Base pair sensitivity and enhanced ON/OFF ratios of DNA-binding: donor-acceptor-donor fluorophores.
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.
Department of Chemistry, University of Miami , 1301 Memorial Drive, Coral Gables, Florida 33146, United States.
James N
JN
Wilson
Jens
J
Wigenius
Demar R G
DR
Pitter
Yanhua
Y
Qiu
Maria
M
Abrahamsson
Fredrik
F
Westerlund
D000241:Adenosine / Q000737:chemistry; D020029:Base Pairing; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D005456:Fluorescent Dyes / Q000737:chemistry*; D057809:HEK293 Cells; D006801:Humans; D008856:Microscopy, Fluorescence; D010879:Piperazines / Q000737:chemistry*; D011407:Propane / Q000031:analogs & derivatives* / Q000737:chemistry; D011743:Pyrimidines / Q000737:chemistry*; D013056:Spectrophotometry, Ultraviolet; D013941:Thymine / Q000737:chemistry
C588239:(1,3-bis(4-(4-methylpiperazin-1-yl)phenyl)-1,3-propandioato-kappaO, kappaO')difluoroboron; C588238:4,6-bis(4-(4-methylpiperazin-1-yl)phenyl)pyrimidin-2-ol; D005456:Fluorescent Dyes; D010879:Piperazines; D011743:Pyrimidines; D004247:DNA; D000241:Adenosine; D013941:Thymine; D011407:Propane