Elementary processes of DNA surface hybridization resolved by single-molecule kinetics: implication for macroscopic device performance

Displacement and dissociation of oligonucleotides during DNA hairpin closure under strain

The hybridization kinetic of an oligonucleotide to its template is a fundamental step in many biological processes such as replication arrest, CRISPR recognition, DNA sequencing, DNA origami, etc. Although single kinetic descriptions exist for special cases of this problem, there are no simple general prediction schemes. In this work, we have measured experimentally, with no fluorescent labelling, the displacement of an oligonucleotide from its substrate in two situations: one corresponding to oligonucleotide binding/unbinding on ssDNA and one in which the oligonucleotide is displaced by the refolding of a dsDNA fork. In this second situation, the fork is expelling the oligonucleotide thus significantly reducing its residence time. To account for our data in these two situations, we have constructed a mathematical model, based on the known nearest neighbour dinucleotide free energies, and provided a good estimate of the residence times of different oligonucleotides (DNA, RNA, LNA) of various lengths in different experimental conditions (force, temperature, buffer conditions, presence of mismatches, etc.). This study provides a foundation for the dynamics of oligonucleotide displacement, a process of importance in numerous biological and bioengineering contexts.

Inferring the energy sensitivity and band gap of electronic transport in a network of carbon nanotubes

Since the industrialization of single-phase nanomaterial-based devices is still challenging, intensive research focus has been given to complex materials consisting of multiple nanoscale entities, including networks and matrices of nanowires, nanotubes, nanoribbons, or other large molecules; among these complex materials, networks of carbon nanotubes are a typical example. Detailed knowledge of the energy sensitivity and band gap of electronic transport in such a material system is difficult to detect, despite its importance in electronic, energetic and sensing applications. Here, we propose a new methodology to obtain these quantities using the measured Seebeck coefficient at a certain temperature but different Fermi levels. We discover that the network consisting of semiconducting (11,10)-carbon nanotubes actually exhibits metallic transport at room temperature. It is also interesting to verify that intrananotube ballistic transport is dominant over diffusive scattering by long-range disorder, as well as the quantum hopping resistance at the contact points. The transport asymmetry ratio between the holes and electrons (1.75) is similar to the value observed in pristine graphene samples (1.50).

Single-molecule determination of chemical equilibrium of DNA intercalation by electrical conductance

We investigated a single-molecule reaction of DNA intercalation as an example of a bimolecular association reaction. Single-molecule conductance values of the product and reactant molecules adsorbed on an Au surface were measured to identify and quantify these molecules. The binding isotherm was constructed, and the association constant of the reaction was determined on a single-molecule basis.