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

We evaluate an AFM-based single molecule force spectroscopy method for mapping sequences in otherwise difficult to sequence heteropolymers, including glycosylated proteins and glycans. The sliding contact force spectroscopy (SCFS) method exploits a sliding contact made between a nanopore threaded over a polymer axle and an AFM probe. We find that for sliding α- and β- cyclodextrin nanopores over a wide range of hydrophilic monomers, the free energy of sliding is proportional to the sum of two dimensionless, easily calculable parameters representing the relative partitioning of the monomer inside the nanopore or in the aqueous phase, and the friction arising from sliding the nanopore over the monomer. Using this relationship we calculate sliding energies for nucleic acids, amino acids, glycan and synthetic monomers and predict on the basis of these calculations that SCFS will detect N- and O-glycosylation of proteins and patterns of sidechains in glycans. For these applications, SCFS offers an alternative to sequence mapping by mass spectrometry or newly-emerging nanopore technologies that may be easily implemented using a standard AFM

Time-reversal symmetry relations for currents in quantum and stochastic nonequilibrium systems

An overview is given of recent advances in the nonequilibrium statistical mechanics of quantum systems and, especially, of time-reversal symmetry relations that have been discovered in this context. The systems considered are driven out of equilibrium by time-dependent forces or by coupling to large reservoirs of particles and energy. The symmetry relations are established for the exchange of energy and particles between the subsystem and its environment. These results have important consequences. In particular, generalizations of the Kubo formula and the Casimir-Onsager reciprocity relations can be deduced beyond linear response properties. Applications to electron quantum transport in mesoscopic semiconducting circuits are discussed.Comment: Chapter contributed to: R. Klages, W. Just, and C. Jarzynski (Eds.), Nonequilibrium Statistical Physics of Small Systems: Fluctuation Relations and Beyond (Wiley-VCH, Weinheim, 2012; ISBN 978-3-527-41094-1

PH-responsive biodegradable amphiphilic networks

Copper-mediated azide - alkyne Huisgen's 1,3-dipolar cycloaddition is a "click" reaction that was successfully used to prepare pH-responsive, amphiphilic and biodegradable networks. Indeed, this reaction proved to be very efficient in the "one pot" grafting of amino alkyne onto azide containing poly(epsilon-caprolactone) and the cross-linking of these chains by alpha,omega-dialkynyl poly(ethylene oxide). The pH-controlled release of guests hosted during the cross-linking step was illustrated with an entrapped model dye

Contribution of "click chemistry" to the synthesis of antimicrobial aliphatic copolyester

A straightforward strategy is proposed to impart antimicrobial properties to biodegradable poly(oxepan-2-one) (poly(epsilon-caprolactone) or PCL), which is based on the grafting of pendant ammonium salts by "click" chemistry. First, statistical copolymerization of 3-chlorooxepan-2-one (alpha-chloro-epsilon-caprolactone or alpha Cl epsilon CL) with oxepan-2-one (epsilon-caprolactone or epsilon CL) was initiated by 2,2-dibutyl-2-stanna-1,3-dioxepane (DSDOP). In a second step, pendant chlorides were converted into azides by reaction with sodium azide (NaN3). Finally, quaternary ammonium containing alkynes were quantitatively added to the pendant azide groups of PCL by the copper-catalyzed Huisgen's 1,3-dipolar cycloaddition, which is a typical "click" reaction. An alternative two-step strategy based on the cycloaddition of the amine containing alkyne onto the pendant azides, followed by quaternization turned out to be less efficient. The antimicrobial activity was analyzed by the "shaking flask method" in the presence of Escherichia col

Contribution of "click chemistry" to the macromolecular engineering of aliphatic polyesters

In this work, click chemistry was sucessfully applied to the chemical modification of aliphatic polyesters with the purpose to tailor their physical properties. The developped strategy was then applied to the synthesis of materials, such as smart partially degradable hydrogels or antibacterial polyesters. Last, the synthesis of amphiphilic star-shaped copolyester was investigated

Mechanical Processes of a Single Synthetic Molecular Machine Studied by AFM-based Force Spectroscopy

Some biomolecules are able to generate directional forces by rectifying random thermal motions. This allows these molecular machines to perform mechanical tasks such as intracellular cargo transport or muscle contraction in plants and animals. Although some artificial molecular machines have been synthesized and used collectively to perform mechanical tasks, so far there have been no direct measurements of mechanical processes at the single-molecule level. Here we report measurements of the mechanical work performed by a synthetic molecule less than 5 nm long. We show that biased Brownian motion of the submolecular components in a hydrogen-bonded [2]rotaxane -a molecular ring threaded onto a molecular axle- can be harnessed to generate significant directional forces. We used the cantilever of an atomic force microscope to apply a mechanical load to the ring during single-molecule pulling-relaxing cycles. The ring was pulled along the axle, away from the thermodynamically favoured binding site, and was then found to travel back to this site against an external load of 30 pN. Using fluctuation theorems, we were able to relate the measurements of the work done at the level of individual molecules to the free energy change measured previously by ensemble measurements. Finally, we used dynamic single-molecule force spectroscopy to probe kinetic information of the interaction between the molecular ring and the preferred binding site. The results also demonstrate that AFM-based single-molecule force spectroscopy, which has been widely used to investigate the mechanochemical behaviour of (bio)macromolecules, can be applied to a molecule that is less than 5 nm in its extended form