Synthesis of labeled oligonucleotides through a new chemically cleavable linker

A synthesis of labeled oligonucleotides incorporating a new chemically cleavable linker (III) via a two-step method is described. The labeled oligomers obtained after cleavage and deprotection reactions [treatment with anhydrous tert-butylamine and dry methanol, 1:1 (v/v) for 12 h at room temperature, and lyophilization followed by subsequent reaction with aq NH₄OH and methylamine (40%), 1:1 (v/v) for 5 min at 65 °C] were analyzed by RP-HPLC. A distinctive feature of this protocol is that free oligomers can be recovered from their labeled analogs under mild conditions (0.2 M NaOH containing 0.5 M NaCl over 30 min at room temperature) and are comparable to the corresponding standard oligonucleotides (HPLC).     

Coordination driven self-assembly of four new molecular boats using a flexible imidazole-containing donor linker

Using a metal-ligand coordination bonding approach, the self-assembly of four new metallamacrocycles from Pd(ii)-based 90 degrees acceptors and a diimidazole donor ligand 1,3-bis(imidazole-1-ylmethyl)-2,4,6-trimethylbenzene (L) has been achieved. The assemblies are characterized fully by NMR and electrospray ionization-mass spectroscopic (ESI-MS) analysis and in two cases the X-ray single-crystal structure analysis established the gross structures. The selective formation of a diimidazole-based linker (L) containing macrocycle [(en)Pd(micro-L)2Pd(en)]4+ from a 1 : 1 : 1 mixture of cis-Pd(en)(NO3)2, and 1,2-bis(4-pyridyl)ethane is also established. Measuring the binding constants established the stronger Pd- binding force compared to traditional Pd-N(pyridyl linker) interaction, which reveals the possibility of using imidazole donor ligands as potential linkers or even better ligands compared to the widely used pyridyl donor ligands in the construction of metal-based large supramolecular assemblies.     

A novel linker for solid-phase synthesis cleavable under neutral conditions

A novel linker cleavable under neutral conditions has been developed for the solid-phase synthesis of base-labile compounds. The linker is comprised of a 3-azidomethyl-4-hydroxybenzyl alcohol moiety, and the azidomethyl group in the linker is readily converted to an aminomethyl group by treatment with a phosphine reagent in the presence of water to result in an intramolecular cyclization to release the compounds. Using the linker, a base-labile dinucleoside methyl phosphate was synthesized on a highly cross-linked polystyrene (HCP) support and cleaved successfully from the resin without decomposition of the product.     

A cleavable amino-thiol linker for reversible linking of amines to DNA

A cleavable heterobifunctional cross-linker for the reversible conjugation of amines to thiol-modified DNA has been developed and tested. The succinimidyl 2-(vinylsulfonyl)ethyl carbonate (SVEC) was prepared in three steps and tested for its ability to react with amines and thiols. The linker was efficient for binding leucine to a thiol-modified DNA sequence and for releasing the amino acid at pH 11.8.     

Reversible aggregation/deaggregation of gold nanoparticles induced by a cleavable dithiol linker

Aqueous solutions of Au colloids (12 +/- 4 nm size) when treated with a blend of mono- and dithiols aggregate forming stable clusters, as evidenced by the shift of their surface plasmon (SP) band from 512 to ca. 600 nm. The presence of carboxylate ester functions on the dithiol allows its cleavage by addition of a cleaving agent, such as hydrazine. The cleavage process results in the breaking down of the clusters of nanoparticles and the shift of the SP band back to lower wavelengths. Further addition of dithiol causes the formation of the clusters again. The aggregation/deaggregation process may be monitored visually by following the color change from pink-red to purple and vice versa in the forward and backward steps, respectively.     

A cleavable linker strategy for optimising enolate alkylation reactions of a polymer-supported Evans' oxazolidin-2-one

A cleavable linker strategy has been used to optimise the enolate alkylation reactions of a recyclable L-tyrosine derived polymer-supported oxazolidin-2-one for the asymmetric synthesis of a series of chiral alpha-alkyl acids.     

Traceless parallel peptide purification by a first-in-class reductively cleavable linker system featuring a safety-release

Hundreds of peptides can be synthesized by automated parallel synthesizers in a single run. In contrast, the most widely used peptide purification method – high-pressure liquid chromatography (HPLC) – only allows one-by-one processing of each sample. The chromatographic purification of many peptides, therefore, remains a time-consuming and costly effort. Catch-and-release methods can be processed in parallel and potentially provide a remedy. However, no such system has yet provided a true alternative to HPLC. Herein we present the development of a side-reaction free, reductively cleavable linker. The linker is added to the target peptide as the last building block during peptide synthesis. After acidic cleavage from synthetic resin, the linker-tagged full-length peptide is caught onto an aldehyde-modified solid support by rapid oxime ligation, allowing removal of all impurities lacking the linker by washing. Reducing the aryl azide to an aniline sensitizes the linker for cleavage. However, scission does not occur at non-acidic pH enabling wash out of reducing agent. Final acidic treatment safely liberates the peptide by an acid-catalysed 1,6-elimination. We showcase this first-in-class reductively cleavable linker system in the parallel purification of a personalized neoantigen cocktail, containing 20 peptides for cancer immunotherapy within six hours.

A first-in-class reductively cleavable linker system that enables parallel and traceless purification of peptides through a safety-release is introduced with three linker types and showcased by rapid production of 20 personalized neoantigen peptides.     

Effect of C-terminal modification on the self-assembly and hydrogelation of fluorinated Fmoc-Phe derivatives

The development of hydrogels resulting from the self-assembly of low molecular weight (LMW) hydrogelators is a rapidly expanding area of study. Fluorenylmethoxycarbonyl (Fmoc) protected aromatic amino acids derived from phenylalanine (Phe) have been shown to be highly effective LMW hydrogelators. It has been found that side chain functionalization of Fmoc-Phe exerts a significant effect on the self-assembly and hydrogelation behavior of these molecules; fluorinated derivatives, including pentafluorophenylalanine (F(5)-Phe) and 3-F-phenylalanine (3-F-Phe), spontaneously self-assemble into fibrils that form a hydrogel network upon dissolution into water. In this study, Fmoc-F(5)-Phe-OH and Fmoc-3-F-Phe-OH were used to characterize the role of the C-terminal carboxylic acid on the self-assembly and hydrogelation of these derivatives. The C-terminal carboxylic acid moieties of Fmoc-F(5)-Phe-OH and Fmoc-3-F-Phe-OH were converted to C-terminal amide and methyl ester groups in order to perturb the hydrophobicity and hydrogen bond capacity of the C-terminus. Self-assembly and hydrogelation of these derivatives was investigated in comparison to the parent carboxylic acid compounds at neutral and acidic pH. It was found that hydrogelation of the C-terminal acids was highly sensitive to solvent pH, which influences the charge state of the terminal group. Rigid hydrogels form at pH 3.5, but at pH 7 hydrogel rigidity is dramatically weakened. C-terminal esters self-assembled into fibrils only slowly and failed to form hydrogels due to the higher hydrophobicity of these derivatives. C-terminal amide derivatives assembled much more rapidly than the parent carboxylic acids at both acidic and neutral pH, but the resultant hydrogels were unstable to shear stress as a function of the lower water solubility of the amide functionality. Co-assembly of acid and amide functionalized monomers was also explored in order to characterize the properties of hybrid hydrogels; these gels were rigid in unbuffered water but significantly weaker in phosphate buffered saline. These results highlight the complex nature of monomer/solvent interactions and their ultimate influence on self-assembly and hydrogelation, and provide insight that will facilitate the development of optimal amino acid LMW hydrogelators for gelation of complex buffered media.     

Light-fueled dissipative self-assembly at molecular and macro-scale enabled by a visible-light-responsive transient hetero-complementary quadruple hydrogen bond

The development of out-of-equilibrium self-assembly systems using light as input fuel is highly desirable and promising for the fabrication of smart supramolecular materials. Herein, we report the construction of new artificial light-fueled dissipative molecular and macroscopic self-assembly systems based on a visible-light-responsive transient quadruple H-bonding array, which consists of an azobenzene-modified ureidopyrimidinone (UPy) module (Azo-O-UPy) and a nonphotoactive diamidonaphthyridine (DAN) derived competitive binder (Napy-1). The visible light (410 nm) irradiation can induce the E to Z isomerization of the azobenzene unit of E-Azo-O-UPy to produce Z-Azo-O-UPy with an opened UPy binding site, which can complex with Napy-1 to form a quadruply H-bonded heterodimer. The heterodimer is metastable and can be quickly disassembled in dark, owing to the fast thermal relaxation of Z-Azo-O-UPy to E-Azo-O-UPy. While introducing such transient quadruple H-bonding interaction into a linear polymer system or a polymeric gel system, light-fueled out-of-equilibrium polymeric assembly both at molecular and macro-scale can be achieved.     

Building addressable libraries: The use of a mass spectrometry cleavable linker for monitoring reactions on a microelectrode array

Time-of-flight secondary ion mass spectrometry (TOF SIMS) has been used in conjunction with a mass spectrometry cleavable linker to determine the percent conversion of reactions that were conducted site-selectively on an addressable microelectrode array. When combined with fluorescence techniques for analysis of the reactions, the TOF SIMS experiment provides a means for optimization of both reaction confinement and reaction efficiency on the microelectrode arrays.     

Screening of polymeric supports and enzymes for the development of an endo enzyme cleavable linker

Several polymeric supports possessing an ester moiety were prepared and a range of enzymes was investigated to hydrolyse the ester linkage and release a signalling group into solution for applications in immunoassays. Pseudomonas lipases were found to most readily cleave the solution-phase analogue and this observation translated well to the corresponding polymeric supports, where the most effective were PEGA resins and the LPOS support PEG-6000.     

Disulfide bond creates a small connecting loop in aminoxy peptide backbone

Disulfide-bond formation between the side chains of cysteine-cysteine pairs is often critical to the folding behavior, stability, and functionality of proteins. In this paper, we report that sulfur atoms can be introduced into the amide groups of aminoxy peptides to form a novel type of disulfide bridge, which creates a connecting loop in the peptide backbone.     

Unsymmetrical p-carborane backbone as a linker for donor-acceptor dyads

Fluorescent nanorods: Donor-acceptor dyads based on novel unsymmetrically disubstituted closo-1,12-dicarbadecaboranes have been prepared in a completely controlled manner by using a three-step procedure. Dyads with different donor-acceptor spacing were thereby obtained. Efficient energy transfer from the donor to the acceptor was determined in fluid solution at room temperature.     

Disulfide bond cleavage induced by a platinum(II) methionine complex

The cleavage of a disulfide bond and the redox equilibrium of thiol/disulfide are strongly related to the levels of glutathione (GSH)/oxidized glutathione (GSSG) or mixed disulfides in vivo. In this work, the cleavage of a disulfide bond in GSSG induced by a platinum(II) complex [Pt(Met)Cl2] (where Met = methionine) was studied and the cleavage fragments or their platinated adducts were identified by means of electrospray mass spectrometry, high-performance liquid chromatography, and ultraviolet techniques. The second-order rate constant for the reaction between [Pt(Met)Cl2] and GSSG was determined to be 0.4 M(-1) s(-1) at 310 K and pH 7.4, which is 100- and 12-fold faster than those of cisplatin and its monoaqua species, respectively. Different complexes were formed in the reaction of [Pt(Met)Cl2] with GSSG, mainly mono- and dinuclear platinum complexes with the cleavage fragments of GSSG. This study demonstrated that [Pt(Met)Cl2] can promote the cleavage of disulfide bonds. The mechanistic insight obtained from this study may provide a deeper understanding on the potential involvement of platinum complexes in the intracellular GSH/GSSG systems.     

A fluorous-assisted synthesis of oligosaccharides using a phenyl ether linker as a safety-catch linker

We report on the fluorous-assisted synthesis of oligosaccharides using a phenyl ether linker. The phenyl ether linker is stable under both acidic and basic conditions but can be cleaved under mildly acidic conditions after reduction to a vinyl ether. The utility of the method was demonstrated by the synthesis of a trisaccharide. A protected trisaccharide with a light-fluorous tag was directly prepared by one-pot glycosylation using three building blocks that contained a building block with a light-fluorous tag though a phenyl ether. A Birch reduction of the trisaccharide provided a fully deprotected trisaccharide with the fluorous tag attached through a vinyl ether, which was easily purified by solid-phase extraction. The tag was cleaved from the sugar portion by treatment with 3% TFA in MeOH.     

Single quintuple bond [PhCrCrPh] molecule as a possible molecular switch

The electronic transport properties of a single quintuple bond [PhCrCrPh] molecule sandwiched between two Au(111) surfaces with the trans-bent and linear configurations are studied by a fully self-consistent nonequilibrium Green's function method combined with density functional theory. The calculated transmission spectra of two chemical isomers are remarkably distinctive. Theoretical results suggest that the current through the trans-bent configuration is significantly larger than the corresponding linear one. The predicted on-off ratio of currents ranging from around 50 to 200 in the applied bias window [-1.5 V, 1.5 V] suggests that multiple bond compounds have attractive potential in molecular switch technology.     

Bolaform superamphiphile based on a dynamic covalent bond and its self-assembly in water

We have employed a dynamic covalent bond to fabricate a bolaform superamphiphile, which can be used as building blocks for controlled assembly and disassembly. In alkaline environment, one building block bearing a benzoic aldehyde group can react with the other building block bearing an amino group to form a bolaform superamphiphile. It is found that the bolaform superamphiphiles can self-assemble in water to form micellar aggregates. When the pH is tuned down to slightly acidic values, the benzoic imine bond can be hydrolyzed, leading to the dissociation of the superamphiphile. The micellar aggregates will also disassemble, and the loaded guest molecules are released subsequently. This line of research has enriched the family of bolaform amphiphiles, and the resulting assemblies may find application in the field of controlled and targetable drug-delivery in a biological environment.