DNA-Codes für die Nanowissenschaften

Assembly of DNA triangles mediated by perylene bisimide caps

Perylene bisimides (PBI) have been synthetically incorporated as caps onto a Y-shaped DNA triple strand. These PBI caps serve as "sticky" ends in the spontaneous assembly of larger DNA ensembles, linking the triangular DNA through stacking interactions. This, in turn, yields a hypsochromic shift in the absorption and a red shift in the fluorescence as characteristic optical readouts. This assembly occurs spontaneously without any enzymatic ligation process and without the use of overhanging DNA as sticky ends. Instead, dimerizations of the PBI chromophores in the assembly are controlled by the DNA as a structural scaffold. Thereby, the PBI-driven assembly is fully reversible. Due to the fact that PBI dimerization does not occur in the single strand, the aggregates can be destroyed by thermal dehybridization of the DNA scaffold and reassembled by reannealing of the DNA construct. In view of the fact that PBI forms stable radical anions, the presented DNA architectures are not only interesting optical biomaterials, but are also promising materials for molecular electronics with DNA.

Synthesis and stretching of rolling circle amplification products in a flow-through system

Enzymatic isothermal rolling circle amplification (RCA) produces long concatemeric single-stranded DNA (ssDNA) molecules if a small circular ssDNA molecule is applied as the template. A method is presented here in which the RCA reaction is carried out in a flow-through system, starting from isolated surface-tethered DNA primers. This approach combines gentle fluidic handling of the single-stranded RCA products, such as staining or stretching via a receding meniscus, with the option of simultaneous (fluorescence) microscopic observation. It is shown that the stretched and surface-attached RCA products are accessible for hybridization of complementary oligonucleotides, which demonstrates their addressability by complementary base pairing. The long RCA products should be well suited to bridge the gap between biomolecular nanoscale building-blocks and structures at the micro- and macroscale, especially at the single-molecule level presented here.

Binding mechanisms in supramolecular complexes

Supramolecular chemistry has expanded dramatically in recent years both in terms of potential applications and in its relevance to analogous biological systems. The formation and function of supramolecular complexes occur through a multiplicity of often difficult to differentiate noncovalent forces. The aim of this Review is to describe the crucial interaction mechanisms in context, and thus classify the entire subject. In most cases, organic host-guest complexes have been selected as examples, but biologically relevant problems are also considered. An understanding and quantification of intermolecular interactions is of importance both for the rational planning of new supramolecular systems, including intelligent materials, as well as for developing new biologically active agents.

Two-dimensional polymers: just a dream of synthetic chemists?

In light of the considerable impact synthetic 2D polymers are expected to have on many fundamental and applied aspects of the natural and engineering sciences, it is surprising that little research has been carried out on these intriguing macromolecules. Although numerous approaches have been reported over the last several decades, the synthesis of a one monomer unit thick, covalently bonded molecular sheet with a long-range ordered (periodic) internal structure has yet to be achieved. This Review provides an overview of these approaches and an analysis of how to synthesize 2D polymers. This analysis compares polymerizations in (initially) a homogeneous phase with those at interfaces and considers structural aspects of monomers as well as possibly preferred connection modes. It also addresses issues such as shrinkage as well as domain and crack formation, and briefly touches upon how the chances for a successful structural analysis of the final product can possibly be increased.

Avidin Decorated Core–Shell Nanoparticles for Biorecognition Studies by Elastic Light Scattering

In this paper, a straightforward method based on elastic light scattering is shown to provide a sensitive and reliable tool for the quantitative determination of protein-ligand interactions that occur at the surface of suitably designed core-shell nanoparticles. The assay makes use of monodisperse nanocolloids that have minimal optical contrast with the aqueous environment. By properly coating the particles with avidin and oligo(ethylene glycol)-based amphiphiles, we developed a hybrid system that combines the availability of standard ligands with the necessary bioinvisibility towards the accidental adsorption of nonspecific macromolecules. This probe was employed to detect interactions between different kinds of biotinylated proteins, and it revealed high specificity and affinities in the low nanomolar range. In particular, we obtained an efficient avidin anchorage of biotinylated protein A on the surface of the nanoparticles, which we exploited as a functional probe for the rapid, quantitative, picomolar detection of human IgG antibodies. Overall, these light-scattering-based nanosensors appear as a simple and highly informative tool for proteomics studies.

Synthetic molecular motors and mechanical machines

The widespread use of controlled molecular-level motion in key natural processes suggests that great rewards could come from bridging the gap between the present generation of synthetic molecular systems, which by and large rely upon electronic and chemical effects to carry out their functions, and the machines of the macroscopic world, which utilize the synchronized movements of smaller parts to perform specific tasks. This is a scientific area of great contemporary interest and extraordinary recent growth, yet the notion of molecular-level machines dates back to a time when the ideas surrounding the statistical nature of matter and the laws of thermodynamics were first being formulated. Here we outline the exciting successes in taming molecular-level movement thus far, the underlying principles that all experimental designs must follow, and the early progress made towards utilizing synthetic molecular structures to perform tasks using mechanical motion. We also highlight some of the issues and challenges that still need to be overcome.

Probing Structural Effects on Replication Efficiency through Comparative Analyses of Families of Potential Self-Replicators

A formidable synthetic apparatus for the creation of nanoscale molecular structures and supramolecular assemblies through molecular structures can potentially be created from systems that are capable of parallel automultiplication (self-replication). In order to achieve this goal, a detailed understanding of the relationship between molecular structure and replication efficiency is necessary. Diastereoisomeric templates that are capable of specific and simultaneous autocatalysis have been synthesised. A systematic experimental and theoretical evaluation of their behaviour and that of structurally-related systems reveals the key determinants that dictate the emergence of self-replicative function and defines the structural space within which this behaviour is observed.

Stable and selective formation of hoogsteen-type triplexes and duplexes using twisted intercalating nucleic acids (TINA) prepared via postsynthetic Sonogashira solid-phase coupling reactions

Bulge insertions of (R)-1-O-[4-(1-pyrenylethynyl)phenylmethyl]glycerol (5) into the middle of homopyrimidine oligodeoxynucleotides (twisted intercalating nucleic acids, TINA) obtained via postsynthetic Sonogashira coupling reaction led to extraordinary high thermal stability of Hoogsteen-type triplexes and duplexes, whereas Watson-Crick-type duplexes of the same nucleotide content were destabilized. Modified oligonucleotides were synthesized using the phosphoramidite of (S)-1-(4,4'-dimethoxytriphenylmethyloxy)-3-(4-iodo-benzyloxy)-propan-2-ol followed by treatment of the oligonucleotide on a CPG-support with the Sonogashira-coupling reaction mixture containing different ethynylaryls. Bulged insertion of the pyrene derivative 5 into oligonucleotides was found to be the best among the tested modifications for binding to the Hoogsteen-type triplexes and duplexes. Thus, at pH 7.2 an oligonucleotide with cytidine content of 36% possessing two bulged insertions of 5 separated by three bases formed a stable triplex (T(m) = 43.0 degrees C), whereas the native oligonucleotide was unable to bind to the target duplex. The corresponding Watson-Crick-type duplex with the same oligonucleotide had T(m) of 38.0 degrees C at pH 7.2, while the T(m) of unmodified dsDNA was 47.0 degrees C. Experiments with mismatched oligonucleotides, luminescent properties, and potential applications of TINA technology is discussed.