Understanding the mechanisms by which DBPs find their target sites (∼10 bp long) within genomes made of millions to billions of base pairs, and quantifying the associated search kinetics, is pivotal to analyse biochemical reactions and their regulation in living cells1,2. The search process ...
We calculated the average mismatch rates by counting the number of base pairs that were not matching between the mapped read and the genome sequence and dividing this number by the length of the mapped read. Mismatches evaluated include soft clipping, insertion, deletion, and substitution mismatches...
Centromeric satellite sequences typically have a monomer size of 100–200 base pairs, often 150 to 180 bp, a length sufficient to wrap a single nucleosome [4]. However, in plants, the origin of these monomers remains unclear. Analysis of ancestral crop species, such as Gossypium raimondii [...
Mutations one, two and three base pairs proximal to the PAM show the lowest binding efficiencies, suggesting that this site has the highest specificity for dCas9 binding for this given probe. As the mutations near the PAM distal region, there is a steady increase in dCas9 binding. This is ...
For any given genome, an individual k-mer is derived from single-base increments along the length of the viral genome (“Methods”). Thus, in a genome with a length of 30 kb, the approximate size of the SARS-CoV-2 genome, there are ~ 30,000 k-mers. If all viral genomes ...
According to Medline Plus, in every cell, humans possess 23 pairs of chromosomes, among which the sex chromosomes constitute one pair. The X chromosome, comprising roughly 155 million DNA base pairs, makes up around 5% of the total DNA incells. ...
Alternative splicing (AS) is a principal mode of genetic regulation and one of the most widely used mechanisms to generate structurally and functionally distinct mRNA and protein variants. Dysregulation of AS may result in aberrant transcription and protein products, leading to the emergence of human...
T-box transcription factors containing other domains than the T-box domain have so far only been described in vertebrates, and in that case the domain in question is another DNA-binding domain [30]. The Response regulator receiver domain functions as receiver of phosphorylation signals in two-...
Large serine recombinases (LSRs) are DNA integrases that facilitate the site-specific integration of mobile genetic elements into bacterial genomes. Only a few LSRs, such as Bxb1 and PhiC31, have been characterized to date, with limited efficiency as tools for DNA integration in human cells. ...
sharpness of the transition in selectivity as a function of the length L of the oligomers at play; the relevance of the constraint of defectless 3′ terminals in PCR primer targeting; and the quantitative estimate of the contribution to miRNA target selectivity provided by processes beyond base ...