On the formation and properties of interstrand DNA-DNA cross-links forged by reaction of an abasic site with the opposing guanine residue of 5'-CAp sequences in duplex DNA

We recently reported that the aldehyde residue of an abasic (Ap) site in duplex DNA can generate an interstrand cross-link via reaction with a guanine residue on the opposing strand. This finding is intriguing because the highly deleterious nature of interstrand cross-links suggests that even small amounts of Ap-derived cross-links could make a significant contribution to the biological consequences stemming from the generation of Ap sites in cellular DNA. Incubation of 21-bp duplexes containing a central 5'-CAp sequence under conditions of reductive amination (NaCNBH(3), pH 5.2) generated much higher yields of cross-linked DNA than reported previously. At pH 7, in the absence of reducing agents, these Ap-containing duplexes also produced cross-linked duplexes that were readily detected on denaturing polyacrylamide gels. Cross-link formation was not highly sensitive to reaction conditions, and the cross-link, once formed, was stable to a variety of workup conditions. Results of multiple experiments including MALDI-TOF mass spectrometry, gel mobility, methoxyamine capping of the Ap aldehyde, inosine-for-guanine replacement, hydroxyl radical footprinting, and LC-MS/MS were consistent with a cross-linking mechanism involving reversible reaction of the Ap aldehyde residue with the N(2)-amino group of the opposing guanine residue in 5'-CAp sequences to generate hemiaminal, imine, or cyclic hemiaminal cross-links (7-10) that were irreversibly converted under conditions of reductive amination (NaCNBH(3)/pH 5.2) to a stable amine linkage. Further support for the importance of the exocyclic N(2)-amino group in this reaction was provided by an experiment showing that installation of a 2-aminopurine-thymine base pair at the cross-linking site produced high yields (15-30%) of a cross-linked duplex at neutral pH, in the absence of NaCNBH(3).

The relative contribution of calcium, zinc and oxidation-based cross-links to the stiffness of Arion subfuscus glue

Metal ions are present in many different biological materials, and are capable of forming strong cross-links in aqueous environments. The relative contribution of different metal-based cross-links was measured in the defensive glue produced by the terrestrial slug Arion subfuscus. This glue contains calcium, magnesium, zinc, manganese, iron and copper. These metals are essential to the integrity of the glue and to gel stiffening. Removal of all metals caused at least a 15-fold decrease in the storage modulus of the glue. Selectively disrupting cross-links involving hard Lewis acids such as calcium reduced the stiffness of the glue, while disrupting cross-links involving borderline Lewis acids such as zinc did not. Calcium is the most common cation bound to the glue (40 mmol l(-1)), and its charge is balanced primarily by sulphate at 82-84 mmol l(-1). Thus these ions probably play a primary role in bringing polymers together directly. Imine bonds formed as a result of protein oxidation also contribute substantially to the stiffness of the glue. Disrupting these bonds with hydroxylamine caused a 33% decrease in storage modulus of the glue, while stabilizing them by reduction with sodium borohydride increased the storage modulus by 40%. Thus a combination of metal-based bonds operates in this glue. Most likely, cross-links directly involving calcium play a primary role in bringing together and stabilizing the polymer network, followed by imine bond formation and possible iron coordination.

Facile route to an all-organic, triply threaded, interlocked structure by templated dynamic clipping

Encaged! Three-terminal interlocked molecular species were obtained by dynamic (2+3) assembly of a cagelike macro-bicycle around a trifurcated trispyridinium π guest. The complex is stabilized by π-π interactions and multiple [C-H⋅⋅⋅O] and [C-H⋅⋅⋅N] interactions. Uncomplexed guest molecules cocrystallize alongside the threaded complexes in the solid state, thus giving extended π-stacked columns.

H-shaped supra-amphiphiles based on a dynamic covalent bond

The imine bond, a kind of dynamic covalent bond, is used to bind two bolaform amphiphiles together with spacers, yielding H-shaped supra-amphiphiles. Micellar aggregates formed by the self-assembly of the H-shaped supra-amphiphiles are observed. When pH is tuned down from basic to slightly acidic, the benzoic imine bond can be hydrolyzed, leading to the dissociation of H-shaped supra-amphiphiles. Moreover, H-shaped supra-amphiphiles have a lower critical micelle concentration than their building blocks, which is very helpful in enhancing the stability of the benzoic imine bond being hydrolyzed by acid. The surface tension isotherms of the H-shaped supra-amphiphiles with different spacers indicate their twisty conformation at a gas-water interface. The study of H-shaped supra-amphiphiles can enrich the family of amphiphiles, and moreover, the pH-responsiveness may make them apply to controlled or targetable drug delivery in a biological environment.

Applications of reversible covalent chemistry in analytical sample preparation

Reversible covalent chemistry (RCC) adds another dimension to commonly used sample preparation techniques like solid-phase extraction (SPE), solid-phase microextraction (SPME), molecular imprinted polymers (MIPs) or immuno-affinity cleanup (IAC): chemical selectivity. By selecting analytes according to their covalent reactivity, sample complexity can be reduced significantly, resulting in enhanced analytical performance for low-abundance target analytes. This review gives a comprehensive overview of the applications of RCC in analytical sample preparation. The major reactions covered include reversible boronic ester formation, thiol-disulfide exchange and reversible hydrazone formation, targeting analyte groups like diols (sugars, glycoproteins and glycopeptides, catechols), thiols (cysteinyl-proteins and cysteinyl-peptides) and carbonyls (carbonylated proteins, mycotoxins). Their applications range from low abundance proteomics to reversible protein/peptide labelling to antibody chromatography to quantitative and qualitative food analysis. In discussing the potential of RCC, a special focus is on the conditions and restrictions of the utilized reaction chemistry.

Efficient long-range stereochemical communication and cooperative effects in self-assembled Fe4L6 cages

A series of large, optically active Fe(4)L(6) cages was prepared from linear 5,5'-bis(2-formylpyridines) incorporating varying numbers (n = 0-3) of oligo-p-xylene spacers, chiral amines, and Fe(II). When a cage was constructed from the ligand bridged by one p-xylene spacer (n = 1) and a bulky chiral amine, both a homochiral Fe(2)L(3) helicate and Fe(4)L(6) cage were observed to coexist in solution due to a delicate balance between steric factors. In contrast, when a less bulky chiral amine was used, only the Fe(4)L(6) cage was observed. In the case of larger cages (n = 2, 3), long-range (>2 nm) stereochemical coupling between metal centers was observed, which was minimally diminished as the ligands were lengthened. This communication was mediated by the ligands' geometries and rigidity, as opposed to gearing effects between xylene methyl groups: the metal-centered stereochemistry was not observed to affect the axial stereochemistry of the ligands.

Adaptation of dynamic covalent systems of imine constituents to medium change by component redistribution under reversible phase separation

A dynamic covalent library of interconverting imine constituents, dissolved in an acetonitrile/water mixture, undergoes constitutional reorganization upon phase separation induced by a physical stimulus (heat) or a chemical effector (inorganic salt, carbohydrate, organic solvent). The process has been made reversible, regenerating the initial library upon phase reunification. It represents the behavior of a dynamic covalent library upon reversible phase separation and its adaptation to a phase change, with up-regulation in each phase of the fittest constituents by component selection. Finally, the system exemplifies the splitting of a 2D (square) constitutional dynamic network into a 3D (cube) one.

Cooperative self-assembly: producing synthetic polymers with precise and concise primary structures

The quest to construct mechanically interlocked polymers, which present precise monodisperse primary structures that are produced both consistently and with high efficiencies, has been a daunting goal for synthetic chemists for many years. Our ability to realise this goal has been limited, until recently, by the need to develop synthetic strategies that can direct the formation of the desired covalent bonds in a precise and concise fashion while avoiding the formation of unwanted kinetic by-products. The challenge, however, is a timely and welcome one, as a consequence of, primarily, the potential for mechanically interlocked polymers to act as dynamic (noncovalent) yet robust (covalent) new materials for a wide array of applications. One such strategy which has been employed widely in recent years to address this issue, known as Dynamic Covalent Chemistry (DCC), is a strategy in which reactions operate under equilibrium and so offer elements of "proof-reading" and "error-checking" to the bond forming and breaking processes such that the final product distribution always reflects the thermodynamically most favourable compound. By coupling DCC with template-directed protocols, which utilise multiple weak noncovalent interactions to pre-organise and self-assemble simpler small molecular precursors into their desired geometries prior to covalent bond formation, we are able to produce compounds with highly symmetric, robust and complex topologies that are otherwise simply unobtainable by more traditional methods. Harnessing these strategies in an iterative, step-wise fashion brings us ever so much closer towards perfecting the controlled synthesis of high order main-chain mechanically interlocked polymers. This tutorial review focuses (i) on the development of DCC-namely, the formation of dynamic imine bonds-used in conjunction with template-directed protocols to afford a variety of mechanically interlocked molecules (MIMs) and ultimately (ii) on the synthesis of highly ordered poly[n]rotaxanes with high conversion efficiencies.