title: Predicting near-UV electronic circular dichroism in nucleosomal DNA by means of DFT response theory.
abstract: It is demonstrated that time-dependent density functional theory (DFT) calculations can accurately predict changes in near-UV electronic circular dichroism (ECD) spectra of DNA as the structure is altered from the linear (free) B-DNA form to the supercoiled N-DNA form found in nucleosome core particles. At the DFT/B3LYP level of theory, the ECD signal response is reduced by a factor of 6.7 in going from the B-DNA to the N-DNA form, and it is illustrated how more than 90% of the individual base-pair dimers contribute to this strong hypochromic effect. Of the several inter-base pair parameters, an increase in twist angles is identified as to strongly contribute to a reduced ellipticity. The present work provides first evidence that first-principles calculations can elucidate changes in DNA dichroism due to the supramolecular organization of the nucleoprotein particle and associates these changes with the local structural features of nucleosomal DNA.
authors.affiliation: Department of Physics, Chemistry and Biology, Linköping University, SE-581 83 Linköping, Sweden. mathieu@ifm.liu.se.
authors.forename: Patrick
authors.initials: P
authors.lastname: Norman
authors.forename: Joseph
authors.initials: J
authors.lastname: Parello
authors.forename: Prasad L
authors.initials: PL
authors.lastname: Polavarapu
authors.forename: Mathieu
authors.initials: M
authors.lastname: Linares
mesh_terms: D020029:Base Pairing; D002942:Circular Dichroism; D059371:DNA, B-Form / Q000737:chemistry*; D004583:Electrons; D008958:Models, Molecular; D009705:Nucleosides / Q000737:chemistry; D009707:Nucleosomes; D011789:Quantum Theory; D013056:Spectrophotometry, Ultraviolet; D013816:Thermodynamics
chemical_list: D059371:DNA, B-Form; D009705:Nucleosides; D009707:Nucleosomes