Predicting near-UV electronic circular dichroism in nucleosomal DNA by means of DFT response theory

• 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.

Subject headings

NATURVETENSKAP  -- Kemi -- Teoretisk kemi (hsv//swe)

NATURAL SCIENCES  -- Chemical Sciences -- Theoretical Chemistry (hsv//eng)

Keyword

DNA B

nucleoside

nucleosome

base pairing

chemical structure

chemistry

circular dichroism

electron

quantum theory

thermodynamics

ultraviolet spectrophotometry

DNA

B-Form

Electrons

Models

Molecular

Nucleosides

Nucleosomes

Spectrophotometry

Ultraviolet

Publication and Content Type

ref (subject category)

art (subject category)