Atomic force microscopy shows that vaccinia topoisomerase IB generates filaments on DNA in a cooperative fashion

Type IB DNA topoisomerases cleave and rejoin one strand of the DNA duplex, allowing for the removal of supercoils generated during replication and transcription. In addition, electron microscopy of cellular and viral TopIB–DNA complexes has suggested that the enzyme promotes long-range DNA–DNA crossovers and synapses. Here, we have used the atomic force microscope to visualize and quantify the interaction between vaccinia topoisomerase IB (vTopIB) and DNA. vTopIB was found to form filaments on nicked-circular DNA by intramolecular synapsis of two segments of a single DNA molecule. Measuring the filament length as a function of protein concentration showed that synapsis is a highly cooperative process. At high protein:DNA ratios, synapses between distinct DNA molecules were observed, which led to the formation of large vTopIB-induced DNA clusters. These clusters were observed in the presence of Mg(2+), Ca(2+) or Mn(2+), suggesting that the formation of intermolecular vTopIB-mediated DNA synapsis is favored by screening of the DNA charge

A Mechanism for Cutting Carbon Nanotubes with a Scanning Tunneling Microscope

We discuss the local cutting of single-walled carbon nanotubes by a voltage pulse to the tip of a scanning tunneling microscope. The tip voltage ($\mid V \mid \ge$~3.8 eV) is the key physical quantity in the cutting process. After reviewing several possible physical mechanisms we conclude that the cutting process relies on the weakening of the carbon-carbon bonds through a combination of localized particle-hole excitations induced by inelastically tunneling electrons and elastic deformation due to the electric field between tip and sample. The carbon network releases part of the induced mechanical stress by forming topological defects that act as nucleation centers for the formation of dislocations that dynamically propagate towards bond-breaking.Comment: 7 pages, 6 postscript figures, submitted to PR

DNA Translocation through Graphene Nanopores

Nanopores -- nanosized holes that can transport ions and molecules -- are very promising devices for genomic screening, in particular DNA sequencing. Both solid-state and biological pores suffer from the drawback, however, that the channel constituting the pore is long, viz. 10-100 times the distance between two bases in a DNA molecule (0.5 nm for single-stranded DNA). Here, we demonstrate that it is possible to realize and use ultrathin nanopores fabricated in graphene monolayers for single-molecule DNA translocation. The pores are obtained by placing a graphene flake over a microsize hole in a silicon nitride membrane and drilling a nanosize hole in the graphene using an electron beam. As individual DNA molecules translocate through the pore, characteristic temporary conductance changes are observed in the ionic current through the nanopore, setting the stage for future genomic screening

Imaging Electron Wave Functions of Quantized Energy Levels in Carbon Nanotubes

Carbon nanotubes provide a unique system to study one-dimensional quantization phenomena. Scanning tunneling microscopy is used to observe the electronic wave functions that correspond to quantized energy levels in short metallic carbon nanotubes. Discrete electron waves are apparent from periodic oscillations in the differential conductance as a function of the position along the tube axis, with a period that differs from that of the atomic lattice. Wave functions can be observed for several electron states at adjacent discrete energies. The measured wavelengths are in good agreement with the calculated Fermi wavelength for armchair nanotubes.Comment: 11 pages, 4 figures in seperate PDF fil

Electron-hole symmetry in a semiconducting carbon nanotube quantum dot

Optical and electronic phenomena in solids arise from the behaviour of electrons and holes (unoccupied states in a filled electron sea). Electron-hole symmetry can often be invoked as a simplifying description, which states that electrons with energy above the Fermi sea behave the same as holes below the Fermi energy. In semiconductors, however, electron-hole symmetry is generally absent since the energy band structure of the conduction band differs from the valence band. Here we report on measurements of the discrete, quantized-energy spectrum of electrons and holes in a semiconducting carbon nanotube. Through a gate, an individual nanotube is filled controllably with a precise number of either electrons or holes, starting from one. The discrete excitation spectrum for a nanotube with N holes is strikingly similar to the corresponding spectrum for N electrons. This observation of near perfect electron-hole symmetry demonstrates for the first time that a semiconducting nanotube can be free of charged impurities, even in the limit of few-electrons or holes. We furthermore find an anomalously small Zeeman spin splitting and an excitation spectrum indicating strong electron-electron interactions.Comment: 12 pages, 4 figure

The current implementation status of the integration of sports and physical activity into Dutch rehabilitation care

Purpose: To describe the current status of the nationwide implementation process of a sports and physical activity stimulation programme to gain insight into how sports and physical activity were integrated into Dutch rehabilitation care. Methods: The current implementation status of a sports and physical activity stimulation programme in 12 rehabilitation centres and 5 hospitals with a rehabilitation department was described by scoring fidelity and satisfaction. Seventy-one rehabilitation professionals filled out a questionnaire on how sports and physical activity, including stimulation activities, were implemented into rehabilitation care. Total fidelity scores (in %) were calculated for each organization. Professionals’ satisfaction was rated on a scale from 1 to 10. Results: In most organizations sports and physical activity were to some extent integrated during and after rehabilitation (fidelity scores: median = 54%, IQR = 23%). Physical activity stimulation was not always embedded as standard component of a rehabilitation treatment. Professionals’ satisfaction rated a median value of 8.0 (IQR = 0.0) indicating high satisfaction rates. Conclusions: The fidelity outcome showed that activities to stimulate sports and physical activity during and after rehabilitation were integrated into rehabilitation care, but not always delivered as standardized component. These findings have emphasized the importance to focus on integrating these activities into routines of organizations.Implications for Rehabilitation Components of an evidence-based programme to stimulate sports and physical activity during and after rehabilitation can be used to measure the current status of the integration of sports and physical activity in rehabilitation care in a structural and effective way. The method described in the current study can be used to compare the content of the rehabilitation care regarding the integration of sports and physical activity among organizations both on a national and international level. Sports and physical activity are seen as important ingredients for successful rehabilitation care in The Netherlands