Pyrene or perylene can be attached to the 5 position of deoxyuridine through a triple bond to form an excited state dimers which know as excimers1 . Förster and Kasper has shown that while dilute solutions of pyrene fluoresce violet, at higher concentrations the fluorescence shifts 100 nm and becomes blue. This long wavelength fluorophore emiison is resulted from a charge-trasnfer between a pyrene in the excited state and another pyrene in the group state such as deoxyuridine base. Since this complex must form within the lifetime of the excited state, by having two pyrene-labeled DNA probes at close proximity, one with the pyrene on the 5’ terminus and the other on the 3’, the two pyrenes could be brought together by hybridizing in tandem to the target sequence, leading to excimer formation.2 This technique has been used recently to probe mRNA in cells, taking advantage of the relatively long fluorescence life time of the pyrene excimer.3

Product Information


Product Name:

Pyrene-dU Fluorescent Base Oligonucleotide Modification

Chemical Name:



Fluorescent Base

Modification Code:


Chemical Formula:


Exact Mass:


Formula Weight:


Extinction Coefficient, ε(λ):



Bio-Synthesis Inc. Oligo Structure



Delivery Format:


Shipping Conditions:

Room Temperature

Storage Conditions:

-20°C To -70°C
Oligonucleotides are stable in solution at 4°C for up to 2 weeks. Properly reconstituted material stored at -20°C should be stable for at least 6 months. Dried DNA (when kept at -20°C) in a nuclease-free environment should be stable for years.


1. T. Förster, Kasper, K., Z. Elektrochem., 1955, 59, 976.
2. P.L. Paris, J.M. Langenhan, and E.T. Kool, Nucleic Acids Res., 1998, 26, 3789-93.
3. A.A. Marti, et al., Nucleic Acids Res, 2006, 34, 3161-8.