Sentence examples for binding sites using the from inspiring English sources
DNA sequences in the promoter region were analysed with the TESS interface (http//:www.cbil.upenn.edu/tess) for putative transcription factors binding sites using the TRANSFAC database.
The UCH L1 promoter was mutated at different TCF4/Lef1 binding sites using the Quik-Change Site Directed Mutagenesis Kit (Stratagene).
We searched for both known transcription factor binding sites using the Transfac database (http://www.cbil.upenn.edu/cgi-bin/tess/tess?RQ=NBqt) and for enrichment of novel sequence motifs.
These sequences were then examined for the presence of ERE binding sites using the latest Dragon ERE Finder version 6.0 (http://apps.sanbi.ac.za/ere/index.php) [10] based upon information present in the transcriptional regulation, from patterns to profiles (TRANSFAC) database [11].
However, we envision that it is feasible to increase the selectivity of bioinformatics searches by modeling higher order cis-regulatory modules (CRMs) [31], consisting of several transcription factor binding sites, using the same HMM statistical principles and software described herein.
The region of GAPDH used to normalize the ChIP data was confirmed to not enrich CTCF by comparing it with another region of the GAPDH gene located far away from any known CTCF binding sites (using the following primers: 5'-TACTAGCGGTTTTACGGGCG-3' and 5'-TCGAACAGGAGGAGCAGAGAGCGA-3').
Namely, first we compute non-equilibrium works generated during pulling ligands from the binding site using the steered molecular dynamics method.
The mutated version of this plasmid (p-zbtb7a 3'UTRm) was generated by utilizing the p-zbtb7a 3'UTR as template and modifying the miR-20a seed binding site using the QuikChange II XL Site-Directed Mutagenesis Kit.
Mutagenesis was used to delete miR-17 binding site using the QuickChange II Kit (Stratagene, La Jolla, CA, USA).
We generated 2D schematic representations of the ligands in the binding site using the LIGX option in MOE (Chemical Computing Group, Montreal, Quebec, Canada).
