Twin Probes as a Novel Tool for the Detection of Single‐Nucleotide Polymorphisms

Abstract

Single‐nucleotide polymorphisms (SNPs) are the most common form of DNA sequence variation. There is a strong interest from both academy and industry to develop rapid, sensitive and cost effective methods for SNP detection. Here we report a novel structural concept for DNA detection based on fluorescence dequenching upon hybridization. The so‐called “twin probe” consists of a central fluorene derivative as fluorophore to which two identical oligonucleotides are covalently attached. This probe architecture is applied in homogeneous hybridization assays with subsequent fluorescence spectroscopic analysis. The bioorganic hybrid structure is well suited for sequence specific DNA detection and even SNPs are identified with high efficiency. Additionally, the photophysical properties of the twin probe were investigated. The covalent attachment of two single stranded oligonucleotides leads to strong quenching of the central fluorescence dye induced by the nucleobases. The twin probe is characterized by supramolecular aggregate formation accompanied by red‐shifted emission and broad fluorescence spectra.

The Chemistry of Organic Nanomaterials

“…A third approach to DNA sensing is to attach two identical sequences of single-stranded DNA to a conjugated rigid rod. [138] Hybridization with the complementary sequences induces a marked augmentation in the fluorescence from the conjugated moiety. Even single nucleotide polymorphisms can be detected efficiently.…”

Multiple Logic Functions Based on Small Molecular Fluorene Derivatives and Their Application in Cell Imaging

“…The result of fluorescence quenching upon hybridization was consistent with that reported in the literature. 38 More interesting, we found that the fluorescence of FSM-modified probe 1 can be quenched by SG I (I 2 ) due to the overlap of the fluorescence spectra of FSM/DNA probe and the absorption spectra of SG I ( Figure S1). However, in the presence of both DNAc and SG I, the SG I preferentially intercalated into the dsDNA and the distance between SG I and FSM was shortened.…”

“…Contrary to the quenching effect upon hybridization, the emission of FSM was just slightly decreased compared with the initial state because the guanine (G) base could be a quencher for fluorene connected to oligonucleotides. 38,58 When the SG I (I 2 ) was added into the solution containing probe 2 and S1, the fluorescence intensity of FSM was quenched by SG I. Only K + and SG I are present at the same time, probe 2 and S1 formed into the G-quadruplex structure and SG I was intercalated into the G-quadruplex, inducing the efficient FRET from FSM to SG I.…”

“…Small molecular fluorene derivatives F(COOH) 2 , FS, and the FSM/DNA probes were synthesized according to literature procedures. 38 A carboxyl group at one end of the F(COOH) 2 was covalently linked to the 5′ end of a ssDNA to form the FSM/DNA probe and then purified by HPLC method. The sequences of the FSM/DNA probes and other oligonucleotides used here are listed in Scheme 1.…”

DNA Meets Synthetic Polymers — Highly Versatile Hybrid Materials

“…The so-called "twin probe" consists of a central fluorene derivative as fluorophore to which two identical oligonucleotides are covalently attached. 80 This probe architecture was applied in a homogenous hybridization assay with subsequent fluorescence spectroscopic analysis. The bioorganic hybrid structure was well-suited for sequence specific DNA detection, and even single-nucleotide polymorphisms (SNPs) were identified with high efficiency.…”