulfoxide. The macrocycles examined herein were designed to include a lanthanide chelate, aromatic spacers that function as antennae, thiourea groups as anion-binding units, and an alkyl or aryl linker between the thioureas that tailors the size and rigidity of the macrocycle. The anion-induced change in the emission intensity (lambda(exc) = 272 nm; lambda(em) = 614 nm) varied across the series of macrocycles and was dependent on the basicity of the anion. The largest luminescence response was observed in Eu(2), whereby the emission increased 77% upon the addition of 8 equiv of fluoride. A change in luminescence was not observed when exciting Eu3+ directly (lambda(exc) = 395 nm) over the course of anion titration experiments with all of the anions studied. These macrocycles contain only slight variations in structure, and insights into the mechanism of the anion interaction have been gained through monitoring of anion titrations via luminescence, absorbance, and luminescence lifetime measurements. In addition, model compounds (2-5) lacking the Eu3+ moiety were synthesized to study the binding pockets of Eu2-Eu5 using absorbance and 1H NMR spectroscopy. These studies indicate that the anions interact with the thiourea moiety of Eu2-Eu5, and the luminescent response is controlled by changes in the morphology of the macrocycle binding pocket.     

Synthesis and adsorption of shape-persistent macrocycles containing polycyclic aromatic hydrocarbons in the rigid framework

Shape-persistent macrocycles with interiors in the nanometer regime were prepared by the oxidative cyclization of the appropriate bisacetylene precursors under high-dilution conditions. These compounds contain polycyclic aromatic hydrocarbons in the ring backbone and are decorated with extra annular oligoalkyl or silyl side groups. Interestingly, after depositing them on different surfaces and investigating the self-assembled structures by means of scanning tunneling microscopy (STM) and atomic force microscopy (AFM), various nanostructures were observed. STM showed that these macrocycles are organized in two-dimensional (2D) layers, whereas AFM showed, in addition, the formation of 2D crystallites and one-dimensional fibrils. These results reveal the importance of the extra annular substitution of the macrocycles in creating patterned surfaces and nanoscale objects.     

Synthesis of orthogonally protected cyclic homooligomers from sugar amino acids

Two new families of orthogonally protected cyclic homooligomers with two to four sugar units were synthesized from pyranoid sugar amino acids. Cyclic oligomers composed of amide-linked sugar amino acids (1-3) were prepared by cyclization of linear oligomers of the novel orthogonally protected pyranoid sugar amino acid 12 using a solution-phase coupling method. These orthogonally protected cyclic molecules can be selectively or fully deprotected, affording the macrocycles ready to further functionalization. The straightforward reduction of the amide bonds in the cyclic oligomers 1-3 gave the corresponding amine-linked macrocycles 4-6. This kind of amine-linked carbohydrate-based cyclic oligomer has never been reported before. These flexible molecular receptors could be studied as molecular hosts for molecular, cationic, and anionic recognition. Conformational analysis by molecular modeling (AM1) showed that all of the deprotected cyclic trimers and tetramers preferred a (4)C(1) chair conformation with oxygen atoms of the sugar ring located on the interior of the cavity and the secondary hydroxyl groups outward. In the amide-linked macrocycles, all of the amide bonds are in s-trans conformation. The estimated size of the internal cavity is about 4.5 A for the cyclic trimer and 6.9 A for the cyclic tetramer. The amine-linked macrocycles displayed similar conformational behavior with a slight decrease in internal cavity.     

Smart macrocyclic molecules: induced fit and ultrafast self-sorting inclusion behavior through dynamic covalent chemistry

A family of macrocycles with oligo(ethylene glycol) chains, 4O, 5O, and 6O, was developed to construct a series of new incorporated macrocycles through dynamic covalent chemistry. These flexible macrocycles exhibited excellent "self-sorting" abilities with diamine compounds, which depended on the "induced-fit" rule. For instance, the host macrocycles underwent conformational modulation to accommodate the diamine guests, affording [1+1] intramolecular addition compounds regardless of the flexibility of the diamine. These macrocycles folded themselves to fit various diamines with different chain length through modulation of the flexible polyether chain, and afforded intramolecular condensation products. However, if the chain of the diamine was too long and rigid, oligomers or polymers were obtained from the mixture of the macromolecule and the diamine. All results demonstrated that inclusion compounds involving conformationally suitable aromatic diamines were thermodynamically favorable candidates in the mixture due to the restriction of the macrocycle size. Furthermore, kinetic and thermodynamic studies of self-sorting behaviors of both mixed 4O-5O and 4O-6O systems were investigated in detail. Finally, theoretical calculations were also employed to further understand such self-sorting behavior, and indicated that the large enthalpy change of H(2)NArArNH(2)@4O is the driving force for the sorting behavior. Our system may provide a model to further understand the principle of biomolecules with high specificity due only to their conformational self-adjusting ability.