Lars Röglin

A Synthetic “Tour de Force”: Well‐Defined Multivalent and Multimodal Dendritic Structures for Biomedical Applications

Dendrimers have several unique properties that make them attractive scaffolds for use in biomedical applications. To date, multivalent and multimodal dendritic structures have been synthesized predominantly by statistical modification of peripheral groups. However, the potential application of such probes in patients demands well-defined and monodisperse materials that have unique structures. Current progress in the field of chemical biology, in particular chemoselective ligation methods, renders this challenge possible. In this Minireview, we outline the different available synthetic strategies, some applications that already make use of this new generation of multivalent and multimodal architectures, and the challenges for future developments.

FIT probes: peptide nucleic acid probes with a fluorescent base surrogate enable real-time DNA quantification and single nucleotide polymorphism discovery.

The ability to accurately quantify specific nucleic acid molecules in complex biomolecule solutions in real time is important in diagnostic and basic research. Here we describe a DNA-PNA (peptide nucleic acid) hybridization assay that allows sensitive quantification of specific nucleic acids in solution and concomitant detection of select single base mutations in resulting DNA-PNA duplexes. The technique employs so-called FIT (forced intercalation) probes in which one base is replaced by a thiazole orange (TO) dye molecule. If a DNA molecule that is complementary to the FIT-PNA molecule (except at the site of the dye) hybridizes to the probe, the TO dye exhibits intense fluorescence because stacking in the duplexes enforces a coplanar arrangement even in the excited state. However, a base mismatch at either position immediately adjacent to the TO dye dramatically decreases fluorescence, presumably because the TO dye has room to undergo torsional motions that lead to rapid depletion of the excited state. Of note, we found that the use of d-ornithine rather than aminoethylglycine as the PNA backbone increases the intensity of fluorescence emitted by matched probe-target duplexes while specificity of fluorescence signaling under nonstringent conditions is also increased. The usefulness of the ornithine-containing FIT probes was demonstrated in the real-time PCR analysis providing a linear measurement range over at least seven orders of magnitude. The analysis of two important single nucleotide polymorphisms (SNPs) in the CFTR gene confirmed the ability of FIT probes to facilitate unambiguous SNP calls for genomic DNA by quantitative PCR.

Proximicins A, B, and C—Antitumor Furan Analogues of Netropsin from the Marine Actinomycete Verrucosispora Induce Upregulation of p53 and the Cyclin Kinase Inhibitor p21

Netropsin (1) and distamycin (2) are naturally occurring gpeptides with antiviral and antibacterial activity (Figure 1). Netropsin, formerly named congocidine, was isolated from S. netropsis in 1951, while distamycin was isolated from S. distallicus in 1964. Both compounds bind in the minor groove of DNA, and they were arguably the first compounds for which AT-selective DNA binding was demonstrated. The design of synthetic derivatives capable of addressing a specific sequence of DNAwould allow the selective inhibition of gene expression and thus result in compounds that act as antitumor agents. As a consequence, netropsin and distamycin were used as the basic structures for the synthesis of numerous analogues to enable the investigation and modulation of their minor-groove binding. This was also achieved by using combinatorial approaches. A particular challenge was to generate selective binders for GC base pairs. One approach was based on the assumption that the introduction of a hydrogen-bond acceptor in the pyrrole

Controlling the activity of peptides and proteins with smart nucleic acid–protein hybrids

Oligonucleotide-peptide conjugates have frequently been used to control the localisation of the conjugate molecule. For example, the oligonucleotide segment has allowed spatially addressed immobilization of peptides and proteins on DNA-arrays via hybridisation while the peptide part has most frequently been used to confer transfer of oligonucleotide cargo into live cells. The regulation of functional properties such as the affinity of these bioconjugates for protein targets has rarely been addressed. This review article describes the current developments in the application of smart oligonucleotide-peptide hybrids. The mutual recognition between nucleic acid segments is used to constrain the structure or control the distance between peptide and protein segments. Application of these new type of oligonucleotide-peptide hybrids allowed not only the regulation of binding affinity of peptide ligands but also control of enzymatic and optical activity of proteins.

DNA and RNA-controlled switching of protein kinase activity.

Constrained: The readily programmable nucleic acid mediated recognition is used to constrain a phosphopeptide that was flanked by PNA segments. RNA‐based switching allows control over the activity of target enzymes such as the protein kinase Src. It might thus be feasible to transduce changes of the concentration of selected RNA molecules to changes of the activity of signal transduction proteins.

Chemical control of biomolecular interaction modules

The mutual recognition of biomacromolecules often is mediated by dedicated interaction modules. We take two main approaches in order to recognize and control nucleic acid-nucleic acid, protein-protein, and protein-nucleic acid interactions. In one, the rules that govern the formation of nucleic acid structures are used to design molecules that respond to the presence of nucleic acid or protein targets by showing changes of conformation or reactivity. For example, hybrid molecules can transduce changes of nucleic acid structure to changes of peptide structure, and vice versa. The other approach takes advantage of protein domains that once may form the basis of sensor materials and control elements. However, the current chemical synthesis methods have still not reached the level of maturity required to provide routine access to folded protein domains. In this article, we also describe recent progress that may facilitate the chemical synthesis of protein interaction domains.

Recognizing and Controlling Biomolecules with “Smart” Hybridization-based Switches

The rules that govern the formation of DNA duplex structures are well known. On one hand, this process is used in the design of probe molecules that report the presence of target nucleic acids by responding to changes of structure and reactivity. On the other hand, molecules may be developed that transduce changes of nucleic acid structure to changes of peptide structure, and vice versa. Applications in the fields of bioanalytical chemistry and synthetic biology are discussed.