Continuous observation of the stochastic motion of an individual small-molecule walker

Abstract

Motion -be it the ability to change shape, rotate or translate -is an important potential asset for functional nanostructures. For translational motion, a variety of DNA-based and small-molecule walkers have been created, but observing the translational motion of individual molecules in real time remains a significant challenge. Here, we show that the movement of a small-molecule walker along a 5-foothold track can be monitored continuously within a protein nanoreactor. The walker is an organoarsenic(III) molecule with exchangeable thiol ligands, and the track a line of cysteine residues 6Å apart within an α-haemolysin protein pore that acts as the nanoreactor. Changes in the flow of ionic current through the pore reflect the individual steps of a single walker, which require the making and breaking of As-S bonds, and occur in aqueous solution at neutral pH and room temperature. The walker moves considerably faster (~0.7 s per step) than previous walkers based on covalent chemistry and is weakly processive (6 ± 1 steps per outing). It shows weak net directional movement, which can be described by a thermodynamic sink arising from the different environments of the cysteines that constitute the track.Creating nanoscale objects that can change shape1, rotate2,3 or translate4 is an important goal in nanotechnology. Examples of translational motion include chemotactic droplets5, chemically propelled objects6, and DNA walkers7, some of which offer the possibility of cargo delivery8-10. The development of small-molecule walkers is also under intense investigation11. The motion of such walkers can be random, or biased directionally through asymmetry of the track or the input of "fuel". Examples of non-covalent small-molecule walkers embrace various rotaxanes and related structures12. Walkers that employ covalent chemistry afford optimal spatial precision13, 14. For example, Leigh and co-workers observed the slow random motion of a functionally symmetric covalent walker, α-methylene-4-nitrostyrene, with a step-time of hours on a 9-foothold oligoethylenimine track15, 16. The walker lingered in a thermodynamic well at a terminal track site, thereby Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:http://www.nature.com/authors/editorial_policies/license.html#terms * Correspondence and requests for materials should be addressed to G.S.P (gokce.pulcu@chem.ox.ac.uk) or H.B (hagan.bayley@chem.ox.ac.uk). Author Contributions: G.S.P. designed and performed experiments, analyzed data and wrote the paper; E.M. prepared the protein samples; L.C. synthesized the molecular walker and performed experiments; H.B. designed experiments, analyzed data and wrote the paper.Author Information: Readers are welcome to comment on the online version of the paper.The authors declare no competing financial interests. Europe PMC Funders GroupAuthor Manuscript Nat Nanotechnol. Author manuscript; available in PMC 2016 ...

Directional control of a processive molecular hopper

“…Dissociation of the hopper from the track was never seen (n > 30 outings on different tracks), which implies that substantial improvements on step numbers would be achieved if the stability of the bilayer were improved. In comparison, previous synthetic small-molecule walkers moved directionally for less than 10 steps (5,12). Wild-type kinesins typically exhibit a mean step number of 75 to 175 before dissociation (2, 3).…”

Semisynthetic protein nanoreactor for single-molecule chemistry

“…Single-molecule chemistry has attracted interest because it provides insights into fundamental chemical processes that cannot be observed at the ensemble scale (6)(7)(8). However, chemistry carried out within the αHL nanoreactor has so far been confined to the reactions of thiolates (i.e., deprotonated Cys side chains) (7)(8)(9)(10)(11)(12) and derivatives of the side chains of Cys residues (13,14). The incorporation of unnatural amino acids into the αHL pore would substantially advance single-molecule chemistry, through the incorporation of a large variety of individual side chains as well as multiple substitutions.…”

Single‐Molecule Observation of Intermediates in Bioorthogonal 2‐Cyanobenzothiazole Chemistry

“…for MESNa, K d1 = k À1 /k 1 = 0.025 m versus K d2 = k À2 /k 2 = 13 m). Because the lifetime of the adduct with one ligand is over 80-times longer than that with two ligands,C BT molecules have the capacity to act as molecular walkers on amulti-thiol track, [22] ap ossibility yet to be tested. It is worth noting that the termination of the reversible chemistry occurred always from the thioimidate level, presumably through hydrolysis.…”

“…[36] Fore xample, am ulti-cysteine track can potentially interact with CBT molecules through consecutive dynamic covalent reactions, for which the association and dissociation kinetics determine the processivity of the mobile molecules. [22,37] When individual aminothiols reacted with aC BT nanoreactor,w ew ere able to resolve for the first time two transient intermediate species in the formation of thiazolidines or dihydrothiazines based on the root-mean-square noise of their current states. Although the current noise associated with molecular structure cannot be predicted at present, our results will add to the data accumulating in this area.…”