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 journalArticle

10 Citations (Scopus)

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, 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
Pages (from-to)12000-12006
Number of pages7
JournalJournal of Physical Chemistry B
Volume117
Issue number40
DOIs
StatePublished - Oct 10 2013

Fingerprint

Fluorophores
DNA
Coloring Agents
Dyes
deoxyribonucleic acid
dyes
sensitivity
AT Rich Sequence
Fluorescence microscopy
Quenching
electron transfer
quenching
Cells
aqueous solutions
microscopy
life (durability)
Wavelength
fluorescence
Electrons
augmentation

ASJC Scopus subject areas

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

Cite this

Base pair sensitivity and enhanced ON/OFF ratios of DNA-binding : Donor-acceptor-donor fluorophores. / Wilson, James N; Wigenius, Jens; Pitter, Demar R G; Qiu, Yanhua; Abrahamsson, Maria; Westerlund, Fredrik.

In: Journal of Physical Chemistry B, Vol. 117, No. 40, 10.10.2013, p. 12000-12006.

Research output: Contribution to journalArticle

Wilson, James N ; Wigenius, Jens ; Pitter, Demar R G ; Qiu, Yanhua ; Abrahamsson, Maria ; Westerlund, Fredrik. / Base pair sensitivity and enhanced ON/OFF ratios of DNA-binding : Donor-acceptor-donor fluorophores. In: Journal of Physical Chemistry B. 2013 ; Vol. 117, No. 40. pp. 12000-12006.
@article{69bdf8fb5c2842ae9994e0cba16626d9,
title = "Base pair sensitivity and enhanced ON/OFF ratios of DNA-binding: Donor-acceptor-donor fluorophores",
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, 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.",
author = "Wilson, {James N} and Jens Wigenius and Pitter, {Demar R G} and Yanhua Qiu and Maria Abrahamsson and Fredrik Westerlund",
year = "2013",
month = "10",
day = "10",
doi = "10.1021/jp406993m",
language = "English",
volume = "117",
pages = "12000--12006",
journal = "Journal of Physical Chemistry B Materials",
issn = "1520-6106",
publisher = "American Chemical Society",
number = "40",

}

TY - JOUR

T1 - Base pair sensitivity and enhanced ON/OFF ratios of DNA-binding

T2 - Donor-acceptor-donor fluorophores

AU - Wilson, James N

AU - Wigenius, Jens

AU - Pitter, Demar R G

AU - Qiu, Yanhua

AU - Abrahamsson, Maria

AU - Westerlund, Fredrik

PY - 2013/10/10

Y1 - 2013/10/10

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=84885643470&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84885643470&partnerID=8YFLogxK

U2 - 10.1021/jp406993m

DO - 10.1021/jp406993m

M3 - Article

VL - 117

SP - 12000

EP - 12006

JO - Journal of Physical Chemistry B Materials

JF - Journal of Physical Chemistry B Materials

SN - 1520-6106

IS - 40

ER -