DNA Condensation-Inspired Assembly of DNA Nanotubes into Reversible Superstructures: A Base Pairing-Orthogonal Way to Create Rings, Bundles, or Vast Networks

Abstract

By offering exquisite programmability, sequence-specific DNA self-assembly is the foundation of structural DNA nanotechnology but necessitates custom-designed DNA strands. Finding assembly principles orthogonal to base pairing is thus desirable not only to organize DNA in a sequence-independent manner but also to bring additional levels of control over preformed DNA self-assembled structures. Here, we report that self-assembled DNA nanotubes, upon the addition of DNA-condensing multivalent cations, including the naturally occurring polyamines spermidine and spermine, spontaneously condense to form higher-order structures including well-defined micrometer-sized rings and 30 to 60 nm wide bundles, in which DNA strands are parallelly packed with an interspacing ranging from 2.5 to 3 nm. In the semidilute regime, a new organization into vast tridimensional networks is observed for a specific range of charge ratios, prior to the formation of highly clustered bundles. We demonstrate that the process is electrostatically driven, conferring a ubiquitous character to this assembly principle. We report in particular a pivotal role of the counterion valency (the higher it is, the lower the charge ratio required), emphasizing the role of DNA neutralization through the entropically driven exchange between DNA counterions and the condensing agents. We also show an important role of DNA concentration for controlling the individual or interconnected nature of the formed structures as well as favoring the nanotube assembly. We finally devise methods for additional control, such as superstructure disassembly upon monovalent ion addition or photocontrol using a photosensitive DNA-condensing agent.