Carbazole modified oligonucleotides: synthesis, hybridization studies and fluorescence properties

Tetraphenylethylene-DNA conjugates: influence of sticky ends and DNA sequence length on the supramolecular assembly of AIE-active vesicles

The supramolecular assembly of DNA conjugates, functionalized with tetraphenylethylene (TPE) sticky ends, into vesicular structures is described. The aggregation-induced emission (AIE) active TPE units allow monitoring the assembly process by fluorescence spectroscopy. The number of TPE modifications in the overhangs of the conjugates influences the supramolecular assembly behavior. A minimum of two TPE residues on each end are required to ensure a well-defined assembly process. The design of the presented DNA-based nanostructures offers tailored functionalization with applications in DNA nanotechnology.

The supramolecular assembly of tetraphenylethylene (TPE)–DNA conjugates is presented. The length of the TPE sticky ends exerts a pronounced effect on the formation of aggregation-induced emission (AIE)-active vesicles.

Complex DNA Architectonics─Self-Assembly of Amphiphilic Oligonucleotides into Ribbons, Vesicles, and Asterosomes

The precise arrangement of structural subunits is a key factor for the proper shape and function of natural and artificial supramolecular assemblies. In DNA nanotechnology, the geometrically well-defined double-stranded DNA scaffold serves as an element of spatial control for the precise arrangement of functional groups. Here, we describe the supramolecular assembly of chemically modified DNA hybrids into diverse types of architectures. An amphiphilic DNA duplex serves as the sole structural building element of the nanosized supramolecular structures. The morphology of the assemblies is governed by a single subunit of the building block. The chemical nature of this subunit, i.e., polyethylene glycols of different chain length or a carbohydrate moiety, exerts a dramatic influence on the architecture of the assemblies. Cryo-electron microscopy revealed the arrangement of the individual DNA duplexes within the different constructs. Thus, the morphology changes from vesicles to ribbons with increasing length of a linear polyethylene glycol. Astoundingly, attachment of a N-acetylgalactosamine carbohydrate to the DNA duplex moiety produces an unprecedented type of star-shaped architecture. The novel DNA architectures presented herein imply an extension of the current concept of DNA materials and shed new light on the fast-growing field of DNA nanotechnology.

Polyamine-Oligonucleotide Conjugates: 2'-OMe-Triazole-Linked 1,4,7,10-Tetraazacyclododecane and Intercalating Dyes and Their Effect on the Thermal Stability of DNA Duplexes

Oligonucleotides with the sequences 5'-GTG AUPA TGC, 5'-GCA TAUP CAC and 5'-GUPG ATA UPGC, where UP is 2'-O-propargyl uridine, were subjected to post-synthetic Cu(I)-catalyzed azide-alkyne cycloaddition to attach 1,4,7,10-tetraazacyclododecane (cyclen) and two well-known DNA intercalating dyes: thioxanthone and 1,8-naphthalimide. We propose a convenient cyclen protection-deprotection strategy that allows efficient separation of the resulting polyamine-oligonucleotide conjugates from the starting materials by RP-HPLC to obtain high-purity products. In this paper, we present hitherto unknown macrocyclic polyamine-oligonucleotide conjugates and their hybridization properties reflected in the thermal stability of thirty-two DNA duplexes containing combinations of labeled strands, their unmodified complementary strands, and strands with single base pair mismatches. Circular dichroism measurements showed that the B-conformation is retained for all dsDNAs consisting of unmodified and modified oligonucleotides. An additive and destabilizing effect of cyclen moieties attached to dsDNAs was observed. Tm measurements indicate that placing the hydrophobic dye opposite to the cyclen moiety can reduce its destabilizing effect and increase the thermal stability of the duplex. Interestingly, the cyclen-modified U showed significant selectivity for TT mismatch, which resulted in stabilization of the duplex. We conclude the paper with a brief review and discussion in which we compare our results with several examples of oligonucleotides labeled with polyamines at internal strand positions known in the literature.

Rational Design and Experimental Analysis of Short-Oligonucleotide Substrate Specificity for Targeting Bacterial Nucleases

An undecamer oligonucleotide probe based on a pair of deoxythymidines flanked by several modified nucleotides is a specific and highly efficient biosensor for micrococcal nuclease (MNase), an endonuclease produced by Staphylococcus aureus. Herein, the interaction mode and cleavage process on such oligonucleotide probes are identified and described for the first time. Also, we designed truncated pentamer probes as the minimum-length substrates required for specific and efficient biosensing. By means of computational (virtual docking) and experimental (ultra-performance liquid chromatography–mass spectrometry and matrix-assisted laser desorption ionization time-of-flight) techniques, we perform a sequence/structure–activity relationship analysis, propose a catalytically active substrate–enzyme complex, and elucidate a novel two-step phosphodiester bond hydrolysis mechanism, identifying the cleavage sites and detecting and quantifying the resulting probe fragments. Our results unravel a picture of both the enzyme–biosensor complex and a two-step cleavage/biosensing mechanism, key to the rational oligonucleotide design process.