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.     

Structural Studies Reveal Enantiospecific Recognition of a DNA G‐Quadruplex by a Ruthenium Polypyridyl Complex

By using X‐ray crystallography, we show that the complexes Λ/Δ‐[Ru(TAP)₂(11‐CN‐dppz)]²⁺ (TAP=1,4,5,8‐tetraazaphenanthrene, dppz=dipyridophenazine) bind DNA G‐quadruplex in an enantiospecific manner that parallels the specificity of these complexes with duplex DNA. The Λ complex crystallises with the normally parallel stranded d(TAGGGTTA) tetraplex to give the first such antiparallel strand assembly in which syn‐guanosine is adjacent to the complex at the 5′ end of the quadruplex core. SRCD measurements confirm that the same conformational switch occurs in solution. The Δ enantiomer, by contrast, is present in the structure but stacked at the ends of the assembly. In addition, we report the structure of Λ‐[Ru(phen)₂(11‐CN‐dppz)]²⁺ bound to d(TCGGCGCCGA), a duplex‐forming sequence, and use both structural models to provide insight into the motif‐specific luminescence response of the isostructural phen analogue enantiomers.     

Thermal Stability of Modified i‐Motif Oligonucleotides with Naphthalimide Intercalating Nucleic Acids

In continuation of our investigation of characteristics and thermodynamic properties of the i‐motif 5′‐d[(CCCTAA)₃CCCT)] upon insertion of intercalating nucleotides into the cytosine‐rich oligonucleotide, this article evaluates the stabilities of i‐motif oligonucleotides upon insertion of naphthalimide (1H‐benzo[de]isoquinoline‐1,3(2H)‐dione) as the intercalating nucleic acid. The stabilities of i‐motif structures with inserted naphthalimide intercalating nucleotides were studied using UV melting temperatures (T_m) and circular dichroism spectra at different pH values and conditions (crowding and non‐crowding). This study indicated a positive effect of the naphthalimide intercalating nucleotides on the stabilities of the i‐motif structures compared to the wild‐type structure which is in contrast to a previous observation for a pyrene‐intercalating nucleotide showing a decrease in T_m values.     

Induced‐Fit Recognition of CCG Trinucleotide Repeats by a Nickel–Chromomycin Complex Resulting in Large‐Scale DNA Deformation

Small‐molecule compounds targeting trinucleotide repeats in DNA have considerable potential as therapeutic or diagnostic agents against many neurological diseases. Ni^II(Chro)₂ (Chro=chromomycin A3) binds specifically to the minor groove of (CCG)_n repeats in duplex DNA, with unique fluorescence features that may serve as a probe for disease detection. Crystallographic studies revealed that the specificity originates from the large‐scale spatial rearrangement of the DNA structure, including extrusion of consecutive bases and backbone distortions, with a sharp bending of the duplex accompanied by conformational changes in the Ni^II chelate itself. The DNA deformation of CCG repeats upon binding forms a GGCC tetranucleotide tract, which is recognized by Ni^II(Chro)₂. The extruded cytosine and last guanine nucleotides form water‐mediated hydrogen bonds, which aid in ligand recognition. The recognition can be accounted for by the classic induced‐fit paradigm.     

A Rotaxane‐like Cage‐in‐Ring Structural Motif for a Metallosupramolecular Pd6L12 Aggregate

A BODIPY‐based bis(3‐pyridyl) ligand undergoes self‐assembly upon coordination to tetravalent palladium(II) cations to form a Pd₆L₁₂ metallosupramolecular assembly with an unprecedented structural motif that resembles a rotaxane‐like cage‐in‐ring arrangement. In this assembly the ligand adopts two different conformations—a C‐shaped one to form a Pd₂L₄ cage which is located in the center of a Pd₄L₈ ring consisting of ligands in a W‐shaped conformation. This assembly is not mechanically interlocked in the sense of catenation but it is stabilized only by attractive π‐stacking between the peripheral BODIPY chromophores and the ligands’ skeleton as well as attractive van der Waals interactions between the long alkoxy chains. As a result, the co‐arrangement of the two components leads to a very efficient space filling. The overall structure can be described as a rotaxane‐like assembly with a metallosupramolecular cage forming the axle in a metallosupramolecular ring. This unique structural motif could be characterized via ESI mass spectrometry, NMR spectroscopy, and X‐ray crystallography.     

Hydrogen bonding in polyamino‐polyalcohols: a monohydrated cocrystal of 1,3‐diamino‐5‐azaniumyl‐1,3,5‐trideoxy‐cis‐inositol iodide and 1,3,5‐triamino‐1,3,5‐trideoxy‐cis‐inositol

In the title monohydrated cocrystal, namely 1,3‐diamino‐5‐azaniumyl‐1,3,5‐trideoxy‐cis‐inositol iodide–1,3,5‐triamino‐1,3,5‐trideoxy‐cis‐inositol–water (1/1/1), C₆H₁₆N₃O₃⁺·I⁻·C₆H₁₅N₃O₃·H₂O, the neutral 1,3,5‐triamino‐1,3,5‐trideoxy‐cis‐inositol (taci) molecule and the monoprotonated 1,3‐diamino‐5‐azaniumyl‐1,3,5‐trideoxy‐cis‐inositol cation (Htaci⁺) both adopt a chair conformation, with the three O atoms in axial and the three N atoms in equatorial positions. The cation, but not the neutral taci unit, exhibits intramolecular O—H...O hydrogen bonding. The entire structure is stabilized by a complex three‐dimensional network of intermolecular hydrogen bonds. The neutral taci entities and the Htaci⁺ cations are each aligned into chains along [001]. In these chains, two O—H...N interactions generate a ten‐membered ring as the predominant structural motif. The rings consist of vicinal 2‐amino‐1‐hydroxyethylene units of neighbouring molecules, which are paired via centres of inversion. The chains are interconnected into undulating layers parallel to the ac plane, and the layers are further held together by O—H...N hydrogen bonds and additional interactions with the iodide counter‐anions and solvent water molecules.     

The hydrogen‐bonded complex bis(tert‐butylammonium) 2,6‐dichlorophenolate 2,4‐dichlorophenol–2,4‐dichlorophenolate tetrahydrofuran disolvate containing a chiral R53(10) hydrogen‐bonded ring as a supramolecular synthon

A fixed hydrogen‐bonding motif with a high probability of occurring when appropriate functional groups are involved is described as a `supramolecular hydrogen‐bonding synthon'. The identification of these synthons may enable the prediction of accurate crystal structures. The rare chiral hydrogen‐bonding motif R₅³(10) was observed previously in a cocrystal of 2,4,6‐trichlorophenol, 2,4‐dichlorophenol and dicyclohexylamine. In the title solvated salt, 2C₄H₁₂N⁺·C₆H₃Cl₂O⁻·(C₆H₃Cl₂O⁻·C₆H₄Cl₂O)·2C₄H₈O, five components, namely two tert‐butylammonium cations, one 2,4‐dichlorophenol molecule, one 2,4‐dichlorophenolate anion and one 2,6‐dichlorophenolate anion, are bound by N—H…O and O—H…O hydrogen bonds to form a hydrogen‐bonded ring, with the graph‐set motif R₅³(10), which is further associated with two pendant tetrahydrofuran molecules by N—H…O hydrogen bonds. The hydrogen‐bonded ring has internal symmetry, with a twofold axis running through the centre of the 2,6‐dichlorophenolate anion, and is isostructural with a previous and related structure formed from 2,4‐dichlorophenol, dicyclohexylamine and 2,4,6‐trichlorophenol. In the title crystal, helical columns are built by the alignment and twisting of the chiral hydrogen‐bonded rings, along and across the c axis, and successive pairs of rings are associated with each other through C—H…π interactions. Neighbouring helical columns are inversely related and, therefore, no chirality is sustained, in contrast to the previous case.     

Stabilization of a Bimolecular Triplex by 3′‐S‐Phosphorothiolate Modifications: An NMR and UV Thermal Melting Investigation

Triplexes formed from oligonucleic acids are key to a number of biological processes. They have attracted attention as molecular biology tools and as a result of their relevance in novel therapeutic strategies. The recognition properties of single‐stranded nucleic acids are also relevant in third‐strand binding. Thus, there has been considerable activity in generating such moieties, referred to as triplex forming oligonucleotides (TFOs). Triplexes, composed of Watson–Crick (W–C) base‐paired DNA duplexes and a Hoogsteen base‐paired RNA strand, are reported to be more thermodynamically stable than those in which the third strand is DNA. Consequently, synthetic efforts have been focused on developing TFOs with RNA‐like structural properties. Here, the structural and stability studies of such a TFO, composed of deoxynucleic acids, but with 3′‐S‐phosphorothiolate (3′‐SP) linkages at two sites is described. The modification results in an increase in triplex melting temperature as determined by UV absorption measurements. ¹H NMR analysis and structure generation for the (hairpin) duplex component and the native and modified triplexes revealed that the double helix is not significantly altered by the major groove binding of either TFO. However, the triplex involving the 3′‐SP modifications is more compact. The 3′‐SP modification was previously shown to stabilise G‐quadruplex and i‐motif structures and therefore is now proposed as a generic solution to stabilising multi‐stranded DNA structures.     

N‐(X‐Chlorophenyl)‐4‐hydroxy‐2‐methyl‐2H‐1,2‐benzothiazine‐3‐carboxamide 1,1‐dioxide (with X = 2 and 4)

The structures of N‐(2‐chlorophenyl)‐4‐hydroxy‐2‐methyl‐2H‐1,2‐benzothiazine‐3‐carboxamide 1,1‐dioxide and N‐(4‐chlorophenyl)‐4‐hydroxy‐2‐methyl‐2H‐1,2‐benzothiazine‐3‐carboxamide 1,1‐dioxide, both C₁₆H₁₃ClN₂O₄S, are stabilized by extensive intramolecular hydrogen bonds. The 4‐chloro derivative forms dimeric pairs of molecules lying about inversion centres as a result of intermolecular N—H...O hydrogen bonds, forming 14‐membered rings representing an R₂²(14) motif; the 2‐chloro derivative is devoid of any such intermolecular hydrogen bonds. The heterocyclic thiazine rings in both structures adopt half‐chair conformations.     

Heterotapes: A Persistent,Dual‐Synthon Hydrogen‐Bonding Motif

The small dinitrile anion carbamoyldicyanomethanide, [C(CN)₂‐(CONH₂)]^? (cdm), reproducibly forms a hydrogen‐bonded tape containing two different supramolecular synthons: a “heterotape”. The tape incorporates both an amide dimer and a nitrile‐containing ring. The robustness of the motif is confirmed by its persistence from an isolated tape in a separated ion‐pair structure, [K(15c5)₂](cdm)? H₂O, to its incorporation into coordination complexes of octahedral metals, thus facilitating the formation of 2D sheets. Complexes containing coligands that occupy the equatorial coordination sites, [Cu(2,2′‐py₂NH)₂(cdm)₂]? 2MeOH, [Ni(cyclam)(cdm)₂], and [Cu(cyclam)(cdm)₂]?2MeOH (cyclam=1,4,8,11‐tetraazacyclotetradecane, 2,2′‐py₂NH=di(2‐pyridyl)amine), show retention of the heterotape motif, whilst the ethylene diamine complex [Cu‐(en)₂(cdm)₂] (en=ethylene diamine) displays an alternative hydrogen‐bonding motif due to interference from the diamine ligands.     

Two new isatin derivatives: 1‐benzyl‐4,5,6‐trimethoxyindoline‐2,3‐dione and 1‐benzyl‐5‐fluoroindoline‐2,3‐dione

Isatin (1H‐indole‐2,3‐dione) derivatives represent synthetically useful substrates which can be used to prepare a broad range of heterocyclic compounds. In the title compounds, C₁₈H₁₇NO₅, (I), and C₁₅H₁₀FNO₂, (II), the isatin ring systems are planar and form a dihedral angle of 73.04 (7)° in (I) and 76.82 (11)° in (II) with the benzyl groups. The bicyclic scaffolds in both compounds are almost superimposable, with an r.m.s. deviation of 0.061 Å. The crystal structures of both derivatives are stabilized by C—H...O interactions. These contacts generate an R¹₂(7) ring motif in (I) and a C(7) chain motif in (II).     

Structural Principles for Anion‐Deficient,Fluorite‐Related Superstructures in the Zirconia‐Scandia System

The concept of the coordination defect (CD) was used recently by Bevan and Martin [6] to describe the fluorite‐related superstructures of the intermediate Pr/Tb oxides. The CD is an octahedron of corner‐shared OM_4/8 tetrahedra enclosing a □M_4/8 tetrahedron, where □ represents an oxygen vacancy. Various linkages of CDs can define a polyhedral prism with contents appropriate to the phase composition, and this is designated the “structural motif”. The identical, parallel top and bottom planes of this prism are the “motif plane”. This concept is now extended to explore the structures of the ordered phases, delta, gamma and beta, which occur in the zirconia‐scandia system, the respective formulae being Zr₃Sc₄O₁₂, Zr₁₀Sc₄O₂₆ and Zr₄₈Sc₁₄O₁₁₇ to Zr₅₀Sc₁₂O₁₁₈. It is shown that the motif plane is the same in each of the known structures (delta and gamma), thus defining the close relationship between them. Possible models for the as‐yet unknown structure of the beta phase, in which this same motif plane occurs, can then be proposed.     

Synthesis,Structure, and Properties of SrC(NH)3, a Nitrogen‐Based Carbonate Analogue with the Trinacria Motif

Strontium guanidinate, SrC(NH)₃, the first compound with a doubly deprotonated guanidine unit, was synthesized from strontium and guanidine in liquid ammonia and characterized by X‐ray and neutron diffraction, IR spectroscopy, and density‐functional theory including harmonic phonon calculations. The compound crystallizes in the hexagonal space group P6₃/m, constitutes the nitrogen analogue of strontium carbonate, SrCO₃, and its structure follows a layered motif between Sr²⁺ ions and complex anions of the type C(NH)₃^2?; the anions adopt the peculiar trinacria shape. A comparison of theoretical phonons with experimental IR bands as well as quantum‐chemical bonding analyses yield a first insight into bonding and packing of the formerly unknown anion in the crystal.     

Polymorphism of methyl 4‐amino‐3‐phenylisothiazole‐5‐carboxylate: an experimental and theoretical study

Being a close analogue of amflutizole, methyl 4‐amino‐3‐phenylisothiazole‐5‐carboxylate (C₁₁H₁₀N₂O₂S) was assumed to be capable of forming polymorphic structures. Noncentrosymmetric and centrosymmetric polymorphs have been obtained by crystallization from a series of more volatile solvents and from denser tetrachloromethane, respectively. Identical conformations of the molecule are found in both structures. The two polymorphs differ mainly in the intermolecular interactions formed by the amino group and in the type of stacking interactions between the π‐systems. The most effective method for revealing packing motifs in structures with intermolecular interactions of different types (hydrogen bonding, stacking, dispersion, etc.) is to study the pairwise interaction energies using quantum chemical calculations. Molecules form a column as the primary basic structural motif due to stacking interactions in both polymorphic structures under study. The character of a column (straight or zigzag) is determined by the orientations of the stacked molecules (in a `head‐to‐head' or `head‐to‐tail' manner). Columns bound by intermolecular N—H…O and N—H…N hydrogen bonds form a double column as the main structural motif in the noncentrosymmetric structure. Double columns in the noncentrosymmetric structure and columns in the centrosymmetric structure interact strongly within the ab crystallographic plane, forming a layer as a secondary basic structural motif. The noncentrosymmetric structure has a lower density and a lower (by 0.59 kJ mol^?1) lattice energy, calculated using periodic calculations, compared to the centrosymmetric structure.     

Cationic Pentaheteroaryls as Selective G‐Quadruplex Ligands by Solvent‐Free Microwave‐Assisted Synthesis

We report herein a solvent‐free and microwaved‐assisted synthesis of several water soluble acyclic pentaheteroaryls containing 1,2,4‐oxadiazole moieties ( 1 – 7 ). Their binding interactions with DNA quadruplex structures were thoroughly investigated by FRET melting, fluorescent intercalator displacement assay (G4‐FID) and CD spectroscopy. Among the G‐quadruplexes considered, attention was focused on telomeric repeats together with the proto‐oncogenic c‐kit sequences and the c‐myc oncogene promoter. Compound 1 , and to a lesser extent 2 and 5 , preferentially stabilise an antiparallel structure of the telomeric DNA motif, and exhibit an opposite binding behaviour to structurally related polyoxazole ( TOxaPy ), and do not bind duplex DNA. The efficiency and selectivity of the binding process was remarkably controlled by the structure of the solubilising moieties.     

Triplet Acceptors with a D‐A Structure and Twisted Conformation for Efficient Organic Solar Cells

Triplet acceptors have been developed to construct high‐performance organic solar cells (OSCs) as the long lifetime and diffusion range of triplet excitons may dissociate into free charges instead of net recombination when the energy levels of the lowest triplet state (T₁) are close to those of charge‐transfer states (³CT). The current triplet acceptors were designed by introducing heavy atoms to enhance the intersystem crossing, limiting their applications. Herein, two twisted acceptors without heavy atoms, analogues of Y6, constructed with large π‐conjugated core and D‐A structure, were confirmed to be triplet materials, leading to high‐performance OSCs. The mechanism of triplet excitons were investigated to show that the twisted and D‐A structures result in large spin–orbit coupling (SOC) and small energy gap between the singlet and triplet states, and thus efficient intersystem crossing. Moreover, the energy level of T₁ is close to ³CT, facilitating the split of triplet exciton to free charges.     

An Unprecedented Knot‐like G‐Quadruplex Peripheral Motif

A knot‐like G‐quadruplex peripheral structure is formed by a 7‐nt DNA sequence DL7 (TGTTGGT), in which six out of its seven nucleobases participate in compact base‐pairing interactions. Here, the solution NMR structure of a 24‐nt DNA oligonucleotide containing the DL7 sequence shows the interaction between a two‐layer anti‐parallel G‐quadruplex core and the peripheral knot‐like structure, including the construction of two sharp turns in the DNA backbone. The formation of this novel structural element highlights the intricate properties of single‐stranded DNA folding in presence of G‐quadruplex‐forming motifs. We demonstrated the compatibility of the DL7 knot‐like structure with various G‐quadruplexes, which could have implications in drug design and DNA engineering.     

Structure‐Based Design of Platinum(II) Complexes as c‐myc Oncogene Down‐Regulators and Luminescent Probes for G‐Quadruplex DNA

A series of platinum(II) complexes with tridentate ligands was synthesized and their interactions with G‐quadruplex DNA within the c‐myc gene promoter were evaluated. Complex 1 , which has a flat planar 2,6‐bis(benzimidazol‐2‐yl)pyridine (bzimpy) scaffold, was found to stabilize the c‐myc G‐quadruplex structure in a cell‐free system. An in silico G‐quadruplex DNA model has been constructed for structure‐based virtual screening to develop new Pt^II‐based complexes with superior inhibitory activities. By using complex 1 as the initial structure for hit‐to‐lead optimization, bzimpy and related 2,6‐bis(pyrazol‐3‐yl)pyridine (dPzPy) scaffolds containing amine side‐chains emerge as the top candidates. Six of the top‐scoring complexes were synthesized and their interactions with c‐myc G‐quadruplex DNA have been investigated. The results revealed that all of the complexes have the ability to stabilize the c‐myc G‐quadruplex. Complex 3 a ([Pt^II L2R ] ⁺ ; L2 =2,6‐bis[1‐(3‐piperidinepropyl)‐1H‐enzo[d]imidazol‐2‐yl]pyridine, R =Cl) displayed the strongest inhibition in a cell‐free system (IC₅₀=2.2 μM ) and was 3.3‐fold more potent than that of 1 . Complexes 3 a and 4 a ([Pt^II L3R ]⁺; L3 =2,6‐bis[1‐(3‐morpholinopropyl)‐1H‐pyrazol‐3‐yl]pyridine, R =Cl) were found to effectively inhibit c‐myc gene expression in human hepatocarcinoma cells with IC₅₀ values of ≈17 μM , whereas initial hit 1 displayed no significant effect on gene expression at concentrations up to 50 μM . Complexes 3 a and 4 a have a strong preference for G‐quadruplex DNA over duplex DNA, as revealed by competition dialysis experiments and absorption titration; 3 a and 4 a bind G‐quadruplex DNA with binding constants (K) of approximately 10⁶–10⁷ dm³ mol^?1, which are at least an order of magnitude higher than the K values for duplex DNA. NMR spectroscopic titration experiments and molecular modeling showed that 4 a binds c‐myc G‐quadruplex DNA through an external end‐stacking mode at the 3′‐terminal face of the G‐quadruplex. Intriguingly, binding of c‐myc G‐quadruplex DNA by 3 b is accompanied by an increase of up to 38‐fold in photoluminescence intensity at λ_max=622 nm.     

Two Histidines in an α‐Helix: A Rigid Co2+‐Binding Motif for PCS Measurements by NMR Spectroscopy

Pseudocontact shifts (PCS) generated by paramagnetic metal ions present valuable long‐range information in the study of protein structural biology by nuclear magnetic resonance (NMR) spectroscopy. Faithful interpretation of PCSs, however, requires complete immobilization of the metal ion relative to the protein, which is difficult to achieve with synthetic metal tags. We show that two histidine residues in sequential turns of an α‐helix provide a binding site for a Co²⁺ ion, which positions the metal ion in a uniquely well‐defined and predictable location. Exchange between the bound and free cobalt is slow on the timescale defined by chemical shifts, but the NMR resonance assignments are nonetheless readily transferred from the diamagnetic to the paramagnetic NMR spectrum by an I_zS_z‐exchange experiment. The double‐histidine‐Co²⁺ motif offers a straightforward, inexpensive, and convenient way of generating precision PCSs in proteins.