DNA binding fluorescent proteins for the direct visualization of large DNA molecules

Direct Visualization of Single-Molecule DNA-Binding Proteins Along DNA to Understand DNA–Protein Interactions

Polymerase synthesis of DNA labelled with benzylidene cyanoacetamide-based fluorescent molecular rotors: fluorescent light-up probes for DNA-binding proteins.

Viscosity-sensitive fluorophores, fluorescent molecular rotors based on aminobenzylidene-cyanoacetamide moiety, were tethered to 2'-deoxycytidine triphosphate via a propargylamine linker and incorporated into DNA by polymerases in primer extension, nicking enzyme amplification or PCR. DNA probes incorporating modified nucleosides show a light-up response upon binding to a protein.

Single-molecule visualization of ROS-induced DNA damage in large DNA molecules.

We present a single molecule visualization approach for the quantitative analysis of reactive oxygen species (ROS) induced DNA damage, such as base oxidation and single stranded breaks in large DNA molecules. We utilized the Fenton reaction to generate DNA damage with subsequent enzymatic treatment using a mixture of three types of glycosylases to remove oxidized bases, and then fluorescent lab...

Investigation of the direct DNA damages irradiated by protons of different energies using geant4-DNA toolkit

Background: The total yields of direct Single-Strand Breaks (SSBs) and Double-Strand Breaks (DSBs) in proton energies varying from 0.1 to 40 MeV were calculated. While other studies in this field have not used protons with energy less than 0.5 MeV, our results show interesting and complicated behavior of these protons. Materials and Methods: The simulation has been done using the Geant4-DNA too...

Systematic evaluation of split-fluorescent proteins for the direct detection of native and methylated DNA.

In order to directly detect nucleic acid polymers, we have designed biosensors comprising sequence-specific DNA binding proteins tethered to split-reporter proteins, which generate signal upon binding a predetermined nucleic acid target, in an approach termed SEquence-Enabled Reassembly (SEER). Herein we demonstrate that spectroscopically distinct split-fluorescent protein variants, GFPuv, EGFP...