Programmable cleavage of linear double-stranded DNA by combined action of Argonaute CbAgo from Clostridium butyricum and nuclease deficient RecBC helicase from E. coli.

Prokaryotic Argonautes (pAgos) use small nucleic acids as specificity guides to cleave single-stranded DNA at complementary sequences. DNA targeting function of pAgos creates attractive opportunities for DNA manipulations that require programmable DNA cleavage. Currently, the use of mesophilic pAgos as programmable endonucleases is hampered by their limited action on double-stranded DNA (dsDNA). We demonstrate here that efficient cleavage of linear dsDNA by mesophilic Argonaute CbAgo from Clostridium butyricum can be activated in vitro via the DNA strand unwinding activity of nuclease deficient mutant of RecBC DNA helicase from Escherichia coli (referred to as RecBexo-C). Properties of CbAgo and characteristics of simultaneous cleavage of DNA strands in concurrence with DNA strand unwinding by RecBexo-C were thoroughly explored using 0.03-25 kb dsDNAs. When combined with RecBexo-C, CbAgo could cleave targets located 11-12.5 kb from the ends of linear dsDNA at 37°C. Our study demonstrates that CbAgo with RecBexo-C can be programmed to generate DNA fragments with custom-designed single-stranded overhangs suitable for ligation with compatible DNA fragments. The combination of CbAgo and RecBexo-C represents the most efficient mesophilic DNA-guided DNA-cleaving programmable endonuclease for in vitro use in diagnostic and synthetic biology methods that require sequence-specific nicking/cleavage of linear dsDNA at any desired location.

Utilizing "Latent" Carbon: Repositioning Hydrogen-Bonded Synthons and Assemblies via Halogen Bonding to π-Systems.

Molecules bearing carboxylic acid, amide, and hydroxyl groups are ubiquitous in crystal engineering, where robust hydrogen-bonded synthons centred on these functionalities enable reliable crystal structure design. We now show that halogen bonding to the carbon π-system of such molecules, traditionally ignored in crystal engineering, permits the recognition and directional assembly of the resulting hydrogen-bonded structural subunits, leaving the archetypal hydrogen-bonded ring, ladder, and chain homosynthons intact, but repositioned in space. When applied to heteromolecular synthons, this enables rearranging more complex hydrogen-bonded motifs and the evolution of binary cocrystals into ternary ones through "latent" carbon-based recognition sites, demonstrating a rational approach to build higher-order solid-state supramolecular assemblies.

Three-in-One: Dye-Volatile Cocrystals Exhibiting Intensity-Dependent Photochromic, Photomechanical, and Photocarving Response.

Cocrystallization of a cis-azobenzene dye with volatile molecules, such as pyrazine and dioxane, leads to materials that exhibit at least three different light-intensity-dependent responses upon irradiation with low-power visible light. The halogen-bond-driven assembly of the dye cis-(p-iodoperfluorophenyl)azobenzene with volatile halogen bond acceptors produces cocrystals whose light-induced behavior varies significantly depending on the intensity of the light applied. Low-intensity (<1 mW·cm-2) light irradiation leads to a color change associated with low levels of cis → trans isomerization. Irradiation at higher intensities (150 mW·mm-2) produces photomechanical bending, caused by more extensive isomerization of the dye. At still higher irradiation intensities (2.25 W·mm-2) the cocrystals undergo cold photocarving; i.e., they can be cut and written on with micrometer precision using laser light without a major thermal effect. Real-time Raman spectroscopy shows that this novel photochemical behavior differs from what would be expected from thermal energy input alone. Overall, this work introduces a rational blueprint, based on supramolecular chemistry in the solid state, for new types of crystalline light-responsive materials, which not only respond to being exposed to light but also change their response based on the light intensity.

Polymorphs and solid solutions: materials with new luminescent properties obtained through mechanochemical transformation of dicyanoaurate(I) salts.

We report the use of mechano- and thermochemical methods to create new solid-state luminescent materials from well-known inorganic salts, potassium dicyanoaurate(I) KAu(CN)2, and potassium dicyanocuprate(I) KCu(CN)2. In particular, manual grinding or ball milling of commercial samples of KAu(CN)2 led to the formation of a novel polymorph of the salt, herein termed m-KAu(CN)2, evident by a significant change in color of the fluorescence emission of the solid material from orange to violet. The formation of m-KAu(CN)2 is reversible upon addition of small amounts of solvents, and powder X-ray diffraction analysis indicates that the structure of m-KAu(CN)2 might be related to that of pristine KAu(CN)2 through a change in ordering of Au(CN)2- ions in a layered structure. Thermal treatment of KAu(CN)2 led to the discovery of another polymorph of this well-known salt, herein termed t-KAu(CN)2, making KAu(CN)2 a rare example of a system in which thermochemical and mechanochemical treatments lead to the formation of different, in each case previously not reported, polymorphic forms. The thermally-induced transformation from KAu(CN)2 to t-KAu(CN)2 takes place around 250 °C and proceeds in a crystal-to-crystal fashion, which enabled the preliminary structural characterisation through single crystal X-ray diffraction, revealing the retention of the layered structure and a change in ordering of Au(CN)2- ions. Milling of the simple salt KAu(CN)2 in the presence of equimolar amounts or less of its copper(I)-based analogue coordination polymer KCu(CN)2 leads to the formation of a series of solid solution materials, isostructural to m-KAu(CN)2 and with visible fluorescence emission distinct from KCu(CN)2 or any herein investigated forms of KAu(CN)2.

The "η-sweet-spot" (ηmax) in liquid-assisted mechanochemistry: polymorph control and the role of a liquid additive as either a catalyst or an inhibitor in resonant acoustic mixing (RAM).

Resonant acoustic mixing (RAM) offers a simple, efficient route for mechanochemical synthesis in the absence of milling media or bulk solvents. Here, we show the use of RAM to conduct the copper-catalysed coupling of sulfonamides and carbodiimides. This coupling was previously reported to take place only by mechanochemical ball milling, while in conventional solution environments it is not efficient, or does not take place at all. The results demonstrate RAM as a suitable methodology to conduct reactions previously accessed only by ball milling and provide a detailed, systematic overview of how the amount of liquid additive, measured by the ratio of liquid volume to weight of reactants (η, in µL mg-1), can affect the course of a mechanochemical reaction and the polymorphic composition of its product. Switching from ball milling to RAM allowed for the discovery of a new polymorph of the model sulfonylguanidine obtained by catalytic coupling of di(cyclohexyl)carbodiimide (DCC) and p-toluenesulfonamide, and the ability to control reaction temperature in RAM enabled in situ control of the polymorphic behaviour of this nascent product. We show that the reaction conversion for a given reaction time does not change monotonically but, instead, achieves a maximum for a well-defined η-value. This "η-sweet-spot" of conversion is herein designated ηmax. The herein explored reactions demonstrate sensitivity to η on the order of 0.01 µL mg-1, which corresponds to an amount of liquid additive below 5 mol% compared to the reactants, and is at least one to two orders of magnitude lower than the η-value typically considered in the design of liquid-assisted ball milling mechanochemical reactions. Such sensitivity suggests that strategies to optimise liquid-assisted mechanochemical reactions should systematically evaluate η-values at increments of 0.01 µL mg-1, or even finer. At η-values other than ηmax the reaction conversion drops off, demonstrating that the same liquid additive can act either as a catalyst or an inhibitor of a mechanochemical reaction, depending on the amount.

Halogen bonding with carbon: directional assembly of non-derivatised aromatic carbon systems into robust supramolecular ladder architectures.

Carbon, although the central element in organic chemistry, has been traditionally neglected as a target for directional supramolecular interactions. The design of supramolecular structures involving carbon-rich molecules, such as arene hydrocarbons, has been limited almost exclusively to non-directional π-stacking, or derivatisation with heteroatoms to introduce molecular assembly recognition sites. As a result, the predictable assembly of non-derivatised, carbon-only π-systems using directional non-covalent interactions remains an unsolved fundamental challenge of solid-state supramolecular chemistry. Here, we propose and validate a different paradigm for the reliable assembly of carbon-only aromatic systems into predictable supramolecular architectures: not through non-directional π-stacking, but via specific and directional halogen bonding. We present a systematic experimental, theoretical and database study of halogen bonds to carbon-only π-systems (C-I⋯πC bonds), focusing on the synthesis and structural analysis of cocrystals with diversely-sized and -shaped non-derivatised arenes, from one-ring (benzene) to 15-ring (dicoronylene) polycyclic atomatic hydrocarbons (PAHs), and fullerene C60, along with theoretical calculations and a systematic analysis of the Cambridge Structural Database. This study establishes C-I⋯πC bonds as directional interactions to arrange planar and curved carbon-only aromatic systems into predictable supramolecular motifs. In >90% of herein presented structures, the C-I⋯πC bonds to PAHs lead to a general ladder motif, in which the arenes act as the rungs and halogen bond donors as the rails, establishing a unique example of a supramolecular synthon based on carbon-only molecules. Besides fundamental importance in the solid-state and supramolecular chemistry of arenes, this synthon enables access to materials with exciting properties based on simple, non-derivatised aromatic systems, as seen from large red and blue shifts in solid-state luminescence and room-temperature phosphorescence upon cocrystallisation.

Halogen bonding to the azulene π-system: cocrystal design of pleochroism.

We describe the rational development of a design for pleochroic molecular solids, by using C-Iπ halogen bonds to pre-organise different chromophores in a cocrystal. Using the structure of a known naphthalene cocrystal as a blueprint, we demonstrate how a highly robust C-Iπ motif permits the systematic exchange of original cocrystal components with azobenzene and azulene, resulting in optically interesting dichroic or pleochroic materials.