bi1c00281_si_001.pdf (3.41 MB)
DNA Minor Groove-Induced cis–trans Isomerization of a Near-Infrared Fluorescent Probe
journal contribution
posted on 2021-06-18, 16:05 authored by Sudakshina Ganguly, N. Arul Murugan, Debasis Ghosh, Nagarjun Narayanaswamy, Thimmaiah Govindaraju, Gautam BasuThe
discovery of small molecules that exhibit turn-on far-red or
near-infrared (NIR) fluorescence upon DNA binding and understanding
how they bind DNA are important for imaging and bioanalytical applications.
Here we report the DNA-bound structure and the DNA binding mechanism
of quinone cyanine dithiazole (QCy-DT), a recently reported AT-specific
turn-on NIR fluorescent probe for double-stranded DNA. The nuclear
magnetic resonance (NMR)-derived structure showed minor groove binding
but no specific ligand–DNA interactions, consistent with an
endothermic and entropy-driven binding mechanism deduced from isothermal
titration calorimetry. Minor groove binding is typically fast because
it minimally perturbs the DNA structure. However, QCy-DT exhibited
unusually slow DNA binding. The cyanine-based probe is capable of cis–trans isomerization due to overlapping
methine bridges, with 16 possible slowly interconverting cis/trans isomers. Using NMR, density functional theory,
and free energy calculations, we show that the DNA-free and DNA-bound
environments of QCy-DT prefer distinctly different isomers, indicating
that the origin of the slow kinetics is a cis–trans isomerization and that the minor groove preferentially
selects an otherwise unstable cis/trans isomer of QCy-DT. Flux analysis showed the conformational selection
pathway to be the dominating DNA binding mechanism at low DNA concentrations,
which switches to the induced fit pathway at high DNA concentrations.
This report of cis/trans isomerization
of a ligand, upon binding the DNA minor groove, expands the prevailing
understanding of unique discriminatory powers of the minor groove
and has an important bearing on using polymethine cyanine dyes to
probe the kinetics of molecular interactions.