Folding dynamics and conformational heterogeneity of human telomeric G-quadruplex structures in Na+ solutions by single molecule FRET microscopy.

G-quadruplex structures can occur throughout the genome, including at telomeres. They are involved in cellular regulation and are potential drug targets. Human telomeric G-quadruplex structures can fold into a number of different conformations and show large conformational diversity. To elucidate the different G-quadruplex conformations and their dynamics, we investigated telomeric G-quadruplex folding using single molecule FRET microscopy in conditions where it was previously believed to yield low structural heterogeneity. We observed four FRET states in Na(+) buffers: an unfolded state and three G-quadruplex related states that can interconvert between each other. Several of these states were almost equally populated at low to medium salt concentrations. These observations appear surprising as previous studies reported primarily one G-quadruplex conformation in Na(+) buffers. Our results permit, through the analysis of the dynamics of the different observed states, the identification of a more stable G-quadruplex conformation and two transient G-quadruplex states. Importantly these results offer a unique view into G-quadruplex topological heterogeneity and conformational dynamics.

A Single Molecule Polyphenylene-Vinylene Photonic Wire.

Nanoscale transport of light through single molecule systems is of fundamental importance for light harvesting, nanophotonic circuits, and for understanding photosynthesis. Studies on organization of molecular entities for directional transfer of excitation energy have focused on energy transfer cascades via multiple small molecule dyes. Here, we investigate a single molecule conjugated polymer as a photonic wire. The phenylene-vinylene-based polymer is functionalized with multiple DNA strands and immobilized on DNA origami by hybridization to a track of single-stranded staples extending from the origami structure. Donor and acceptor fluorophores are placed at specific positions along the polymer which enables energy transfer from donor to polymer, through the polymer, and from polymer to acceptor. The structure is characterized by atomic force microscopy, and the energy transfer is studied by ensemble fluorescence spectroscopy and single molecule TIRF microscopy. It is found that the polymer photonic wire is capable of transferring light over distances of 24 nm. This demonstrates the potential residing in the use of conjugated polymers for nanophotonics.

Controlled aggregation of DNA functionalized poly(phenylene-vinylene).

The morphology of conjugated polymers strongly influences their optical and electronic properties and affects their performance in polymer devices. Using optical spectroscopy and atomic force microscopy, we investigate the fluorescence properties and the aggregation state of DNA-functionalized poly(phenylene-vinylene). We show that polymer aggregation can be controlled in solution through ion and DNA interactions; aggregation is induced in the presence of divalent cations and can be reversed by adding sequence specific DNA. These interactions provide ways to tune polymer aggregation on the timescale of minutes and allows tuning of the polymer's optical properties.

Tailored protein encapsulation into a DNA host using geometrically organized supramolecular interactions.

The self-organizational properties of DNA have been used to realize synthetic hosts for protein encapsulation. However, current strategies of DNA-protein conjugation still limit true emulation of natural host-guest systems, whose formation relies on non-covalent bonds between geometrically matching interfaces. Here we report one of the largest DNA-protein complexes of semisynthetic origin held in place exclusively by spatially defined supramolecular interactions. Our approach is based on the decoration of the inner surface of a DNA origami hollow structure with multiple ligands converging to their corresponding binding sites on the protein surface with programmable symmetry and range-of-action. Our results demonstrate specific host-guest recognition in a 1:1 stoichiometry and selectivity for the guest whose size guarantees sufficient molecular diffusion preserving short intermolecular distances. DNA nanocontainers can be thus rationally designed to trap single guest molecules in their native form, mimicking natural strategies of molecular recognition and anticipating a new method of protein caging.

Programmed Switching of Single Polymer Conformation on DNA Origami.

DNA nanotechnology offers precise geometrical control of the positioning of materials, and it is increasingly also being used in the development of nanomechanical devices. Here we describe the development of a nanomechanical device that allows switching of the position of a single-molecule conjugated polymer. The polymer is functionalized with short single-stranded (ss) DNA strands that extend from the backbone of the polymer and serve as handles. The DNA polymer conjugate can be aligned on DNA origami in three well-defined geometries (straight line, left-turned, and right-turned pattern) by DNA hybridization directed by single-stranded guiding strands and ssDNA tracks extending from the origami surface and polymer handle. We demonstrate switching of a conjugated organic polymer conformation between left- and right-turned conformations of the polymer on DNA origami based on toehold-mediated strand displacement. The switching is observed by atomic force microscopy and by Förster resonance energy transfer between the polymer and two different organic dyes positioned in close proximity to the respective patterns. Using this method, the polymer conformation can be switched six times successively. This controlled nanomechanical switching of conjugated organic polymer conformation demonstrates unique control of the shape of a single polymer molecule, and it may constitute a new component for the development of reconfigurable nanophotonic and nanoelectronic devices.

Routing of individual polymers in designed patterns.

Synthetic polymers are ubiquitous in the modern world, but our ability to exert control over the molecular conformation of individual polymers is very limited. In particular, although the programmable self-assembly of oligonucleotides and proteins into artificial nanostructures has been demonstrated, we currently lack the tools to handle other types of synthetic polymers individually and thus the ability to utilize and study their single-molecule properties. Here we show that synthetic polymer wires containing short oligonucleotides that extend from each repeat can be made to assemble into arbitrary routings. The wires, which can be more than 200 nm in length, are soft and bendable, and the DNA strands allow individual polymers to self-assemble into predesigned routings on both two- and three-dimensional DNA origami templates. The polymers are conjugated and potentially conducting, and could therefore be used to create molecular-scale electronic or optical wires in arbitrary geometries.