Ultra-specific discrimination of single-nucleotide mutations using sequestration-assisted molecular beacons

Abstract

A sequestration-assisted molecular beacon strategy was proposed for highly specific discrimination and detection of single-nucleotide mutations at low abundance.

Enhanced SNP-sensing using DNA-templated reactions through confined hybridization of minimal substrates (CHOMS)

“…4-mer PNA targeting sequences having any types of SNV were functionalized with pyridinium coumarin (DC-A sequences) for second signalling and medically relevant T variations in KRAS, BCR-ABL1, and JAK2 were selected as test SNVs. 16,27 Aer 10 min of irradiation, a sample containing both coumarin and rhodamine substrates selectively afforded a uorescence signal exclusively for the fully matched sequences (WT for rhodamine and SNV for coumarin). Other variants afforded a negligible signal gain in either channel.…”

“…12,13 The need to achieve more costeffective, faster analysis and higher single nucleotide resolution continues to drive technological developments. 14 Recent examples include amendments to existing technologies such as molecular beacons, 15,16 melting analysis, 17,18 environmentally sensitive uorescent nucleobases, [19][20][21][22][23][24] and strand displacement probes 25,26 or new technologies such as polymerase-amplied release of ATP (POLARA) 27 or graphene-based biosensors for real-time kinetic monitoring of hybridization. 28 The analysis of SNVs requires technologies with the highest nucleotide resolution to ascertain the polymorphism or variation.…”

Target-Triggered Polymerization of Branched DNA Enables Enzyme-free and Fast Discrimination of Single-Base Changes

“…Spherical nucleic acid conjugates possessing the periphery of high-dense nucleic acid probes and the core of inorganic nanoparticles are used as visible detection platform through color change generated by particle aggregation (Cutler et al., 2012, Rouge et al., 2015). Consequently, DNA nanostructures can serve as simultaneous target recognizer and signal amplifiers (Li et al., 2018), becoming effective elements for the discrimination of single-base changes (Hu et al., 2017). Given that the fine DNA nanostructure increased the difficulty of design and use, it is necessary to develop an enzyme-free, simply designed, low-cost, and easily manipulated method for the discrimination of single-base changes.…”

Locus-patterned sequence oriented enrichment for multi-dimensional gene analysis

“…[6][7][8] Toward that end, considerable efforts are focused on the discrimination of single-nucleotide variants (SNVs) during multi-dimensional gene analysis. [9][10][11] DNA strand branch migration provides opportunities to recognize SNVs, relying on the specicity of Watson-Crick hybridization between different dynamic DNA complexes at some step of strand displacement workow. [12][13][14][15] However, the effects are impaired by the small thermodynamic penalty from a single base mismatch and are always vulnerable to environmental perturbation.…”