Synthesis of Eight-Arm, Branched Oligonucleotide Hybrids and Studies on the Limits of DNA-Driven Assembly

Abstract

Oligonucleotide hybrids with organic cores as rigid branching elements and four or six CG dimer strands have been shown to form porous materials from dilute aqueous solution. In order to explore the limits of this form of DNA-driven assembly, we prepared hybrids with three or eight DNA arms via solution-phase syntheses, using H-phosphonates of protected dinucleoside phosphates. This included the synthesis of (CG)8TREA, where TREA stands for the tetrakis[4-(resorcin-5-ylethynyl)phenyl]adamantane core. The ability of the new compounds to assemble in a DNA-driven fashion was studied by UV-melting analysis and NMR, using hybrids with self-complementary CG zipper arms or non-self-complementary TC dimer arms. The three-arm hybrid failed to form a material under conditions where four-arm hybrids did so. Further, the assembly of TREA hybrids appears to be dominated by hydrophobic interactions, not base pairing of the DNA arms. These results help in the design of materials forming by multivalent DNA-DNA interactions.

Solution‐Phase Synthesis of Branched Oligonucleotides with up to 32 Nucleotides and the Reversible Formation of Materials

“…One challenge is to handle richly-functionalized, labile biomacromolecules. The first target molecule contained a tetrakis(p-hydroxyphenyl)adamantane (TPA) core, which is considerably smaller than those studied earlier, [35,36] but features the phenols as reactive nucleophiles, for which much of our earlier solution-phase work had been optimized. Further, simultaneous couplings at the termini of all arms of the branched constructs call for high-yielding reactions, a problem known from dendrimer chemistry.…”

“…Sequences as short as CG dimers can act as "zippers" and bring about the assembly process at a high concentration of divalent cations. [36] This prompted us to shift our attention to branched DNA hybrids with a smaller, entirely aliphatic core, hoping to build materials with larger pore size without losing the ability to steer the assembly process through choice of the sequence and length of the DNA arms. [35] But, when the number of arms was increased to eight and the size of the rigid and lipophilic core increased, the sequence dependence of the assembly process was lost, indicating that it was no longer dominated by Watson-Crick base pairing.…”

The competing effects of core rigidity and linker flexibility in the nanoassembly of trivalent small molecule-DNA hybrids (SMDH3s)–a synergistic experimental-modeling study

“…30 The specific matching of the sequences between complementary comonomers imposed an orientation control that favors the formation of caged dimers over face-to-face analogs. 9 The high GC content of the arms stabilizes duplex formation, which also promotes the formation of caged dimers via intramolecular hybridization between complementary comonomers.…”

“…Together, these design features can help to counter interactions between the hydrophobic cores and prevent the formation of large-oligomer networks via hydrophobic nucleation mechanism. 30 …”

Encapsulating Active Pharmaceutical Ingredients in Self‐Assembling Adamantanes with Short DNA Zippers

“…Because of multivalent interactions, dinucleotide arms of the sequence 5′‐CG‐3′ suffice to induce the formation of materials upon hybridization of hybrids with four, six or eight arms in aqueous buffer containing magnesium ions 24, 25. Efficient and scalable solution‐phase syntheses make these compounds available at a fraction of the cost of linear oligonucleotides 26, 27.…”