Branched DNA nanostructures efficiently stabilised and monitored by novel pyrene–perylene 2′-α-l-amino-LNA FRET pairs

Abstract

Novel pyrene-perylene α-L-LNA FRET pairs described herein effectively detect assembly of 2- and 3-way branched DNA nanostructures prepared by postsynthetic microwave-assisted CuAAC click chemistry. The fluorescent signalling of assembly by internally positioned FRET pairs is achieved with low to no fluorescence background signal, remarkably low limit of target detection values and stabilization of the resulting nanostructures.

Toward Non-Enzymatic Ultrasensitive Identification of Single Nucleotide Polymorphisms by Optical Methods

“…Amplified DNA targets can be analyzed for the presence of SNP by different direct and indirect hybridization strategies including intercalator dyes in allele-specific digital PCR (dPCR) [17], sequence-specific fluorogenic probes [18], electrochemical sensors [19][20][21][22][23][24] and diagnostic nano-materials [25]. Electrochemical sensing is a promising approach for SNP detection which takes advantage of synthetic oligonucleotide probes and the large thermodynamic changes in enthalpy and entropy.…”

“…nano-particles and fluorescence spectroscopy [17][18][19][20][21][22][23][24][25]. Next several efficient colorimetric assays for SNP sensing in amplified DNA have been developed based on modified gold nano-particles (Au-nps; Figure 2) [26].…”

Fluorescent Nucleic Acid Analogues in Research and Clinical Diagnostics

“…In doing this, the choice of a fluorophore becomes a critical factor. The optimal groove-binding fluorophore is highly sensitive to the local microenvironment, stable under conditions of oligonucleotide synthesis or postsynthetic labeling, water soluble, and bright (Lindegaard et al 2008;Umemoto et al 2007;Astakhova et al 2008aAstakhova et al , b, 2010Astakhova et al , 2012Astakhova et al , 2013aAstakhova 2014;Østergaard et al 2010a, b;Sau and Hrdlicka 2012;Kumar et al 2013). Notably, the chemistry and length of a linker play an important role for the attachment of groove-binding dyes to oligonucleotides.…”

RNA and DNA Diagnostics

“…ONTs containing fluorophores are commonly used for real-time analysis of DNA sequences being amplified in a polymerase chain reaction (PCR) as well as for sequencing by hybridization, fluorescence in situ hybridization, fluorescence resonance energy transfer, molecular beacons, TaqMan probes, and DNA chips (Erlich et al 1991;Mirzabekov 1994;Dumont et al 2012;Singh et al 2000;Astakhova et al 2013;Ke et al 2012;Tan et al 2012;Ryazantsev et al 2012;Benitez et al 2012;Schulze et al 2012). They are also commonly used as probes to detect specific DNA or RNA sequences in homogeneous solution, and such measurements are required in various fields such as basic research, drug development, and medical diagnosis.…”