Base Pair
Sensitivity and Enhanced ON/OFF Ratios of
DNA-Binding: Donor–Acceptor–Donor Fluorophores
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Abstract
The photophysical properties of two
recently reported live cell
compatible, DNA-binding dyes, 4,6-bis(4-(4-methylpiperazin-1-yl)phenyl)pyrimidin-2-ol, <b>1</b>, and [1,3-bis[4-(4-methylpiperazin-1-yl)phenyl]-1,3-propandioato-κ<i>O</i>, κ<i>O</i>′]difluoroboron, <b>2</b>, are characterized. Both dyes are quenched in aqueous solutions,
while binding to sequences containing only AT pairs enhances the emission.
Binding of the dyes to sequences containing only GC pairs does not
produce a significant emission enhancement, and for sequences containing
both AT and GC base pairs, emission is dependent on the length of
the AT pair tracts. Through emission lifetime measurements and analysis
of the dye redox potentials, photoinduced electron transfer with GC
pairs is implicated as a quenching mechanism. Binding of the dyes
to AT-rich regions is accompanied by bathochromic shifts of 26 and
30 nm, respectively. Excitation at longer wavelengths thus increases
the ON/OFF ratio of the bound probes significantly and provides improved
contrast ratios in solution as well as in fluorescence microscopy
of living cells