Molecular probes of DNA bulges: Functional assay and spectroscopic analysis

A chemo- and regioselective Pd(0)-catalyzed three-component spiroannulation

A chemo- and regioselective Pd(0)-catalyzed spiroannulation has been successfully developed. The key feature of this method is the use of readily available 1,2-dihaloarenes, alkynes and 2-naphthols for the rapid assembly of spirocarbocyclic molecules. Mechanistic studies revealed that this domino reaction proceeded through a cascade of oxidative addition to Pd(0), alkyne migratory insertion, and 2-naphthol-facilitated dearomatizing [4+1] spiroannulation.

A novel cross-linked nanoparticle with aggregation-induced emission properties for cancer cell imaging

Fluorescent probes have been widely used in bioimaging as an efficient and convenient analytical tool. From the initial inorganic nanoparticles and small organic molecules to polymeric nanoparticles, scientific researchers have been trying to develop a probe with strong fluorescence and excellent biocompatibility. In this study, a tetraphenylethylene derivative with AIE properties and hyaluronic acid modified by methacrylic anhydride were combined to prepare a novel nanoparticle (HA-Ac-Pha-C) as a fluorescent probe by a photochemical cross-linking reaction. The fluorescence intensity and size of the nanoparticles were characterized by different techniques. It was confirmed that cross-linked nanoparticles not only showed stronger fluorescence, but also had better photostability while still maintaining 85.9% of the initial intensity after seven days. Moreover, cells and zebrafish imaging experiments also demonstrated that nanoparticles show specific fluorescence labeling for cancer cells and excellent biocompatibility in living organisms.

Synthesis of Polycyclic Spirocarbocycles via Acid-Promoted Ring-Contraction/Dearomative Ring-Closure Cascade of Oxapropellanes

We report herein the development of an acid-promoted rearrangement of oxa[4.3.2]propellanes to afford polyaromatic-fused spiro[4.5]carbocycles. DFT calculations suggest that the reaction pathway involves generation of a cyclobutyl cation, ring contraction to the cyclopropylcarbinyl cation, and dearomative ring closure by an internal 2-naphthol moiety. The resulting spirocarbocycles are synthetically valuable, as they could be transformed into two different polycyclic aromatic hydrocarbons via skeletal rearrangement. Syntheses of optically pure spirocarbocycles via a central-to-axial-to-central chirality transfer are also described.

Ag nanoclusters as probes for turn-on fluorescence recognition of TpG dinucleotide with a high selectivity

CpG dinucleotide in DNA has a great tendency to mutate to TpG dinucleotide and this transition can cause some serious diseases. In this work, fluorescent Ag nanoclusters (Ag NCs) were employed as useful inorganic fluorophores for the potential of selectively discriminating TpG dinucleotide from CpG dinucleotide. Opposite the base Y of interest in YpG dinucleotide (Y=C or T), a bulge site was introduced so as to make the base Y to be unpaired and ready for Ag(+) binding. Such that the unpaired Y and context base pairs can provide a specific space suitable for creating fluorescent Ag NCs. We found that in comparison with CpG dinucleotide, TpG dinucleotide is much more efficient in growing fluorescent Ag NCs. Therefore, mutation of CpG dinucleotide to TpG can be identified by a turn-on fluorescence response and a high selectivity. More interestingly, Ag NCs exhibit a better performance in the TpG recognition over the other dinucleotides (Y=A and G) than the previously used organic fluorophores. Additionally, the effectiveness of the bulge site design in discriminating these dinucleotides was evidenced by control DNAs having the abasic site structure. We expect that a practical method for TpG dinucleotide recognition with a high selectivity can be developed using the bulge site-grown fluorescent Ag NCs as novel probes.

Recent advances in synthesis of bacterial rare sugar building blocks and their applications

This Highlight describes recent advances in the synthesis of the bacterial deoxy amino hexopyranoside building blocks and their application in constructing various biologically important bacterial O-glycans.

De novo synthesis of D- and L-fucosamine containing disaccharides

The availability of rare monosaccharides that cannot be isolated from natural sources is currently limiting the access to the synthesis and the biological evaluation of complex bacterial cell-surface glycans. Here, we report the synthesis of D- and L-fucosamine building blocks by a de novo approach from L- and D-Garner aldehydes. These differentially protected monosaccharide building blocks were utilized to prepare disaccharides present on the surface of Pseudomonas aeruginosa bacteria.

Designed DNA probes from the neocarzinostatin family: impact of glycosyl linkage stereochemistry on bulge base binding

Bulged sites in DNA and RNA have become targets for rational drug design due to their suspected involvement in a number of key biomolecular processes. A lead compound, derived from the enediyne natural product NCS-chrom has been used to inform chemical synthesis of a family of designed probes of DNA bulges, one of which shows 80 nM affinity for a two base bulged target. Key contributors to binding of these spirocyclic compounds have been studied in order to correlate affinity and specificity with structural features. Herein, we demonstrate that the glycosyl linkage stereochemistry of the pendant aminofucosyl group plays a pivotal role in binding, and coupled with insight obtained with various bulged targets, will allow rational design of second generation ligands.

Solution structure of a designed spirocyclic helical ligand binding at a two-base bulge site in DNA

The solution structure of the complex formed between an oligodeoxynucleotide containing a two-base bulge (5'-CCATCGTCTACCTTTGGTAGGATGG) and SCA-alpha2, a designed spirocyclic helical molecule, has been elucidated. SCA-alpha2, a close mimic of the metabolite, NCSi-gb, of the DNA bulge-specific enediyne antibiotic neocarzinostatin, differs in possessing a more stable spirocyclic ring system and in lacking certain bulky groupings that compromise bulged DNA binding. This study provides a detailed comparison of the binding modes of the two complexes and provides new insights into the importance of shape and space, as opposed to simple nucleotide sequence, in complex formation at the bulge site. The two rigidly held aromatic rings of SCA-alpha2 form a right-handed helical molecular wedge that specifically penetrates the bulge-binding pocket and immobilizes the two bulge residues (GT), which point toward the minor groove, rather than the major groove as in the NCSi-gb.bulged DNA complex. The ligand aromatic ring systems stack on the DNA bulge-flanking base pairs that define the long sides of the triangular prism binding pocket. Like NCSi-gb, SCA-alpha2 possesses the natural N-methylfuranose moiety, alpha-linked to the benzindanol (BI) moiety. The amino sugar anchors in the major groove of the DNA and points toward the 3'-bulge-flanking base pair. Lacking the bulky cyclocarbonate of NCSi-gb, the SCA-alpha2.bulged DNA complex has a much less twisted and buckled 3'-bulge-flanking base pair (dG20.dC8), and the G20 residue stacks directly above the BI ring platform. Also, the absence of the methyl group and the free rotation of the methoxy group on the dihydronaphthanone (NA) moiety of SCA-alpha2 allow better stacking geometry of the NA ring above the 5'-bulge-flanking dG21.dC5 base pair. These and other considerations help to explain why NCSi-gb binds very poorly to bulged RNA and are consistent with the recent observation of good binding with SCA-alpha2. Thus, although the two complexes resemble each other closely, they differ in important local environmental details. SCA-alpha2 has a better hand-in-glove fit at the bulge site, making it an ideal platform for the placement of moieties that can react covalently with the DNA and for generating congeners specific for bulges in RNA.