DNA duplex–quadruplex exchange as the basis for a nanomolecular machine

TLDR

Nanodevices that perform linear or rotary movements are of great interest, and nucleic acids have recently been proposed as potential nanomolecular machines capable of rotation and scissors‑like opening and closing. The authors present a nanomachine that performs an extension–contraction movement. The device is a single 21‑base oligonucleotide that uses a duplex–quadruplex equilibrium, driven by sequential addition of DNA strands and producing a duplex by‑product. The duplex–quadruplex interconversion drives a 5‑nm two‑stroke linear motor‑type movement, observed via FRET spectroscopy.

Abstract

There is currently great interest in the design of nanodevices that are capable of performing linear or rotary movements. Protein molecular machines are abundant in biology but it has recently been proposed that nucleic acids could also act as nanomolecular machines in model systems. Several types of movements have been described with DNA machines: rotation and “scissors-like” opening and closing. Here we show a nanomachine that is capable of an extension–contraction movement. The simple and robust device described here is composed of a single 21-base oligonucleotide and relies on a duplex–quadruplex equilibrium that may be fueled by the sequential addition of DNA single strands, generating a DNA duplex as a by-product. The interconversion between two well defined topological states induces a 5-nm two-stroke, linear motor-type movement, which is detected by fluorescence resonance energy transfer spectroscopy.