Tuning knot abundance in semiflexible chains with crowders of different sizes: a Monte Carlo study of DNA chains

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To assess the effect of an 8-oxoguanine (8OG) defect base on the vertical ionization energies (VIEs) and electron affinities (VEAs) of DNA, density functional theory calculations were carried out for native and defect DNA bases and nucleotides, as well as ...

Cells possess remarkable control of the folding and entanglement topology of long and flexible chromosomal DNA molecules. It is thought that structural maintenance of chromosome (SMC) protein complexes play a crucial role in this, by organizing long DNAs i ...

We study the dynamics of knotted deformable closed chains sedimenting in a viscous fluid. We show experimentally that trefoil and other torus knots often attain a remarkably regular horizontal toroidal structure while sedimenting, with a number of intertwi ...

Transcription factors (TFs) regulate gene expression by binding to specific short DNA sequences of 5 to 20-bp to regulate the rate of transcription of genetic information from DNA to messenger RNA. We present PWMScan, a fast web-based tool to scan server-r ...

Since the origins of DNA-based life, the enzyme ribonucleotide reductase (RNR) has spurred proliferation because of its rate-limiting role in de novo deoxynucleoside-triphosphate (dNTP) biosynthesis. Paradoxically, the large subunit, RNR-alpha, of this obl ...

We investigate properties of spatial graphs on the standard torus. It is known that nontrivial embeddings of planar graphs in the torus contain a nontrivial knot or a non-split link due to [2, 3]. Building on this and using the chirality of torus knots and ...

Interactions of proteins with DNA are essential for carrying out DNA's biological functions and performing a cellular cycle. Such processes as DNA replication, expression and repair are performed by an organised action of various proteins. To better unders ...

In living cells, DNA is highly confined in space with the help of condensing agents, DNA binding proteins and high levels of supercoiling. Due to challenges associated with experimentally studying DNA under confinement, little is known about the impact of ...

Polycomb repressive complex 2 (PRC2) trimethylates histone H3 at lysine 27 to mark genes for repression. We measured the dynamics of PRC2 binding on recombinant chromatin and free DNA at the single-molecule level using total internal reflection fluorescenc ...

Although all Type II restriction endonucleases catalyze phosphodiester bond hydrolysis within or close to their DNA target sites, they form different oligomeric assemblies ranging from monomers, dimers, tetramers to higher order oligomers to generate a dou ...

Tuning knot abundance in semiflexible chains with crowders of different sizes: a Monte Carlo study of DNA chains

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Vertical Ionization Energies and Electron Affinities of Native and Damaged DNA Bases, Nucleotides, and Pairs from Density Functional Theory Calculations: Model Assessment and Implications for DNA Damage Recognition and Repair

DNA-segment-capture model for loop extrusion by structural maintenance of chromosome (SMC) protein complexes

Periodic Motion of Sedimenting Flexible Knots

Evaluation of Auramine O staining and conventional PCR for leprosy diagnosis: A comparative cross-sectional study from Ethiopia

PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix

Nuclear RNR-alpha antagonizes cell proliferation by directly inhibiting ZRANB3

On chirality of toroidal embeddings of polyhedral graphs

Nanocapillaries combined with optical tweezers as a single molecule technique for studying DNA-protein complexes

Spatial confinement induces hairpins in nicked circular DNA

DNA binding by PHF1 prolongs PRC2 residence time on chromatin and thereby promotes H3K27 methylation

Restriction endonuclease AgeI is a monomer which dimerizes to cleave DNA