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

Inciting protocols

This paper studies patenting decisions by firms in relation to the negotiation and signing of the Helsinki and Oslo protocol as part of the Convention on Long-Range Transboundary Air Pollution. We use a uniquely constructed patent data set on SO 2 abatement technologies filed in 15 signatory and non-signatory countries in the period 1970-1997. The data distinguish between so-called 'mother' patents, or original inventions, and 'family' patents, which represent the same invention but are patents filed in foreign countries. Our analysis suggests that not only local environmental regulations matter for patenting decisions. International environmental agreements provide incentives for additional inventive activity in and the diffusion of knowledge towards signatory countries by reducing investment uncertainty for inventing firms

Label-Free Detection of Post-translational Modifications with a Nanopore

Post-translational modifications (PTMs) of proteins play key roles in cellular processes. Hence, PTM identification is crucial for elucidating the mechanism of complex cellular processes and disease. Here we present a method for PTM detection at the single-molecule level using FraC biological nanopores. We focus on two major PTMs, phosphorylation and glycosylation, that mutually compete for protein modification sites, an important regulatory process that has been implicated in the pathogenic pathways of many diseases. We show that phosphorylated and glycosylated peptides can be clearly differentiated from nonmodified peptides by differences in the relative current blockade and dwell time in nanopore translocations. Furthermore, we show that these PTM modifications can be mutually differentiated, demonstrating the identification of phosphorylation and glycosylation in a label-free manner. The results represent an important step for the single-molecule, label-free identification of proteoforms, which have tremendous potential for disease diagnosis and cell biology