Related papers: Embedded transfer RNA Genes
Tight regulation of messenger RNA (mRNA) stability is essential to ensure accurate gene expression in response to developmental and environmental cues. mRNA stability is controlled by mRNA decay pathways, which have traditionally been…
The distribution of transversely polarized quarks inside a transversely polarized nucleon, known as transversity, encodes a basic piece of information on the nucleon structure, sharing the same status with the more familiar unpolarized and…
The significant role of epigenetic mechanisms within natural systems has become increasingly clear. This paper uses a recently presented abstract, tunable Boolean genetic regulatory network model to explore aspects of epigenetics. It is…
RNA editing can be crucial for the expression of genetic information via inserting, deleting, or substituting a few nucleotides at specific positions in an RNA sequence. Within coding regions in an RNA sequence, editing usually occurs with…
The genes of eukaryotes are characterized by protein coding fragments, the exons, interrupted by introns, i.e. stretches of DNA which do not carry any useful information for the protein synthesis. We have analyzed the melting behavior of…
RNA secondary structures of increasing complexity are probed combining single molecule stretching experiments and stochastic unfolding/refolding simulations. We find that force-induced unfolding pathways cannot usually be interpretated by…
Given an Eulerian digraph, we consider the genus distribution of its face-oriented embeddings. We prove that such distribution is log-concave for two families of Eulerian digraphs, thus giving a positive answer for these families to a…
microRNAs (miRNAs) regulate gene expression at post-transcriptional level by repressing target RNA molecules. Competition to bind miRNAs tends in turn to correlate their targets, establishing effective RNA-RNA interactions that can…
Proteins are known to locate their specific targets on DNA up to two orders of magnitude faster than predicted by the Smoluchowski three-dimensional diffusion rate. One of the mechanisms proposed to resolve this discrepancy is termed…
The computer-aided folding of biomolecules, particularly RNAs, is one of the most difficult challenges in computational structural biology. RNA tetraloops are fundamental RNA motifs playing key roles in RNA folding and RNA-RNA and…
The dysregulation of transcripts is characterized as one of the main mechanisms in tumor pathogenesis. The recent discovery developed a new hypothesis, competitive endogenous RNAs (ceRNAs), which could regulate other RNA transcripts via…
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…
The kinetic folding of RNA sequences into secondary structures is modeled as a complex adaptive system, the components of which are possible RNA structural rearrangements (SRs) and their associated bases and base pairs. RNA bases and base…
Nanopores -- nanosized holes that can transport ions and molecules -- are very promising devices for genomic screening, in particular DNA sequencing. Both solid-state and biological pores suffer from the drawback, however, that the channel…
We present a comparative analysis of large-scale topological and evolutionary properties of transcription networks in three species, the two distant bacteria E. coli and B. subtilis, and the yeast S. cerevisiae. The study focuses on the…
In this paper we study properties of topological RNA structures, i.e.~RNA contact structures with cross-serial interactions that are filtered by their topological genus. RNA secondary structures within this framework are topological…
The bioinformatical methods to detect lateral gene transfer events are mainly based on functional coding DNA characteristics. In this paper, we propose the use of DNA traits not depending on protein coding requirements. We introduce several…
Cytoskeletal crowding plays a key role in the diffusion of DNA molecules through the cell, acting as a barrier to effective intracellular transport and conformational stability required for such processes as transfection, viral infection,…
Recent experiments and simulations have demonstrated that proteins can fold on the ribosome. However, the extent and generality of fitness effects resulting from co-translational folding remain open questions. Here we report a genome-wide…
Electron transmission through nanosystems is blocked if there are no states connecting the left and the right reservoir. Electron-electron scattering can lift this blockade and we show that this feature can be conveniently implemented by…