Nanoscale Structure and Interaction of Condensed Phases of DNA–Carbon Nanotube Hybrids

Abstract

Condensation of DNA–carbon nanotube (CNT) hybrids dispersed in aqueous solutions can be induced by elevated hybrid concentrations, salts, or crowding agents. DNA–CNT condensates exhibit either nematic ordering or amorphous aggregates, dependent on the nature of interhybrid interactions. This study employed X-ray diffraction (XRD) to determine nanoscale structures of the condensates, including the presence of positional ordering, interaxial distances, and the range of ordered domains. To probe the effects of DNA sequence, two types of CNT hybrids, dispersed by genomic DNA of random sequence and synthetic oligonucleotides respectively, were studied under identical conditions. The osmotic stress method was further used to quantify force–distance dependencies of the DNA–CNT hybrids to elucidate the relation between interhybrid interactions and condensate structures. We observed that, independent of DNA sequence, lyotropic DNA–CNT phases showed weak positional ordering with long interhybrid distances, salt-induced condensates were amorphous, crowding-condensed DNA–CNTs were the most ordered with pronounced XRD peaks, and interhybrid interactions were defined by short-range hydration repulsion and long-range electrostatic repulsion. Conversely, the effects of DNA sequence became evident as to their quantitative force–distance relationships. Genomic DNA of random sequence consistently gave longer interhybrid distances than synthetic oligonucleotides, which we attribute to the likely differences in their hybrid diameters