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A possible explanation for this phenomenon could be that these LexA-like binding sites are recognized by other transcription factors that have similar DNA-binding domains to that of LexA.
In human promoters, SP1 and EBOX transcription factor binding sites are recognized by the transcription factors NF-Y, SP1, and USF which are known to be constitutive TFs participating in basal gene transcription [ 31].
Ancestral binding sites as well as novel binding sites are recognized by the heterozygous population, which therefore experience no deleterious effects from mismatch binding, and at the same time benefit from improved binding with the novel variant.
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The 2935 binding sites were recognized by TFs associated with 1422 unique human genes, most of which (1129) were associated with the Gene Ontology terms "TF activity", "Cofactor activity", or "DNA Binding" (Additional file 3).
The 110 different putative c-Myc binding sites were recognized partly by different matrices.
An electrophoretic mobility shift assay confirmed that an oligonucleotide containing the binding site is recognized by DBP, but a point mutant version is not (Figure 7B).
The SP1 binding site is recognized by a family of transcription factors, and has similar binding affinity with SP1, SP3, and SP4 factors.
For example, the cryptic heparin-binding site is recognized by conformationally sensitive epitope antibody 8E6, while antibodies 13H1 and 16A7 that per se did not react with plasma VTNC recognize VTNC treated with heparin, chaotropes, detergent, low pH, heating at 56°C, and by immobilization [14].
Editing sites are recognized by RNA binding proteins that bind sequence elements immediately upstream of the C-residue to be edited.
Specific nuclear DNA κB binding sites are efficiently recognized by RelB/p52 DNA heterodimers, allowing for transcription of certain κB-regulated target genes [49], [51].
MicroRNA binding sites are most likely recognized by nucleotide sequences in the 3'-untranslated regions (3′-UTR) of target mRNAs.
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