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There is evidence that many lncRNAs act as scaffolds that regulate the molecular (that is, protein, RNA, and DNA) interactions required for various signalling networks, which is accomplished, in part, via interactions with chromatin-modifying complexes and the epigenetic regulation of the expression of multiple genes (Mercer et al, 2009; Ponting et al, 2009; Li et al, 2013b).
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Mutations in TF binding sites (TFBSs) can disrupt the essential protein-DNA interactions required for the appropriate patterning or magnitude of gene expression.
The accumulation of large-scale interaction data on multiple organisms, such as protein-protein and protein-DNA interactions, requires novel computational techniques that will be able to analyze these data together with information collected through other means.
Since biological targets (e.g., protein receptors, enzymes and DNA) are three-dimensional structures, the interactions require appropriate complementary placement of the pharmacophoric groups in three-dimensional space.
Social interactions require polite conversation.
These interactions require extensive additional theoretical analysis.
Monitoring protein protein and protein DNA interactions requires complex techniques, such as pull-down assays.
The available structures for CFP1, MLL (mixed lineage leukaemia protein) 1, KDM2A and DNMT1 (DNA methyltransferase 1) suggest that the KFGG motif is not involved in sequence-specific DNA interactions, but may be required to provide rigidity to the ZF-CxxC domain fold.
A detailed characterization of chromatin-DNA interactions is therefore required for understanding the molecular mechanisms behind gene regulation.
Our findings indicate that there is a minimum time required for formaldehyde fixation of protein DNA interactions, below which interpretation of ChIP and microscopy becomes problematical.
Some mobility of the WH domain may be required to allow for flexibility in DNA interactions to accommodate different promoters.
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