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Spectroscopic investigation of a FRET molecular beacon containing two fluorophores for probing DNA/RNA sequences

Steffen Jockusch; Angel A. Martí; Nicholas J. Turro; Zengmin Li; Xiaoxu Li; Jingyue Ju; Nathan Stevens; Daniel L. Akins

Title:
Spectroscopic investigation of a FRET molecular beacon containing two fluorophores for probing DNA/RNA sequences
Author(s):
Jockusch, Steffen
Martí, Angel A.
Turro, Nicholas J.
Li, Zengmin
Li, Xiaoxu
Ju, Jingyue
Stevens, Nathan
Akins, Daniel L.
Date:
Type:
Articles
Department:
Chemistry
Volume:
5
Permanent URL:
Book/Journal Title:
Photochemical & Photobiological Sciences
Abstract:
We report the design, synthesis, and characterization of a molecular beacon (MB) consisting of two fluorescent dyes (Alexa 488 and RedX) for DNA and RNA analysis. In the absence of the target DNA or RNA the MB is in its stem-closed form and shows efficient energy transfer from the donor (Alexa) to the acceptor (RedX), generating mostly fluorescence from RedX. In the presence of the complementary target DNA the MB opened efficiently, hybridizes with the target DNA, and energy transfer is blocked in the stem-open form. This attachment to the target generates a fluorescence signature, which is clearly distinguishable from the fluorescence signature of the stem-closed form, allowing for ratiometric analysis of the fluorescence signal. In addition to steady-state fluorescence analysis, time resolved fluorescence (ps time range) and fluorescence depolarization studies were performed. We show that fluorescence lifetime and fluorescence depolarization measurements are useful analytical tools to optimize the MB design.
Subject(s):
Chemistry
Publisher DOI:
http://dx.doi.org/10.1039/b600213g
Item views:
236
Metadata:
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