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Sequence-specific nucleic acid binding proteins do not recognize one sequence out of all possibilities; rather, they bind to many sequences with a range of affinities.
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This could reflect the lower binding specificity of C/EBPα, since it is easier to create a new site if the factor can bind to many different sequences.
While numerous papers suggest that flexibility could enable one protein to bind to many partners, we might have been the first to suggest that flexibility would provide a means for multiple sequences to bind to a common partner.
Deadpan and Snail bind to many neuroblast genes.
Recently we studied the detailed structures for a one-to-many example (namely, p53 using its disordered regions to bind to many partners), and we also studied the structures of a many-to-one example (namely, 14-3-3 usinglets single binding site to associate with many different disordered partners having different amino acid sequences).
Most of the proteins bound to methylated DNA in a sequence-dependent manner; however, a minority bound to many different methylated DNA probes, indicating that binding can sometimes occur independent of DNA sequence.
The adaptor region of Vav1 binds to many different proteins.
To generate the amplicon library for bacteria and archaea, specific primers were selected according to two criteria: (a) the fragment should span 600 bases of the 16S rRNA gene to receive sufficient phylogenetic information and (b) the primers should bind to as many bacterial/archaeal sequences as possible without detecting non-target groups.
Many well represented domains recognize and bind to primary sequences less than 10 amino acids in length called Short Linear Motifs (SLiMs).
Besides GR and AP-1 motifs, many additional 8-mers, such as the CRE TGACGTCAandand CTCF motif (AGGGGGCG) have a high INOS, which indicates that many TFs bind to the same sequences calculated to be well-bound by the nucleosome and produce an intrinsic competition between TF and nucleosomes for binding the same DNA.
Some chromatin factors including many transcription factors bind to specific DNA sequences only in nucleosome free regions.
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