Related papers: Direct homologous dsDNA-dsDNA pairing: how, where …
In many organisms, homologous (or repetitive) chromosomal regions can associate or/and undergo concerted epigenetic changes in the absence of DNA breakage and recombination. The direct specific pairing of DNA duplexes with similar…
Molecular recognition between two double stranded (ds) DNA with homologous sequences may not seem compatible with the B-DNA structure because the sequence information is hidden when it is used for joining the two strands. Nevertheless, it…
Genetic stability is a key factor in maintaining, survival and reproduction of biological cells. It relies on many processes, but one of the most important is a {\it homologous recombination}, in which the repair of breaks in…
Homologous gene shuffling between DNA promotes genetic diversity and is an important pathway for DNA repair. For this to occur, homologous genes need to find and recognize each other. However, despite its central role in homologous…
Homologous recombination plays a key role in generating genetic diversity, while maintaining protein functionality. The mechanisms by which RecA enables a single-stranded segment of DNA to recognize a homologous tract within a whole genome…
Most proteins involved in processing DNA accomplish their activities as a monomer or as a component of a multimer containing a relatively small number of other elements. They generally act locally, binding to one or a few small regions of…
Homologous recombination facilitates the exchange of genetic material between homologous DNA molecules. This crucial process requires detecting a specific homologous DNA sequence within a huge variety of heterologous sequences. The…
Most living systems rely on double-stranded DNA (dsDNA) to store their genetic information and perpetuate themselves. This biological information has been considered the main target of evolution. However, here we show that symmetries and…
The utility of DNA sequence substrings (k-mers) in alignment-free phylogenetic classification, including that of bacteria and viruses, is increasingly recognized. However, its biological basis eludes many twenty-first century practitioners.…
It is not known how a cell manages to find a specific DNA sequence sufficiently fast to repair a broken chromosome through homologous recombination. I propose that the solution is based on a parallelized search implemented by freely…
Complementary DNA strands in solution reliably hybridize to form stable duplexes. We study the kinetics of the hybridization process and the mechanisms by which two initially isolated strands come together to form a stable double helix. We…
The structure of DNA Binding Proteins enables a strong interaction with their specific target site on DNA. However, recent single molecule experiment reported that proteins can diffuse on DNA. This suggests that the interactions between…
While the thermodynamics of DNA hybridization is well understood, much less is known about the kinetics of this classic system. Filling this gap in our understanding has new urgency because DNA nanotechnology often depends critically on…
Analysis of single-molecule micromanipulation experiments of DNA unzipping process shows some features of the force-distance curve, namely two consequent plateaus in the area of ${\sim}12-14pN$ dependent on nucleotide sequence structure, as…
High-density oligonucleotide arrays are among the most rapidly expanding technologies in biology today. In the {\sl GeneChip} system, the reconstruction of the target concentration depends upon the differential signal generated from…
At the onset of X Chromosomes Inactivation, the vital process whereby female mammal cells equalize X products with respect to males, the X chromosomes are colocalized along their Xic (X-Inactivation Center) regions. The mechanism inducing…
A novel mechanism for sympatric speciation that takes into account complex bio-processes within each individual organism is proposed. According to dynamical systems theory, organisms with identical genotypes can possess differentiated…
Single molecule studies, at constant force, of the separation of double-stranded DNA into two separated single strands may provide information relevant to the dynamics of DNA replication. At constant applied force, theory predicts that the…
The formation of DNA loops by proteins and protein complexes that bind at distal DNA sites plays a central role in many cellular processes, such as transcription, recombination, and replication. Here we review the basic thermodynamic…
Double-strand breaks (DSBs) in DNA are naturally occurring destructive events in all organisms that may lead to genome instability. Cells employ various repair methods known as non-homologous end joining (NHEJ), microhomology mediated end…