Design and DNA binding of an extended triple-stranded metallo-supramolecular cylinder

A new tetracationic triple-stranded supramolecular cylinder is prepared from a bis(pyridylimine) ligand containing a diphenylmethane and two ketimine groups in the spacer. The cylinder is longer and slightly wider than the corresponding cylinder containing just diphenylmethane spacers. Inter-strand CH...pi interactions are not observed and this affects the relay of the chiral information within the cylinder; a mixture of rac and meso isomers results, with the meso isomer being the dominant solution species and characterised in the solid state by crystallography. This new cylinder does bind to DNA as confirmed by induced circular dichroism signals in both the metal-to-ligand charge transfer (MLCT) and in-ligand bands of the cylinder. Flow linear dichroism demonstrates that the cylinder binds to DNA in a specific orientation(s) and is consistent with (major) groove-binding as seen for the shorter cylinder. Some DNA bending/coiling is observed but the effect is much less dramatic than observed for the cylinder with diphenylmethane spacers confirming that coiling is not solely a consequence of the tetracationic charge, but rather is related to the precise size and shape of the cylinder.     

Centromeric Alpha‐Satellite DNA Adopts Dimeric i‐Motif Structures Capped by AT Hoogsteen Base Pairs

Human centromeric alpha‐satellite DNA is composed of tandem arrays of two types of 171 bp monomers; type A and type B. The differences between these types are concentrated in a 17 bp region of the monomer called the A/B box. Here, we have determined the solution structure of the C‐rich strand of the two main variants of the human alpha‐satellite A box. We show that, under acidic conditions, the C‐rich strands of two A boxes self‐recognize and form a head‐to‐tail dimeric i‐motif stabilized by four intercalated hemi‐protonated C:C⁺ base pairs. Interestingly, the stack of C:C⁺ base pairs is capped by T:T and Hoogsteen A:T base pairs. The two main variants of the A box adopt a similar three‐dimensional structure, although the residues involved in the formation of the i‐motif core are different in each case. Together with previous studies showing that the B box (known as the CENP‐B box) also forms dimeric i‐motif structures, our finding of this non‐canonical structure in the A box shows that centromeric alpha satellites in all human chromosomes are able to form i‐motifs, which consequently raises the possibility that these structures may play a role in the structural organization of the centromere.     

A Halogen‐Bond‐Induced Triple Helicate Encapsulates Iodide

The self‐assembly of higher‐order anion helicates in solution remains an elusive goal. Herein, we present the first triple helicate to encapsulate iodide in organic and aqueous media as well as the solid state. The triple helicate self‐assembles from three tricationic arylethynyl strands and resembles a tubular anion channel lined with nine halogen bond donors. Eight strong iodine???iodide halogen bonds and numerous buried π‐surfaces endow the triplex with remarkable stability, even at elevated temperatures. We suggest that the natural rise of a single‐strand helix renders its linear halogen‐bond donors non‐convergent. Thus, the stringent linearity of halogen bonding is a powerful tool for the synthesis of multi‐strand anion helicates.     

Bifacial Base‐Pairing Behaviors of 5‐Hydroxyuracil DNA Bases through Hydrogen Bonding and Metal Coordination

A novel bifacial ligand‐bearing nucleobase, 5‐hydroxyuracil ( U^OH ), which forms both a hydrogen‐bonded base pair ( U^OH –A) and a metal‐mediated base pair ( U^OH –M– U^OH ) has been developed. The U^OH –M– U^OH base pairs were quantitatively formed in the presence of lanthanide ions such as Gd^III when U^OH – U^OH pairs were consecutively incorporated into DNA duplexes. This result established metal‐assisted duplex stabilization as well as DNA‐templated assembly of lanthanide ions. Notably, a duplex possessing U^OH –A base pairs was destabilized by addition of Gd^III ions. This observation suggests that the hybridization behaviors of the U^OH ‐containing DNA strands are altered by metal complexation. Thus, the U^OH nucleobase with a bifacial base‐pairing property holds great promise as a component for metal‐responsive DNA materials.     

Catalytic Hairpin Assembly‐Programmed DNA Three‐Way Junction for Enzyme‐Free and Amplified Electrochemical Detection of Target DNA

DNA three‐way junctions (DNA 3WJ) have been widely used as important building blocks for the construction of DNA architectures and dynamic assemblies. Herein, we describe for the first time a catalytic hairpin assembly‐programmed DNA three‐way junction (CHA‐3WJ) strategy for the enzyme‐free and amplified electrochemical detection of target DNA. It takes full advantage of the target‐catalyzed hairpin assembly‐induced proximity effect of toehold and branch‐migration domains for the ingenious execution of the strand displacement reaction to form the DNA 3WJ on the electrode surface. A low detection limit of 0.5 pM with an excellent selectivity was achieved for target DNA detection. The developed CHA‐3WJ strategy also offers distinct advantages of simplicity in probe design and biosensor fabrication, as well as enzyme‐free operation. Thus, it opens a promising avenue for applications in bioanalysis, design of DNA‐responsive devices, and dynamic DNA assemblies.     

Duplex‐Selective Ruthenium‐Based DNA Intercalators

We report the design and synthesis of small molecules that exhibit enhanced luminescence in the presence of duplex rather than single‐stranded DNA. The local environment presented by a well‐known [Ru(dipyrido[3,2‐a:2′,3′‐c]phenazine)L₂]²⁺‐based DNA intercalator was modified by functionalizing the bipyridine ligands with esters and carboxylic acids. By systematically varying the number and charge of the pendant groups, it was determined that decreasing the electrostatic interaction between the intercalator and the anionic DNA backbone reduced single‐strand interactions and translated to better duplex specificity. In studying this class of complexes, a single Ru^II complex emerged that selectively luminesces in the presence of duplex DNA with little to no background from interacting with single‐stranded DNA. This complex shows promise as a new dye capable of selectively staining double‐ versus single‐stranded DNA in gel electrophoresis, which cannot be done with conventional SYBR dyes.     

Rapid Formation of a Supramolecular Polypeptide–DNA Hydrogel for In Situ Three‐Dimensional Multilayer Bioprinting

A rapidly formed supramolecular polypeptide–DNA hydrogel was prepared and used for in situ multilayer three‐dimensional bioprinting for the first time. By alternative deposition of two complementary bio‐inks, designed structures can be printed. Based on their healing properties and high mechanical strengths, the printed structures are geometrically uniform without boundaries and can keep their shapes up to the millimeter scale without collapse. 3D cell printing was demonstrated to fabricate live‐cell‐containing structures with normal cellular functions. Together with the unique properties of biocompatibility, permeability, and biodegradability, the hydrogel becomes an ideal biomaterial for 3D bioprinting to produce designable 3D constructs for applications in tissue engineering.     

Self‐assembly and Cycling of a Three‐state PdxLy Metallosupramolecular System

The use of stimuli to induce reversible structural transformations in metallosupramolecular systems is of keen interest to chemists seeking to mimic the way that Nature effects conformational changes in biological machinery. While a wide array of stimuli have been deployed towards this end, stoichiometric changes have only been explored in a handful of examples. Furthermore, switching has generally been between only two distinct states. Here we use a simple 2‐(1‐(pyridine‐4‐methyl)‐1H‐1,2,3‐triazol‐4‐yl)pyridine “click” ligand in combination with Pd^II in various stoichiometries and concentrations to quantitatively access and cycle between three distinct species: a [PdL₂]²⁺ monomer, a [Pd₂L₂]⁴⁺ dimer, and a [Pd₉L₁₂]¹⁸⁺ cage.     

Kinetic Control in the Chiral Recognition of Three‐Bladed Propellers

The ion pair of the stereolabile C₃‐symmetric, i⁺o proton complex [ 1? H]⁺ of diaza‐macropentacycle 1 and the configurationally stable Δ‐TRISPHAT ([Δ‐ 3 ]^?) anion exists in the form of two diastereomers, namely, [Δ‐( 1? H)][Δ‐ 3 ] and [Λ‐( 1? H)][Δ‐ 3 ], the ratio of which, in terms of diastereomeric excess (de) decreases in the order [D₈]THF (28 %)>CD₂Cl₂ (22 %)>CDCl₃ (20 %)>[D₈]toluene (16 %)>C₆D₆ (7 %)>[D₆]acetone (0 %) at thermodynamic equilibrium. Except in the case of [D₆]acetone, the latter is reached after a period of time that increases from 1 h ([D₈]THF) to 24 h (CDCl₃). Moreover, the initial value of the de of [ 1? H][Δ‐ 3 ] in CDCl₃, before the thermodynamic equilibrium is reached, depends on the solvent in which the sample has been previously equilibrated (sample “history”). This property has been used to show that the crystals of [ 1? H][Δ‐ 3 ] formed by slow evaporation of CH₂Cl₂/CH₃OH mixtures had 100 % de, which indicates that [ 1? H][Δ‐ 3 ] has enjoyed a crystallization‐induced asymmetric transformation. Structural studies in solution (NMR spectroscopy) and in the gas phase by calculations at the semiempirical PM6 level of theory suggest that the optically active anion is docked on the i⁺ (endo) external side of the proton complex such that one of the aromatic rings of [Δ‐ 3 ]^? is inserted into a groove of [ 1? H]⁺, a second aromatic ring being placed astride the outside i⁺ pocket. Solvent polarity controls the thermodynamics of inversion of the [ 1? H]⁺ propeller. However, both polarity and basicity control its kinetics. Therefore, the rate‐limiting steps correspond to the ion‐pair separation/recombination and [ 1? H]⁺/ 1 deprotonation/protonation processes, rather than the inversion of [ 1? H]⁺, the latter being likely to take place in the deprotonated form ( 1 ).     

Self‐Assembly of a Four‐Helix Bundle on a DNA Quadruplex

Come together : A novel method for assembling monomers and controlling structure of a de novo helix bundle protein is described. A guanine (G)‐rich oligodeoxynucleotide scaffold forms a hydrogen‐bonded DNA quadruplex in the presence of potassium counterions, thereby inducing a helical structure and fourfold stoichiometry in conjugated, amphiphilic peptide sequences. The DNA scaffold shows potential for rapidly assembling designed proteins.