Base pair sensitivity and enhanced ON/OFF ratios of DNA-binding: Donor-acceptor-donor fluorophores

James N. Wilson, Jens Wigenius, Demar R.G. Pitter, Yanhua Qiu, Maria Abrahamsson, Fredrik Westerlund

Research output: Contribution to journalArticlepeer-review

13 Scopus citations


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, 1, and [1,3-bis[4-(4-methylpiperazin-1-yl)phenyl]-1,3-propandioato-κO, κO′]difluoroboron, 2, 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.

Original languageEnglish (US)
Pages (from-to)12000-12006
Number of pages7
JournalJournal of Physical Chemistry B
Issue number40
StatePublished - Oct 10 2013

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Surfaces, Coatings and Films
  • Materials Chemistry


Dive into the research topics of 'Base pair sensitivity and enhanced ON/OFF ratios of DNA-binding: Donor-acceptor-donor fluorophores'. Together they form a unique fingerprint.

Cite this