Mapping the positions of beads on a string: dethreading rotaxanes by molecular force spectroscopy

Abstract

The direct manipulation by atomic force microscopy (AFM) of individual macrocycles within a rotaxane offers a potential route to a new sequencing tool for complex macromolecules such as polysaccharides, glycoproteins and nucleic acids. In this paper we demonstrate for the first time that a sliding contact made between a macrocycle, α-cyclodextrin, and its polymer axle by an AFM tip can be used to map the positions of specific groups along the polymer as if they were beads along a string, thereby generating sequence information. We find very good agreement (linear fit with slope = 1.03, R(2) = 0.968) between the calculated and measured positions of phenylenediamine and benzenetricarboxylic acid groups within polymers of polyethylene oxide (PEO). The rupture force profiles attributable to the dethreading interactions of phenylenediamine and benzenetricarboxylic acid differ observably from each other and, in the latter case, from the rupture of the corresponding host-guest complex. As well as opening the way to a macromolecular sequencing technique, the ability demonstrated by this method to manipulate the dethreading of a rotaxane offers a new tool for investigating the process energetics in a wide array of spontaneously forming and forced rotaxane systems.

Polymer sequencing by molecular machines: a framework for predicting the resolving power of a sliding contact force spectroscopy sequencing method

“…Previous analyses of the challenges to polymer sequencing by single molecule force spectroscopy (SMFS), with or without a sliding contact, have focused on DNA sequencing. 22,23 We have shown previously that measurements made with the SCFS approach described here yielded excellent agreement with the predicted positions of aromatic rings substituted into PEG polymers based upon the measured molecular weights of the polymers, 8 and that the CD bead could be used to unzip interactions between the polymer axle and molecules bound to specific sequences within that polymer. 9 Thus the available evidence suggests that SCFS may offer a method for mapping or sequencing long, linear polymers where there are large differences between monomers or blocks, or where specific sequences are recognised by other molecules.…”

“…Analysing sliding contact force spectra In addition to previously published 8,9 datasets using α-CD and stations 1, 2, 4 and 5 on PEG axles ( pyromellitic acid, aminoaniline, guluronic and mannuronic acid respectively; see Fig. 2 for structures), we have conducted SCFS experiments using β-CD beads in order to probe the effect of differences in pore size.…”

“…Recently, the emergence of sequence-defined synthetic polymers has created a new class of materials in which relevant properties may be controlled with much greater precision than before, where sequence directly controls function. [5][6][7] Previously the authors 8,9 and others 10 explored the feasibility of a new route, here called sliding contact force spectroscopy (SCFS), to obtaining sequence information in linear heteropolymers by atomic force microscopy (AFM), but the limits and applicability of the method have not been fully explored. Here we set out to describe the parameters that determine how easy or difficult it is to pass a cyclodextrin (CD)-based macrocycle over a particular monomer, and from that basis derive a framework within which we can predict whether the monomers in a particular copolymer are distinguishable using this method.…”

“…18 The most common terminology 19 for describing the processes occurring in a rotaxane depicts a macrocyclic 'bead' shuttling between 'stations' on the polymer axle. In the SCFS method described here and previously, [8][9][10] the bead is α-or β-cyclodextrin (α-CD and β-CD hereafter) and the stations are the individual monomers comprising the polymer axle, while the AFM probe supplies the unidirectional driving force for shuttling the bead between stations (hereafter 'sliding') under a load generated by the controlled separation of probe and sample. Fig.…”

Sliding Contact Dynamic Force Spectroscopy Method for Interrogating Slowly Forming Polymer Cross-Links

“…Iterations of this 120 approach have been used to manipulate α-CD beads forming a polyrotaxane with PEG back 121 and forth along the PEG axle 19 , and to measure the force required to drive a bead between 122 two stations in a rotaxane 20,21 . It has also been considered as a potential sequencing tool for 123 DNA and other polymers [22][23][24][25] . 124 While SCFS offers the opportunity to measure the difference in interaction between the 138 sliding CD and the monomers in the polymer axle during sliding, the CD may also be used as 139 a molecular 'zipper' to unzip molecules bound to sites incorporated into the polymer.…”