DNA nanomachines and nanostructures involving quadruplexes

TLDR

DNA’s self‑assembly and structural polymorphism, including G‑quadruplexes and i‑DNA, have enabled the design of nanomachines since 2002. The study introduces the G‑quadruplex and i‑DNA structures used in nanomachines and details the opening and closing steps that enable their cyclic operation. A quadruplex–duplex molecular machine is described, outlining its formation rules, opening/closing kinetics, and the physicochemical parameters that influence its efficiency.

Abstract

DNA is an attractive component for molecular recognition, because of its self-assembly properties. Its three-dimensional structure can differ markedly from the classical double helix. For example, DNA or RNA strands carrying guanine or cytosine stretches associate into four-stranded structures called G-quadruplexes or i-DNA, respectively. Since 2002, several groups have described nanomachines that take advantage of this structural polymorphism. We first introduce the unusual structures that are involved in these devices (i.e., i-DNA and G-quadruplexes) and then describe the opening and closing steps that allow cycling. A quadruplex–duplex molecular machine is then presented in detail, together with the rules that govern its formation, its opening/closing kinetics and the various technical and physico-chemical parameters that play a role in the efficiency of this device. Finally, we review the few examples of nanostructures that involve quadruplexes.