Modular DNA-Programmed Assembly of Linear and Branched Conjugated Nanostructures

Abstract

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.

Rational Design of DNA Nanoarchitectures

“…Gothelf et al attached DNA oligomers to salicylaldehyde groups of two-and threearmed compounds, called linear oligonucleotide-functionalized modules (LOMs; Figure 11 c) and tripoidal OMs (TOMs; Figure 11 d), respectively. [78] In their approach, the DNA strands guide the self-assembly of linear and branched structures by positioning the branch-point modules in proximity to one another. The actual assembly is then carried out by covalent linkage of the individual compounds and the DNA oligomers can subsequently be removed from the assembled products.…”

“…To this end, building blocks with an inherent tendency to form curved structures were used, which is realized in modified 4 4 tiles, [50] DAE-DX tiles (30 in Figure 12), [89,90] and TX tiles. [91] Interestingly, tubular DNA assemblies which were obtained from motifs 11 and 20, respectively, were metalized by electroless silver deposition and resulted in the production [77] compounds with salicylaldehyde groups (c, d), [78] a branched alkane containing a quaternary carbon atom (e), [80] and a porphyrin derivative (f). [85] The stars in images (b-f) mark the attachment points of the DNA oligomers.…”

Chemistry on Nucleic Acid Templates

“…Calderone, Liu, and co-workers then expanded the repertoire of NA-templated chemistry to an impressive range of chemical reactions, including [2 þ 3] dipolar cycloadditions, Wittig olefinations, or Pdmediated coupling (Heck) reactions [67], but also chemistries that had already been used to create NA-related structures like amine acylations and reductive aminations ( [72]. Carell, Shionoya, and co-workers have reported the DNAtemplated synthesis of interstrand salen complexes, thereby creating metallo-salen base pairs with potential applications in nanoelectronics [82].…”

Pore Size Variability of DNA Nanomeshes by Polymerase Chain Reaction

“…[19][20][21][22][23][24][25] Synthesis of oligonucleotides has routinely been carried out from 3' to 5' terminus, because the primary 5'-hydroxyl group is significantly more reactive than the secondary 3'-hydroxyl group, making it straightforward to protect the 5'-hydroxyl group with the DMT group and leaving the 3'-hydroxyl group available to form the phosphoramidite. In this work, we, however, used four deoxynucleotide-5'-CE phosphoramidites in order to synthesize the required primers from the 5'-"Trebler" phosphoramidite, which contained 3'-OH ends essential for the PCR processes.…”