Issue 5, 2006

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

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.

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

Supplementary files

Article information

Article type
Paper
Submitted
09 Jan 2006
Accepted
08 Mar 2006
First published
21 Mar 2006

Photochem. Photobiol. Sci., 2006,5, 493-498

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

S. Jockusch, A. A. Martí, N. J. Turro, Z. Li, X. Li, J. Ju, N. Stevens and D. L. Akins, Photochem. Photobiol. Sci., 2006, 5, 493 DOI: 10.1039/B600213G

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