Related papers: G-quadruplexes and mRNA localization
DNA and RNA quadruplexes are extensively studied for the key roles they are suspected to play in the cellular regulation networks at both genomic and transcriptomic levels. The reliable detection of quadruplexes in cells was and remains a…
G-quadruplexes are non-canonical DNA structures rather ubiquitous in human genome, which are thought to play a crucial role in the development of 85-90 % of cancers. Here, we present a novel coarse-grained approach in modeling…
The subcellular localization of RNAs, including long non-coding RNAs (lncRNAs), messenger RNAs (mRNAs), microRNAs (miRNAs) and other smaller RNAs, plays a critical role in determining their biological functions. For instance, lncRNAs are…
Water molecules play an important role in providing unique environments for biological reactions on cell membranes. It is widely believed that water molecules form bridges that connect lipid molecules and stabilize cell membranes. Using…
Quaternions are an important tool to describe the orientation of a molecule. This paper considers the use of quaternions in matching two conformations of a molecule, in interpolating rotations, in performing statistics on orientational…
While studying nucleic acids to reveal the weak interactions responsible for their three-dimensional structure and for their interactions with drugs, we also contributed to the field of biomolecular mass spectrometry, both in terms of…
Genomes contain rare guanine-rich sequences capable of assembling into four-stranded helical structures, termed G-quadruplexes, with potential roles in gene regulation and chromosome stability. Their mechanical unfolding has only been…
G-quadruplexes (G4s) are helical four-stranded structures forming from guanine-rich nucleic acid sequences, which are thought to play a role in cancer development and malignant transformation. Most current studies focus on G4 monomers, yet…
Cell membranes are anchored to the cytoskeleton via immobile inclusions. We investigate the effect of such anchors on the in-plane dynamics of a fluid membrane and mobile inclusions (proteins) embedded in it. The immobile particles lead to…
Interaction with divalent cations is of paramount importance for RNA structural stability and function. We here report a detailed molecular dynamics study of all the possible binding sites for Mg$^{2+}$ on a RNA duplex, including both…
Water molecules confined between biological membranes exhibit a distinctive non-Gaussian displacement distribution, far different from bulk water. Here, we introduce a new transport equation for water molecules in the intermembrane space,…
Many biological, physical, and social interactions have a particular dependence on where they take place. In living cells, protein movement between the nucleus and cytoplasm affects cellular response (i.e., proteins must be present in the…
Droplet formation has emerged as an essential concept for the spatiotemporal organisation of biomolecules in cells. However, classical descriptions of droplet dynamics based on passive liquid-liquid phase separation cannot capture the…
A theoretical calculation is presented to describe the confined motion of transmembrane molecules in cell membranes. The study is analytic, based on Master equations for the probability of the molecules moving as random walkers, and leads…
Diffusion is a fundamental phenomenon that occurs ubiquitously in nature and remains the subject of continuous research interest. Understanding diffusion is a key to understanding leaving systems. In this Chapter, I discuss diffusion of…
Small non-coding RNAs can exert significant regulatory activity on gene expression in bacteria. In recent years, substantial progress has been made in understanding bacterial gene expression by sRNAs. However, recent findings that…
Molecular chaperones play a prominent role in signaling and transcriptional regulatory networks of the cell. Recent advances uncovered that chaperones act as genetic buffers stabilizing the phenotype of various cells and organisms and may…
The dynamics of a tracer molecule near a fluid membrane is investigated, with particular emphasis given to the interplay between the instantaneous position of the particle and membrane fluctuations. It is found that hydrodynamic…
When the motion of a motile cell is observed closely, it appears erratic, and yet the combination of nonequilibrium forces and surfaces can produce striking examples of organization in microbial systems. While most of our current…
Nanoparticle (NP)-based applications are becoming increasingly important in the biomedical field. However, understanding the interactions of NPs with biofluids and cells is a major issue in order to develop novel approaches aimed at…