Related papers: Viral RNA as a branched polymer
The mechanical properties of DNA play a critical role in many biological functions. For example, DNA packing in viruses involves confining the viral genome in a volume (the viral capsid) with dimensions that are comparable to the DNA…
Selected ribonucleotide sequences bind well to zwitterionic phospholipid bilayer membranes, though randomized RNAs do not. There are no evident repeated sequences in selected membrane binding RNAs. This implies small and varied motifs…
DNA plays a special role in polymer science not just because of the highly selective recognition of complementary single DNA strands but also because bacteria can express DNA chains that are very long yet perfectly monodisperse. The latter…
The statistical mechanics of heteropolymer structure formation is studied in the context of RNA secondary structures. A designed RNA sequence biased energetically towards a particular native structure (a hairpin) is used to study the…
The formation of a viral capsid -- the highly-ordered protein shell that surrounds the genome of a virus -- is the canonical example of self-assembly. The capsids of many positive-sense RNA viruses spontaneously assemble from in vitro…
The aim of the study is to analyze viruses using parameters obtained from distributions of nucleotide sequences in the viral RNA. Seeking for the input data homogeneity, we analyze single-stranded RNA viruses only. Two approaches are used…
In biology, predicting RNA secondary structures plays a vital role in determining its physical and chemical properties. Although we have powerful energy models to predict them as well as parametric analysis to understand the models…
Defective interfering particles arise spontaneously during a viral infection as mutants lacking essential parts of the viral genome. Their ability to replicate in the presence of the wild-type (WT) virus (at the expense of viable viral…
Recent studies have shown that single-stranded viral RNAs fold into more compact structures than random RNA sequences with similar chemical composition and identical length. Based on this comparison it has been suggested that wild-type…
Single-stranded (ss) RNA viruses self-assemble spontaneously in solutions that contain the viral RNA genome molecules and the viral capsid proteins. The self-assembly of empty capsids can be understood on the basis of free energy…
In-vivo DNA organization at large length scales ($\sim 100nm$) is highly debated and polymer models have proved useful to understand the principle of DNA-organization. Here, we show that $<2$% cross-links at specific points in a ring…
Understanding how virus capsids assemble around their nucleic acid (NA) genomes could promote efforts to block viral propagation or to reengineer capsids for gene therapy applications. We develop a coarse-grained model of capsid proteins…
During the lifecycle of many single-stranded RNA viruses, including many human pathogens, a protein shell called the capsid spontaneously assembles around the viral genome. Understanding the mechanisms by which capsid proteins selectively…
The structural organisation of the viral genome within its protein container, called the viral capsid, is an important aspect of virus architecture. Many single-stranded (ss) RNA viruses organise a significant part of their genome in a…
We study RNA foldings and investigate their topology using a combination of knot theory and embedded rigid vertex graphs. Knot theory has been helpful in modeling biomolecules, but classical knots place emphasis on a biomolecule's…
We propose a novel characterization method of randomly branched polymers based on the geometrical property of such objects in confined spaces. The central idea is that randomly branched polymers exhibit passing/clogging transition across…
This contribution focuses on the fascinating RNA molecule, its sequence-dependent folding driven by base-pairing interactions, the interplay between these interactions and natural evolution, and its multiple regulatory roles. The four of us…
What can cells gain by using disordered, rather than folded, proteins in the architecture of their skeleton? Disordered proteins take multiple co-existing conformations, and often contain segments which act as random-walk-shaped polymers.…
Single-stranded (ss) RNA viruses self-assemble spontaneously in solutions that contain the viral RNA genome molecules and viral capsid proteins. The self-assembly of empty capsids can be understood on the basis of free energy minimization.…
RNA-RNA binding is an important phenomenon observed for many classes of non-coding RNAs and plays a crucial role in a number of regulatory processes. Recently several MFE folding algorithms for predicting the joint structure of two…