Chemistries for DNA Nanotechnology.

The predictable nature of DNA interactions enables the programmable assembly of highly advanced 2D and 3D DNA structures of nanoscale dimensions. The access to ever larger and more complex structures has been achieved through decades of work on developing structural design principles. Concurrently, an increased focus has emerged on the applications of DNA nanostructures. In its nature, DNA is chemically inert and nanostructures based on unmodified DNA mostly lack function. However, functionality can be obtained through chemical modification of DNA nanostructures and the opportunities are endless. In this review, we discuss methodology for chemical functionalization of DNA nanostructures and provide examples of how this is being used to create functional nanodevices and make DNA nanostructures more applicable. We aim to encourage researchers to adopt chemical modifications as part of their work in DNA nanotechnology and inspire chemists to address current challenges and opportunities within the field.

Preparation, Single-Molecule Manipulation, and Energy Transfer Investigation of a Polyfluorene-graft-DNA polymer.

Conjugated polymers have been intensively studied due to their unique optical and electronic properties combined with their physical flexibility and scalable bottom up synthesis. Although the bulk qualities of conjugated polymers have been extensively utilized in research and industry, the ability to handle and manipulate conjugated polymers at the nanoscale lacks significantly behind. Here, the toolbox for controlled manipulation of conjugated polymers was expanded through the synthesis of a polyfluorene-DNA graft-type polymer (poly(F-DNA)). The polymer possesses the characteristics associated with the conjugated polyfluorene backbone, but the protruding single-stranded DNA provides the material with an exceptional addressability. This study demonstrates controlled single-molecule patterning of poly(F-DNA), as well as energy transfer between two different polymer-DNA conjugates. Finally, highly efficient DNA-directed quenching of polyfluorene fluorescence was shown.

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.

Revealing the structural detail of individual polymers using a combination of electrospray deposition and UHV-STM.

A phenylene vinylene polymer derivative is deposited onto a Au(111) surface under Ultra-High Vacuum (UHV) conditions using electrospray ionisation deposition and characterised using Scanning Tunnelling Microscopy (STM). High resolution STM images reveal the polymer structure on the monomeric scale, allowing the identification of regioisomerism, the intricate isomerisations of the polymer side-chains, as well as the larger-scale topologies of the polymer strands.

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.

Long-term follow-up after triple treatment of prostate cancer stage pT3.

OBJECTIVE: Radical prostatectomy (RP) has become the most common treatment for localized prostate cancer in Sweden. Outcome is extremely good for pT2 stage with Gleason score 6 or less, but more than every fourth operated patient will have a pT3 stage on full amount specimen histology. According to several reports the risk of biochemical recurrence is quite high, especially in stage pT3, on active surveillance after surgery alone. In 1994 the authors recognized this fact at their clinic and decided to apply a new multimodality treatment concept. MATERIAL AND METHODS: During 10 years, between 1 January 1995 and 1 January 2005, 98 pT3 patients were treated with a triple treatment: 8 months of neoadjuvant/adjuvant luteinizing hormone-releasing hormone (LH-RH) analogue treatment, RP and immediate adjuvant radiotherapy (RT) 3 months after RP. RT was delivered to 60 Gy in 30 fractions to the prostatic bed to all the patients. The cumulative risk of progression was calculated with the Kaplan-Meier method. The impact of risk factors was evaluated by the Cox proportional hazard model. RESULTS: Ninety-eight (74 pT3a and 24 pT3b) patients were followed with a mean observation time from operation until October 2007 of 71.6 (median 65.5, range 35-146) months. The mean follow-up time to biochemical failure, death or last measurement of prostate-specific antigen (PSA) was 57.8 (median 57.0, range 3-132) months. Fifteen patients out of 98 had experienced biochemical failure. Only Gleason score had an independent impact on the risk of PSA progression. Complications were mild and temporary and no serious adverse events were registered. CONCLUSIONS: Patients with locally advanced prostate cancer have a high risk of progression after RP as single therapy. Postoperative RT has been shown to improve the outcome. Neoadjuvant/adjuvant hormonal therapy has been shown to improve the outcome after RT. Bringing this knowledge together offering a multimodality therapy with neoadjuvant/adjuvant hormonal therapy, RP followed by postoperative immediate RT seems to offer a high chance of biochemical-free survival.