title: Biomolecular structure manipulation using tailored electromagnetic radiation: a proof of concept on a simplified model of the active site of bacterial DNA topoisomerase.
abstract: We report on the viability of breaking selected bonds in biological systems using tailored electromagnetic radiation. We first demonstrate, by performing large-scale simulations, that pulsed electric fields cannot produce selective bond breaking. Then, we present a theoretical framework for describing selective energy concentration on particular bonds of biomolecules upon application of tailored electromagnetic radiation. The theory is based on the mapping of biomolecules to a set of coupled harmonic oscillators and on optimal control schemes to describe optimization of temporal shape, the phase and polarization of the external radiation. We have applied this theory to demonstrate the possibility of selective bond breaking in the active site of bacterial DNA topoisomerase. For this purpose, we have focused on a model that was built based on a case study. Results are given as a proof of concept.
authors.affiliation: Institute of Physics, FB 10, University of Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany. garcia@physik.uni-kassel.de.
authors.forename: Daungruthai
authors.initials: D
authors.lastname: Jarukanont
authors.forename: João T S
authors.initials: JT
authors.lastname: Coimbra
authors.forename: Bernd
authors.initials: B
authors.lastname: Bauerhenne
authors.forename: Pedro A
authors.initials: PA
authors.lastname: Fernandes
authors.forename: Shekhar
authors.initials: S
authors.lastname: Patel
authors.forename: Maria J
authors.initials: MJ
authors.lastname: Ramos
authors.forename: Martin E
authors.initials: ME
authors.lastname: Garcia
mesh_terms: D020134:Catalytic Domain; D004264:DNA Topoisomerases, Type I / Q000737:chemistry* / Q000378:metabolism; D004574:Electromagnetic Fields; D004926:Escherichia coli / Q000201:enzymology*; D008958:Models, Molecular; D011487:Protein Conformation
chemical_list: D004264:DNA Topoisomerases, Type I