Elucidating DNA binding of dithienylethenes from molecular dynamics and dichroism spectra
Journal article, 2019

DNA binding modes of the stereoisomeric rotamers of two dithenylethene derivatives (DTE1 and DTE2) representing candidate molecular photoswitches of great promise for photopharmacology and nanotechnology have been identified and characterized in terms of their binding energies and electronic circular dichroism (CD) responses. In the open form, two binding modes are identified namely minor-groove binding of the lowest-energy conformer with an anti-parallel arrangement of methyl groups and major-groove double-intercalation of the P-enantiomers of an intermediate-state rotamer. Only the latter binding mode is found to be enantiomerically selective and expected to have an overall negative linear dichroism (LD) as observed in the experiment for DTE1 (Angew. Chem., Int. Ed., 2013, 52, 4393). In the closed form, the most favorable binding mode is found to be minor groove binding. Also this binding mode is found to be enantiomerically selective and for DTE1, it is the M-enantiomer that binds the strongest, showing a positive theoretical signature CD band in the long wavelength region with origin in pyridinium ligands. The theoretical CD spectrum is found to be in good agreement with the experimental one, which provides an indirect evidence for a correct identification of the binding mode in the closed form.

Author

M. Linares

Royal Institute of Technology (KTH)

Haofan Sun

Royal Institute of Technology (KTH)

East China University of Science and Technology

Michal Biler

Royal Institute of Technology (KTH)

Joakim Andreasson

Chalmers, Chemistry and Chemical Engineering, Chemistry and Biochemistry

Patrick Norman

Royal Institute of Technology (KTH)

Physical Chemistry Chemical Physics

1463-9076 (ISSN) 1463-9084 (eISSN)

Vol. 21 7 3637-3643

Subject Categories

Structural Biology

Theoretical Chemistry

Organic Chemistry

DOI

10.1039/c8cp05326j

PubMed

30379159

More information

Latest update

7/20/2019