Deletion of the LBD/dimerization domain leads to an inactive, monomeric DBD in which function can be restored via dimerization driven by fusing the proteins of interest. The new DNAPLOT extension is not only applicable for the analysis of naturally occuring immune repertoires but also for the analysis of artificial antibody populations isolated from phage display libraries. DNA binding of transcriptional regulators is generally dependent on dimerization of the DBD through the LBD. Thus, by removing redundant information on the FRs, essential information about the antigen binding sites is displayed, and critical amino acids can be viewed at a glance. In this way, the essential information on the docking sites of a given antibody population is easily visible. The new extended DNAPLOT version loads a list of variable domain DNA sequences, extracts the CDR regions and presents them as a color-coded string of amino acids. These molecular mediators, along with transcription factors, form a network that governs gene expression. Their evolution is influenced by a large number of factors, including epigenetic mechanisms, gene regulatory elements and molecular cofactors. The adjacent regions, the so called framework regions (FRs), build the antibody structure and provide a frame to expose the 3 CDR regions of each variable domain of the antibody. TFs are proteins that can bind specific DNA sequences and regulate gene expression. Looking at antibody structures, it is well known that mainly the so called complementary determining regions (CDRs) contain the information of the interface between a given antibody and its antigen.

Thus, DNAPLOT is now able to demonstrate the dynamics of the expressed repertoire, e.g., during the time course of the antibody response against a certain pathogen. The new features allow the systematic analysis and visualization of the expressed immune repertoire of an organism. We have now introduced a major extension to the functionality of DNAPLOT.

Dna binding repertoire biology meaning