Modular DNA-programmed assembly of linear and branched conjugated nanostructures

A new strategy for self-assembly and covalent coupling of encoded molecular modules into nanostructures with predetermined connectivity has been developed. The method uses DNA-functionalized oligo(phenylene ethynylene)-derived organic modules for controlling the assembly and covalent coupling of multiple modules. Rigid linear modules (LM) and tripoidal modules (TM) were functionalized with short oligonucleotides at each terminus. They can hybridize and thereby link up modules containing complementary sequences. Each terminus of the oligo(phenylene ethynylene) modules also consists of a salicylaldehyde moiety, which can form metal-salen complexes with other modules. The salicylaldehyde groups of two modules are brought in proximity when their adjoining DNA sequences are complementary, and they selectively form a manganese-salen complex in the presence of ethylenediamine and manganese acetate. The resulting structures consist of a matrix of linear and branched oligo(phenylene ethynylene)s which are linked by conjugated and rigid manganese-salen complexes. These nanostructures are potential conductors for applications in molecular electronics.     

Upregulation of the SERCA-type Ca2+ pump activity in response to endoplasmic reticulum stress in PC12 cells

Background  

Ca²⁺-ATPases of endoplasmic reticulum (SERCAs) are responsible for maintenance of the micro- to millimolar Ca²⁺ ion concentrations within the endoplasmic reticulum (ER) of eukaryotic cells. This intralumenal Ca²⁺ storage is important for the generation of Ca²⁺ signals as well as for the correct folding and posttranslational processing of proteins entering ER after synthesis. ER perturbations such as depletion of Ca²⁺ or abolishing the oxidative potential, inhibition of glycosylation, or block of secretory pathway, activate the Unfolded Protein Response, consisting of an upregulation of a number of ER-resident chaperones/stress proteins in an effort to boost the impaired folding capacity.     

Toehold-Mediated Strand Displacement in a Triplex Forming Nucleic Acid Clamp for Reversible Regulation of Polymerase Activity and Protein Expression

Triplex forming oligonucleotides are used as a tool for gene regulation and in DNA nanotechnology. By incorporating artificial nucleic acids, target affinity and biological stability superior to that of natural DNA may be obtained. This work demonstrates how a chimeric clamp consisting of acyclic (L)-threoninol nucleic acid (aTNA) and DNA can bind DNA and RNA by the formation of a highly stable triplex structure. The (L)-aTNA clamp is released from the target again by the addition of a releasing strand in a strand displacement type of reaction. It is shown that the clamp efficiently inhibits Bsu and T7 RNA polymerase activity and that polymerase activity is reactivated by displacing the clamp. The clamp was successfully applied to the regulation of luciferase expression by reversible binding to the mRNA. When targeting a sequence in the double stranded plasmid, 40 % downregulation of protein expression is achieved.     

DNA-templated covalent coupling of G4 PAMAM dendrimers

Generation-4 polyamidoamine (PAMAM) dendrimers were surface-functionalized with azides or alkynes and conjugated to one DNA strand. DNA-controlled self-assembly of alternating azide and alkyne dendrimers on a DNA template enabled the coupling of the dendrimers by the azide-alkyne "click" reaction to form covalently coupled dimers, trimers, and tetramers. Polymerization of the DNA-dendrimer conjugates was also demonstrated, as well as assembly in a circular structure on DNA origami and imaging by atomic force microscopy.     

Controlled formation and topologies of thiophenolate-based macrocycles: rings, cylinders and bowls

The Schiff-base condensations of 1,3-diaminopropane with a protected thiophenol dialdehyde in the presence of Ni(2+), Pd(2+) or Zn(2+) can be controlled to yield either mononuclear acyclic, or 2 + 2 and 4 + 4 macrocyclic complexes by the choice of both metal cation and counteranion. The Ni(2+) complex of the 2 + 2 macrocycle contains two square-planar nickel ions and shows an arrangement similar to one observed previously: the mu-S atoms of the thiophenolate groups are pyramidal and lie on the same side of the plane defined by the four N atoms of the macrocycle to give a V-shaped molecule. By contrast, the Zn(2+) complex of the 2 + 2 macrocycle undergoes oligomerization to yield a bowl-shaped hexanuclear complex that includes a mu(3)-carbonate anion. Essential for this topology is the presence of three mu(3)-S-thiophenolato groups that link the three macrocyclic units to form a Zn(3)S(3) ring that seals the bottom part of the bowl. In this arrangement, one of the pyramidal mu(3)-S atoms in each dinuclear Zn(2+) complex is inverted relative to the arrangement observed for the dinickel complexes. Molecular modelling suggests that inversion about the mu-S atoms of the 2 + 2 macrocyclic complexes is readily accessible at room temperature and that the contrasting arrangements observed for the Ni(2+) and Zn(2+) complexes are those energetically most favourable for the respective metal ions. Rare 4 + 4 macrocyclic complexes are isolated as neutral dinuclear complexes for Ni(2+) and Pd(2+) and as a tetranuclear complex cation for Zn(2+). The topologies of these systems contrast significantly: those with two square-planar Ni(2+) or Pd(2+) ions form extended rings, while that with Zn(2+) forms a sulfur-lined cylinder which hosts acetonitrile molecules in the crystalline state. Reaction conditions can also be optimised to produce 2 + 1 acyclic ligands as their mononuclear Ni(2+) and Pd(2+) complexes, providing potentially useful building blocks for production of more complicated macrocyclic and supramolecular systems.     

A modular approach to DNA-programmed self-assembly of macromolecular nanostructures

DNA-programmed organic reactions are new and powerful tools for assembling chemical compounds into predetermined complex structures and a brief review of their use is given. This approach is particular efficient for the selection and covalent coupling of multiple components. DNA-templated synthesis is used for polymerization of PNA tetramers and for copying of the connectivity information in DNA. Direct DNA-programmed multicomponent coupling of custom designed organic modules is described. The macromolecular structures obtained are highly conjugated potentially conducting nanoscaffolds. Some future developments in this area are discussed.     

Self-assembly of aluminium-salen coupled nanostructures from encoded modules with cleavable disulfide DNA-linkers

DNA-directed coupling of organic modules by formation of stable aluminium-salen complexes, makes possible the subsequent reductive cleavage of disulfide linkers and release of the two oligonucleotide chains attached to each building-block.