Pyrene binary probes for unambiguous detection of mRNA using time-resolved fluorescence spectroscopy.
We report here the design, synthesis and application of pyrene binary oligonucleotide probes for selective detection of cellular mRNA. The detection strategy is based on the formation of a fluorescent excimer when two pyrene groups are brought into close proximity upon hybridization of the probes with the target mRNA. The pyrene excimer has a long fluorescence lifetime (>40 ns) compared with that of cellular extracts (approximately 7 ns), allowing selective detection of the excimer using time-resolved emission spectra (TRES). Optimized probes were used to target a specific region of sensorin mRNA yielding a strong excimer emission peak at 485 nm in the presence of the target and no excimer emission in the absence of the target in buffer solution. While direct fluorescence measurement of neuronal extracts showed a strong fluorescent background, obscuring the detection of the excimer signal, time-resolved emission measurements indicated that the emission decay of the cellular extracts is approximately 8 times faster than that of the pyrene excimer probes. Thus, using TRES of the pyrene probes, we are able to selectively detect mRNA in the presence of cellular extracts, demonstrating the potential for application of pyrene excimer probes for imaging mRNAs in cellular environments that have background fluorescence.
Martí
Angel A
AA
Department of Chemistry, Columbia University, New York, NY 10027, USA.
Li
Xiaoxu
X
Jockusch
Steffen
S
Li
Zengmin
Z
Raveendra
Bindu
B
Kalachikov
Sergey
S
Russo
James J
JJ
Morozova
Irina
I
Puthanveettil
Sathyanarayanan V
SV
Ju
Jingyue
J
Turro
Nicholas J
NJ
D000818:Animals; D001048:Aplysia / Q000235:genetics; D002457:Cell Extracts / Q000737:chemistry; D005456:Fluorescent Dyes / Q000138:chemical synthesis / Q000737:chemistry*; D019476:Insect Proteins / Q000235:genetics; D009474:Neurons / Q000737:chemistry; D009479:Neuropeptides / Q000235:genetics; D015345:Oligonucleotide Probes / Q000138:chemical synthesis / Q000737:chemistry*; D011721:Pyrenes / Q000737:chemistry*; D012333:RNA, Messenger / Q000032:analysis*; D013050:Spectrometry, Fluorescence / Q000379:methods*; D013997:Time Factors
D002457:Cell Extracts; D005456:Fluorescent Dyes; D019476:Insect Proteins; D009479:Neuropeptides; D015345:Oligonucleotide Probes; D011721:Pyrenes; D012333:RNA, Messenger