Noncovalent Spin-Labeling of DNA and RNA Triplexes.

Studying nucleic acids often requires labeling. Many labeling approaches require covalent bonds between the nucleic acid and the label, which complicates experimental procedures. Noncovalent labeling avoids the need for highly specific reagents and reaction conditions, and the effort of purifying bioconjugates. Among the least invasive techniques for studying biomacromolecules are NMR and EPR. Here, we report noncovalent labeling of DNA and RNA triplexes with spin labels that are nucleobase derivatives. Spectroscopic signals indicating strong binding were detected in EPR experiments in the cold, and filtration assays showed micromolar dissociation constants for complexes between a guanine-derived label and triplex motifs containing a single-nucleotide gap in the oligopurine strand. The advantages and challenges of noncovalent labeling via this approach that complements techniques relying on covalent links are discussed.

Turning DNA Binding Motifs into a Material for Flow Cells.

Nanoscale assemblies of DNA strands are readily designed and can be generated in a wide range of shapes and sizes. Turning them into solids that bind biomolecules reversibly, so that they can act as active material in flow cells, is a challenge. Among the biomolecular ligands, cofactors are of particular interest because they are often the most expensive reagents of biochemical transformations, for which controlled release and recycling are desirable. We have recently described DNA triplex motifs that bind adenine-containing cofactors, such as NAD, FAD and ATP, reversibly with low micromolar affinity. We sought ways to convert the soluble DNA motifs into a macroporous solid for cofactor binding. While assemblies of linear and branched DNA motifs produced hydrogels with undesirable properties, long DNA triplexes treated with protamine gave materials suitable for flow cells. Using exchangeable cells in a flow system, thermally controlled loading and discharge were demonstrated. Employing a flow cell loaded with ATP, bioluminescence was induced through thermal release of the cofactor. The results show that materials generated from functional DNA structures can be successfully employed in macroscopic devices.

Tyrosine-Based Ionic Liquid Crystals: Switching from a Smectic A to a Columnar Mesophase by Exchange of the Spherical Counterion.

Synthetic strategies were developed to prepare l-tyrosine-based ionic liquid crystals with structural variations at the carboxylic and phenolic OH groups as well as the amino functionality. Salt metathesis additionally led to counterion variation. The liquid-crystalline properties were investigated by differential scanning calorimetry (DSC), polarizing optical microscopy (POM) and X-ray diffraction (WAXS, SAXS). The symmetrical ILC chlorides bearing the same alkyl chain at both the ester and ether but either an acyclic or cyclic guanidinium group displayed enantiotropic SmA2 mesophases with phase widths of 31-88 K irrespective of the head group. It was particularly the replacement of chloride in the acyclic guanidinium ILC by hexafluorophosphate that induced a phase change from SmA2 to Colr . This phase change was attributed to a higher curvature of the interface due to the larger anion, which increased the effective head group cross-sectional area of the amphiphilic ILC. The unsymmetrical acyclic guanidinium chlorides, bearing a constant C14 ester and variable alkyl chains on the phenolic position, formed enantiotropic SmA2 phases. The derivative with the largest difference in chain lengths, however, displayed a Colr phase, resulting from discoid aggregates of the cone-shaped guanidinium chloride. The results are discussed in terms of the packing parameters, which indicate that the phase behaviour of the thermotropic tyrosine-based ILCs shows analogies to those of lyotropic liquid crystals.

Stabilizing DNA nanostructures through reversible disulfide crosslinking.

Designed DNA nanostructures can be generated in a wide range of sizes and shapes and have the potential to become exciting tools in material sciences, catalysis and medicine. However, DNA nanostructures are thermally labile assemblies of delicate biomacromolecules, and the lability hampers the use in many applications. Disulfide crosslinking is nature's successful approach to stabilize folded proteins against denaturation. It is therefore interesting to ask whether similar approaches can be used to stabilize DNA nanostructures. Here we report the synthesis of two 2'-deoxynucleoside phosphoramidites and two nucleosides linked to controlled pore glass that can be used to prepare oligodeoxynucleotides with protected thiol groups via automated DNA synthesis. Strands with one, two, three or four thiol-bearing nucleotides were prepared. One nicked duplex and three different nanostructures were assembled, the protected thiols were liberated under non-denaturing conditions, and disulfide crosslinking was induced with oxygen. Up to 19 crosslinks were thus placed in folded DNA structures up to 1456 nucleotides in size. The crosslinked structures had increased thermal stability, with UV-melting points 9-50 °C above that of the control structure. Disulfides were converted back to free thiols under reducing conditions. The redox-dependent increase in stability makes crosslinked DNA nanostructures attractive for the construction of responsive materials and biomedical applications.