From Ribbons to Networks: Hierarchical Organization of DNA-Grafted Supramolecular Polymers

Abstract

DNA-grafted supramolecular polymers (SPs) allow the programmed organization of DNA in a highly regular, one-dimensional array. Oligonucleotides are arranged along the edges of pyrene-based helical polymers. Addition of complementary oligonucleotides triggers the assembly of individual nanoribbons resulting in the formation of extended supramolecular networks. Network formation is enabled by cooperative coaxial stacking interactions of terminal GC base pairs. The process is accompanied by structural changes in the pyrene polymer core that can be followed spectroscopically. Network formation is reversible and disassembly into individual ribbons is realized either via thermal denaturation or by addition of a DNA separator strand.The creation of functional nanoscale structures represents a major goal of today's nanotechnology. DNA-based materials are of primary interest for the construction of functional platforms. [1][2][3][4] Proper choice of the nucleotide sequence provides control over aromatic stacking and hydrogen bonding interactions, 5-7 thus enabling the assembly of systems with a high degree of complexity. [8][9][10][11] Approaches towards the preparation of functional DNA materials include the designed DNA self-assembly, 12-15 the grafting of oligonucleotides onto metal nanoparticles (NPs) 16 and other surfaces, [17][18][19] as well as polymers. [20][21][22][23] The latter class, DNA-grafted polymers, has been pioneered by Nguyen and Mirkin and gained increasing attention over the last years. 24,25 We have recently introduced DNA-grafted supramolecular polymers (SPs). 26 These self-assembled structures appear as one-dimensional (1D) ribbons, consisting of an oligopyrenotide core 27 with arrays of singlestranded oligonucleotides appended onto its edges. The non-covalent nature of SPs brings the additional feature of reversibility of the polymerization process. [28][29][30][31][32][33][34] Furthermore, it enables the formation of polymers with a high DNA grafting density. 25,26 Herein we describe the hierarchical organization of DNA-grafted SPs. It is shown that individual ribbons assemble into extended networks through a highly cooperative mesh of DNA blunt end stacking interactions.Chimeric oligomers Py-a, Py-b and Py-c (Scheme 1) are all composed of a heptapyrenotide part and an appended oligonucleotide.They were prepared via solid-phase synthesis, purified by RP-HPLC and characterized by MS (SI). The two complementary oligonucleotides 1a (separator strand) and 1b (connector strand) have the same nucleobase sequence as the respective corresponding chimeric oligomers Py-a and Py-b; 1c is complementary to the oligonucleotide part of Py-c. DNA-grafted SPs are typically performed by slow annealing. Thus, a 2 μM solution of Py-a in aqueous buffer (10 mM sodium phosphate, pH=7.0 and 250 mM sodium chloride) is cooled from 95° to 20°C using a gradient of 0.1°C/min. Stacking interactions between pyrenes drive the self-assembly of polymeric ribbons. The polymerization process leads to the development ...

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“…Here pyrene modified DNA hybrids as building blocks are capable to form supramolecular complexes. In 2015, Häner group developed that the chimeric oligomers composed of a heptapyrenotide part and an appended DNA strand were assembled into helical nanoribbons, driven by aromatics tacking interactions among pyrene units [35]. The nanoribbons could be changed to extended networks via DNA hybridization [35,36].…”

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