Related papers: Single-molecule imaging of DNA gyrase activity in …
Single-molecule experiments provide new insights into biological processes hitherto not accessible by measurements performed on bulk systems. We report on a study of the kinetics of a triple-branch DNA molecule with four conformational…
Gel electrophoresis, a widely used technique to separate DNA according to their size and weight, generates images that can be analyzed automatically. Manual or semiautomatic image processing presents a bottleneck for further development and…
The cell cycle is one of the most fundamental biological processes important for understanding normal physiology and various pathologies such as cancer. Single cell RNA sequencing technologies give an opportunity to analyse the cell cycle…
Nanochannels provide means for detailed experiments on the effect of confinement on biomacromolecules, such as DNA. We here introduce a model for the complete unfolding of DNA from the circular to linear configuration. Two main ingredients…
While the statistical mechanical description of DNA has a long tradition, renewed interest in DNA melting from a physics perspective is nourished by measurements of the fluctuation dynamics of local denaturation bubbles by single molecule…
We use optical tweezers to perform stretching experiments on DNA molecules when interacting with the drugs daunomycin and ethidium bromide, which intercalate the DNA molecule. These experiments are performed in the low-force regime from…
Background: In Escherichia coli, overlapping rounds of DNA replication allow the bacteria to double in faster times than the time required to copy the genome. The precise timing of initiation of DNA replication is determined by a regulatory…
Synthetic DNA approaches 227.5 exabytes per gram of storage density with stability over millennial timescales. Realising this capacity requires error-correction codes that recover data from substantial synthesis and sequencing errors.…
Biological cells replicate their genomes in a well-planned manner. The DNA replication program of an organism determines the timing at which different genomic regions are replicated, with fundamental consequences for cell homeostasis and…
Double-stranded DNA translocates through sufficiently large nanopores either in a linear, single-file fashion or in a folded hairpin conformation when captured somewhere along its length. We show that the folding state of DNA can be…
Fast 3D super-resolution imaging is essential for decoding rapidly occurring biological processes. Encoding single molecules to their respective planes enable simultaneous multi-plane super-resolution volume imaging. This saves the…
Structural-Maintenance-of-Chromosome (SMC) complexes such as condensins organise the folding of chromosomes. However, their role in modulating the entanglement of DNA and chromatin is not fully understood. To address this question, we…
We present a single-molecule tool called the CoPro (Concentration of Proteins) method that uses millisecond imaging with convolution analysis, automated image segmentation and super-resolution localization microscopy to generate robust…
Background: The short reads output by first- and second-generation DNA sequencing instruments cannot completely reconstruct microbial chromosomes. Therefore, most genomes have been left unfinished due to the significant resources required…
It is hypothesized that nonlinear solid friction between the gel matrix and DNA molecules inhibits the motion of DNA through the nanopores of the gel during electrophoresis. In this article, it is demonstrated that external noise can…
SAXS studies of four 60 base-pair DNA duplexes with sequences closely related to part of the GAGE6 (G-antigen 6) promoter have been performed to study the role of DNA conformations in solution and their potential relationship to DNA-protein…
We propose a stochastic model for gene transcription coupled to DNA supercoiling, where we incorporate the experimental observation that polymerases create supercoiling as they unwind the DNA helix, and that these enzymes bind more…
Single-molecule FRET is widely used to study helicases by detecting distance changes between a fluorescent donor and an acceptor anchored to overhangs of a forked DNA duplex. However, it has lacked single-base pair (1-bp) resolution…
The ejection of DNA from a bacterial virus (``phage'') into its host cell is a biologically important example of the translocation of a macromolecular chain along its length through a membrane. The simplest mechanism for this motion is…
In this work, we show that by varying the experimental conditions, the driving amplitude, a dynamic force microscope allows DNA properties to be selectively imaged. The substrate on which the DNA is fixed is a silica surface grafted with…