Cooperative Melting in Caged Dimers of Rigid Small Molecule-DNA Hybrids

Abstract

Rigid small-molecule DNA hybrids (rSMDHs) have been synthesized with three DNA strands attached to a rigid tris(phenylacetylene) core. When combined under dilute conditions, complementary rSMDHs form cage dimers that melt at >10 degrees C higher and much sharper than either unmodified DNA duplexes or rSMDH aggregates formed at higher concentrations. With a 2.97 average number of cooperative duplexes, these caged dimers constitute the first example of cooperative melting in well-defined DNA-small-molecule structures, demonstrating the important roles that local geometry and ion concentration play in the hybridization/dehybridization of DNA-based materials.

Two Base Pair Duplexes Suffice to Build a Novel Material

“…Their hybridization properties are also different from three-arm DNA hybrids with a large planar core. [19] The melting point of our hybrids is much higher than that of linear control duplexes, and the transitions are not highly cooperative. Further, the smaller the designed lattice constant, the greater the effect of salt on the stability of the assemblies.…”

“…Hybrids with longer DNA strands give higher melting points than their linear counterparts, statistically coated nanoparticles, or three-arm hybrids. [19] We expect the effect of multivalent binding to be even more pronounced for octahedral cores inducing the formation of six duplexes per hybrid.…”

“…At 4 mm, no precipitate forms, at 15 mm the onset of precipitation is approximately 15 8C, and at 120 mm, precipitation starts at approximately 20 8C. According to the available data from solutions ranging from 4-15 mm (hexamer and tetramer hybrid) and 4-150 mm (dimer hybrid), no signs of sharpening of the transition [19] are seen when lowering the concentration. Further, the temperature of the onset of precipitation increases both with increasing salt concentration and with increasing hybrid concentration for (CG) 4 TPM, again showing no signs of caged dimer formation.…”

Pore Size Variability of DNA Nanomeshes by Polymerase Chain Reaction

“…phosphoramidite by a DNA synthesizer, [14][15][16][17][18] because organic hubs has been proved to be amenable to the generation of multiplearmed DNA structures. [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.…”

“…Multiple-armed DNA structures consisting of oligonucleotides have been reported previously to generate high molecular-weight assemblies. [14][15][16][17][18]23,24 Their structural information has not been drawn yet in detail, but McLaughlin suggested an idealized, periodic DNA lattice with regular and defined pores. 12 We postulate that the structures were composed of many self-assembled nanomeshes with a broad range of size scales.…”