AUTHOR=Oiwa Nestor N. , Cordeiro Claudette E. , Heermann Dieter W. TITLE=The Electronic Behavior of Zinc-Finger Protein Binding Sites in the Context of the DNA Extended Ladder Model JOURNAL=Frontiers in Physics VOLUME=4 YEAR=2016 URL=https://www.frontiersin.org/journals/physics/articles/10.3389/fphy.2016.00013 DOI=10.3389/fphy.2016.00013 ISSN=2296-424X ABSTRACT=
Instead of ATCG letter alignments, typically used in bioinformatics, we propose a new alignment method using the probability distribution function of the bottom of the occupied molecular orbital (BOMO), highest occupied molecular orbital (HOMO), and lowest unoccupied orbital (LUMO). We apply the technique to transcription factors with Cys2His2 zinc fingers. These transcription factors search for binding sites, probing for the electronic patterns at the minor and major DNA groves. The eukaryotic Cys2His2 zinc finger proteins bind to DNA ubiquitously at highly conserved domains. They are responsible for gene regulation and the spatial organization of DNA. To study and understand these zinc finger DNA-protein interactions, we use the extended ladder in the DNA model proposed by Zhu et al. [