Related papers: Probing DNA interactions with proteins using a sin…
Despite more than 100 years of study, it is unclear if the movement of proteins inside the cell is best described as a mosh pit or an exquisitely choreographed dance. Recent studies suggest the latter. Local interactions induce molecular…
Fluorescence microscopy reveals that the contents of many (membrane-free) nuclear "bodies" exchange rapidly with the soluble pool whilst the underlying structure persists; such observations await a satisfactory biophysical explanation. To…
DNA-functionalized particles have great potential for the design of complex self-assembled materials. The major hurdle in realizing crystal structures from DNA-functionalized particles is expected to be kinetic barriers that trap the system…
DNA nanotechnology uses predictable interactions of nucleic acids to precisely engineer complex nanostructures. Characterizing these self-assembled structures at the single-structure level is crucial for validating their design and…
DNA nanocompartment is a typical DNA-based machine whose function is dependent of molecular collective effect. Fundamental properties of the device have been addressed via electrochemical analysis, fluorescent microscopy, and atomic force…
Trapping, linearization, and imaging of single molecule DNA is of broad interest to both biophysicists who study polymer physics and engineers who build nucleic acid analyzing methods such as optical mapping. In this study, single DNA…
There are many problems in biochemistry that are difficult to study experimentally. Simulation methods are appealing due to direct availability of atomic coordinates as a function of time. However, direct molecular simulations are…
Biological molecules, like all active matter, use free energy to generate force and motion which drive them out of thermal equilibrium, and undergo inherent dynamic interconversion between metastable free energy states separated by levels…
Time-resolved single-molecule biophysical experiments yield data that contain a wealth of dynamic information, in addition to the equilibrium distributions derived from histograms of the time series. In typical force spectroscopic setups…
The evolution, regulation and sustenance of biological complexity is determined by protein-protein interaction network that is filled with dynamic events. Recent experimental evidences point out that clustering of proteins has a vital role…
In this paper, a new method to efficiently simulate diffusion controlled second order chemical reactions is derived and applied to site-specific DNA-binding proteins. The protein enters a spherical cell and propagates via two competing…
We present the first proof-of-concept simulations of detectors using biomaterials to detect particle interactions. The essential idea behind a "DNA detector" involves the attachment of a forest of precisely-sequenced single or…
Human physiology and pathology arise from the coordinated interactions of diverse single cells. However, analyzing single cells has been limited by the low sensitivity and throughput of analytical methods. DNA sequencing has recently made…
The effective DNA-DNA interaction force is calculated by computer simulations with explicit tetravalent counterions and monovalent salt. For overcharged DNA molecules, the interaction force shows a double-minimum structure. The positions…
The full understanding of cellular functions requires information about protein numbers for various biomolecular assemblies and their dynamics, which can be partly accessed by super-resolution fluorescence microscopy. Yet, many protein…
When nanoparticles (NPs) are introduced into a biological solution, layers of biomolecules form on their surface, creating a corona. Understanding how the structure of the protein evolves into the corona is essential for evaluating the…
Topology affects physical and biological properties of DNA and impacts fundamental cellular processes, such as gene expression, genome replication, chromosome structure and segregation. In all organisms DNA topology is carefully modulated…
DNA supercoiling is central to many fundamental processes of living organisms. Its average level along the chromosome and over time reflects the dynamic equilibrium of opposite activities of topoisomerases, which are required to relax…
As proof-of-principle for generating superresolution structural information from DNA we applied a method of localization microscopy utilizing photoblinking comparing intercalating dye YOYO-1 against minor groove binding dye SYTO-13, using a…
The binding of proteins onto DNA contributes to the shaping and packaging of genome as well as to the expression of specific genetic messages. With a view to understanding the interplay between the presence of proteins and the deformation…