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However, gp2 also inhibited RNAP binding to promoter fragments that lacked downstream promoter DNA that interacts with the β′ jaw.
The cross-linked SUMO-TF-DNA complexes were extracted and contained the DNA that interacts with either the SUMOylated-TFs or the SUMOylated transcription complexes.
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Matrix attachment regions (MAR) are the sites on genomic DNA that interact with the nuclear matrix.
The SMC proteins usually act as heterodimers (that is, SMC1 and 3 in cohesin, SMC2 and 4 in condensin, SMC5 and 6 in an unnamed complex involved in DNA repair) that interact through their hinge domains.
Another family of commonly used recognition molecules are DNA aptamers, which are short pieces of DNA that interact with specific targets, depending on the aptamer sequence.
Chromatin Immuno Precipitation (ChIP) is a biochemical method to identify binding sites on DNA that interact with proteins.
Lambda relies heavily on a processive exonuclease that produces extended tracks of single stranded DNA that interact, while RecA mediates pairing between duplex molecules.
Another method used to build 3D structures, called DNA origami, is tougher to use to build complex shapes, Yin said, because it relies on a long "scaffold" strand of DNA that folds to interact with hundreds of shorter "staple" strands – and each new shape requires a new scaffold routing strategy and hence new staples.
Premature senescence of A549 cells was induced by their exposure to 2 nM DNA topoisomerase inhibitor mitoxantrone (Mxt), the drug that interacts with DNA by intercalation and is a type II DNA topoisomerase inhibitor [ 44].
In silico analysis and DNA shift assays showed that SimReg1 is a DNA-binding autoregulatory protein that interacts directly with putative promoter regions of the structural sim genes, both transporter genes simX and simEx2, and the putative regulatory gene simReg3.
SogR1 is a DNA-binding transcriptional regulator that interacts with OHHL and modulates the expression of target genes in accordance with bacterial population density.
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