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

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. molecular machine ͉ FRET ͉ DNA structure ͉ G-quartet

Two-repeat Tetrahymena Telomeric d(TGGGGTTGGGGT) Sequence Interconverts Between Asymmetric Dimeric G-quadruplexes in Solution

“…[41][42][43] In addition, we note that understanding G-quadruplex structural elements (G-tetrad core and loops), as well as their folding/unfolding kinetics, would also help in designing new scaffolds for useful molecular shapes 10,44 or for basis of nanodevices. 45,46 …”

A DNA Nanotransport Device Powered by Polymerase ϕ29

“…In recent years, there has been tremendous progress in DNA based nanodevices [3,11,12,19,20,25,26,29,30,42,43,[53][54][55]. Recent research has explored DNA as a material for self-assembly of nanoscale objects [10,18,21,24,35,49,51,52], for performing computation [2, 6-8, 22, 23, 47, 48, 50], and for the construction of nanomechanical devices [3, 11-13, 19, 25, 29, 36-39, 42, 44, 45, 53, 56, 57].…”

Biomolecules and Pure Carbon Aggregates: An Application Towards “Green Electronics”

“…Nanowires known as G4-wires [34] (or quadruplexes), consist of stacked guanine (G) tetrads (G4). These one-dimensional polymers act as prospective candidates for bio-molecular electronics because, due to the low ionization potential of guanine (the lowest among nucleicacid bases), they might be suitable to mediate charge transport by hole conduction along the helix, and have even been suggested as nano-mechanical extension-contraction machines [35].…”