Dual Sensing of Hairpin and Quadruplex DNA Structures Using Multicolored Peptide Nucleic Acid Fluorescent Probes

Abstract

Synthesis of water-soluble 5-mer Peptide Nucleic Acids (PNAs) functionalized at their 5' and 3'-ends with two original precursors of pentamethine cyanine dye synthesis is reported. The successful use of these PNA probes for sensing DNA hairpin structures in vitro was also demonstrated where specific hairpin formation was associated with the appearance of a characteristic fluorescence signal at 660 nm. A comparative study between three different strategies where PNAs were targeting either the stem or the loop of the hairpin was carried out. Best sensitivity was obtained using PNA sequences complementary to the loop sequence and directing both functional moieties toward the base of loop. Unprecedented proof-of-concept for the simultaneous sensing of hairpin and quadruplex DNAs with a nonoverlapping two-color system (C3 and C5) is also demonstrated.

Nucleic Acid Templated Reactions for Chemical Biology

“…The introduction of a modified aldehyde derivative led to the formation of a pentamethine cyanine dye (Cy5) in a similar fashion. Cy3 and Cy5 were used for simultaneous sensing of DNA hairpins and quadruplexes (fluorescence emission recorded at 540 and 660 nm, respectively) …”

A streptavidin paramagnetic-particle based competition assay for the evaluation of the optical selectivity of quadruplex nucleic acid fluorescent probes

“…Finally, the use of a different quadruplex structure as competitor is a tool in the quest for the molecular Holy Grail that a probe with specificity for a single type of quadruplex structure would represent (for recent examples, see Refs. [49,50]). …”

Fluorescence Detection of Intron Lariat RNA with Reduction‐Triggered Fluorescent Probes

“…[13] Furthermore, this is the first example for the detection of higher-order-structured RNA by using a nucleic acid templated chemical reaction, although the DNA-templated detection of G-quadruplex or hairpin DNA was recently reported. [14] Studies on the realtime detection of LaRNA with RETF probes both in vitro and in vivo are currently under way. .…”