Related papers: Positioning Crenarchaeal tRNA-Introns
Atomic Force Microscopy analysis is employed to study the geometrical and topological properties of $3000$kbp DNA molecules fixed in mica substrates with $MgCl_{2}$. We found that the aggregates on the substrate surface for certain salt…
Many physical systems can be mapped onto solved or "solvable" models of magnetism. In this work, we have mapped the statistical mechanics of columnar phases of ideally helical rigid DNA -- subject to the earlier found unusual, frustrated…
Given a random RNA secondary structure, $S$, we study RNA sequences having fixed ratios of nuclotides that are compatible with $S$. We perform this analysis for RNA secondary structures subject to various base pairing rules and minimum arc-…
The speed of site-specific binding of transcription factor (TFs) proteins with genomic DNA seems to be strongly retarded by the randomly occurring sequence traps. Traps are those DNA sequences sharing significant similarity with the…
We explore the large-scale behavior of nucleotide compositional strand asymmetries along human chromosomes. As we observe for 7 of 9 origins of replication experimentally identified so far, the (TA+GC) skew displays rather sharp upward…
Chromosomal rearrangements, which shuffle DNA throughout the genome, are an important source of divergence across taxa. Using a paired-end read approach with Illumina sequence data for archaic humans, I identify changes in genome structure…
We consider the classical and local thermodynamic stability of non- and near-extremal Dp-branes smeared on a transverse direction. These two types of stability are connected through the correlated stability conjecture for which we give a…
Site-specific recombination on supercoiled circular DNA yields a variety of knotted or catenated products. We develop a model of this process, and give extensive experimental evidence that the assumptions of our model are reasonable. We…
We searched for Technetium (Tc) in a sample of bright oxygen-rich asymptotic giant branch (AGB) stars located in the outer galactic bulge. Tc is an unstable element synthesised via the s-process in deep layers of AGB stars, thus it is a…
During evolution of microorganisms genomes underwork have different changes in their lengths, gene orders, and gene contents. Investigating these structural rearrangements helps to understand how genomes have been modified over time. Some…
An odd-odd nucleus is treated as the core-particle-hole system. The core is described by the Bohr Hamiltonian. Different collective potentials of the core are investigated. The odd particle and hole are assumed to be in the symmetric…
Understanding how viral mutant spectra organize and explore genotype space is essential for unraveling the mechanisms driving evolution at the finest scale. Here we use deep-sequencing data of an amplicon in the A2 protein of the RNA…
Transcriptional activity has been shown to relate to the organization of chromosomes in the eukaryotic nucleus and in the bacterial nucleoid. In particular, highly transcribed genes, RNA polymerases and transcription factors gather into…
In this work it is shown that 20 canonical amino acids (AAs) within genetic code appear to be a whole system with strict AAs positions; more exactly, with AAs ordinal number in three variants; first variant 00-19, second 00-21 and third…
Recently, structural analysis of the human transferrin and growth hormone (GH) amino acid sequences has unravelled that they harbor a motif identical to a pattern found in viral oncoproteins known to bind the primarily nuclear tumor…
Protein structures are a very special class among all possible structures. It was suggested that a ``designability principle'' plays a crucial role in nature's selection of protein sequences and structures. Here we provide a theoretical…
Symmetry breaking governs most fascinating phenomena in crystals, such as ferroelectricity, nonlinear optics, piezoelectricity, ferromagnetism, and superconductivity. In two-dimensional materials, a wide variety of tuning knobs presents…
Graphene nanoribbons (GNRs) are promising two-dimensional materials with various technological applications, in particular for the armchair GNR families that have a semiconductor character. Recently, methods that allowed for the control of…
Over the past few years, microRNAs (miRNAs) have emerged as a new prominent class of gene regulatory factors that negatively regulate expression of approximately one-third of the genes in animal genomes at post-transcriptional level.…
We present McGenus, an algorithm to predict RNA secondary structures with pseudoknots. The method is based on a classification of RNA structures according to their topological genus. McGenus can treat sequences of up to 1000 bases and…