Sensitive Surface Enhanced Raman Scattering-Based Detection of a BIGH3 Point Mutation Associated with Avellino Corneal Dystrophy

Surface enhanced Raman scattering (SERS) is highly useful for sensitive analytical sensing; however, its practical availability for detecting a point mutation associated with disease in clinical sample was rarely proved. Herein, we present a toehold-mediated, DNA displacement-based, SERS sensor for detecting point mutations in the BIGH3 gene associated with the most common corneal dystrophies (CDs) in a clinical setting. To diagnose Avellino corneal dystrophy (ACD), selectivity was ensured by exploring optimal DNA displacement conditions such as length of toehold and hybridization temperature. A SERS-efficient Ag@Au bimetallic nanodendrite was employed to ensure sensitivity. Optimization for a clinical setting showed that discrimination was maximized when toehold length was 6-mer (T6), and hybridization temperature was 36 °C. On the basis of tests that used clinical homozygous and heterozygous CD samples, a single-base mismatched DNA sequence was identifiable within 30 min with a limit of detection (LOD) of 400 fM. From the results, we conclude that our toehold-mediated, DNA displacement-based, SERS sensor allows a rapid and sensitive detection of a BIGH3 gene point mutation associated with Avellino corneal dystrophy, indicating the practical ability of the method to diagnose genetic diseases caused by point mutations.

Stereochemistry-Guided DNA Probe for Single Nucleotide Polymorphisms Analysis

Single nucleotide polymorphisms (SNPs) are the most abundant genetic polymorphisms and are responsible for many genetic diseases and cancers. In general, SNPs detection is performed by a single probe system (SPS), in which a single probe specifically hybridizes to one target. However, with the use of this method it is hard to improve the hybridization specificity and single mismatched discrimination factors (DF). In addition, the multiprobe system (MPS) requires complex probe designs and introduces at least one auxiliary probe except for the probe complementary to the target, resulting in a complicated detection system. Faced with these difficulties, we perform the SNP detection using a d/l-tryptophan (Trp) guided DNA probe and regulate the DF of electrochemical DNA (E-DNA) sensors by molecular chirality. We show that the DF of the d-Trp incubated E-DNA sensor (d-sensor) is larger than that of the l-sensor. More importantly, we achieve the high specificity by coupling d-Trp and l-Trp incubated E-DNA sensors, and the median DF is 7.21. Furthermore, the specificity of SNP detection can be further improved by supersandwich assay, and the median DF is enlarged to 37.23, which is comparable to that obtained with a multiprobe detection system.

An efficient DNA-fueled molecular machine for the discrimination of single-base changes

A new strategy for single-base polymorphism (SNP) detection based on the assembly of DNA-AuNPs (gold nanoparticles) driven by a DNA-fueled molecular machine, is established and optimized. It is highly efficient, works at room temperature, and is easy to handle. A single-base change on an oligonucleotide strand is unambiguously discriminated for either SNPs or insertions and deletions (indels). The strategy is demonstrated to detect a mutation in the breast cancer gene BRCA1 in homogeneous solution at room temperature.

Amplified single base-pair mismatch detection via aggregation of exonuclease-sheared gold nanoparticles

Single nucleotide polymorphism (SNP) detection is important for early diagnosis, clinical prognostics, and disease prevention, and a rapid and sensitive low-cost SNP detection assay would be valuable for resource-limited clinical settings. We present a simple platform that enables sensitive, naked-eye detection of SNPs with minimal reagent and equipment requirements at room temperature within 15 min. SNP detection is performed in a single tube with one set of DNA probe-modified gold nanoparticles (AuNPs), a single exonuclease (Exo III), and the target in question. Exo III’s apurinic endonucleolytic activity differentially processes hybrid duplexes between the AuNP-bound probe and DNA targets that are perfectly matched or contain a single-base mismatch. For perfectly matched targets, Exo III’s exonuclease activity facilitates a process of target recycling that rapidly shears DNA probes from the particles, generating an AuNP aggregation-induced color change, whereas no such change occurs for mismatched targets. This color change is easily observed with as little as 2 nM of target, 100-fold lower than the target concentration required for reliable naked eye observation with unmodified AuNPs in well-optimized reaction conditions. We further demonstrate that this system can effectively discriminate a range of different mismatches.

Novel (phenylethynyl)pyrene-LNA constructs for fluorescence SNP sensing in polymorphic nucleic acid targets

We describe fluorescent oligonucleotide probes labeled with novel (phenylethynyl)pyrene dyes attached to locked nucleic acids. Furthermore, we prove the utility of these probes for the effective detection of single-nucleotide polymorphisms in natural nucleic acids. High-affinity hybridization of the probes and excellent fluorescence responses to single-base mismatches in DNA/RNA targets are demonstrated in model dual-probe and doubly labeled probe formats. This stimulated us to develop two diagnostic systems for the homogeneous detection of a drug-resistance-causing mutation in HIV-1 protease cDNA and RNA gene fragments. Target sequences were obtained by analysis of 200 clinical samples from patients currently receiving anti-HIV/AIDS combination therapy at the Russian Federal AIDS Center. Using these fluorescent oligonucleotides, we were able to detect the target mutation despite all the challenges of the natural targets, that is, the presence of additional mutations, neighboring sequence variation, and low target concentration, which typically reduce binding and effectiveness of sensing by fluorescent oligonucleotides.

A two-color, self-controlled molecular beacon

Control yourself! A two-color molecular beacon with non-nucleosidic chromophores in a triplex stem is presented. Pyrene and PDI fluorophores act as mutual quenchers by formation of a donor-acceptor complex in the closed form. Hybridization with the target results in two independent fluorescence signals. The two-color read-out provides a "self-control" feature, which helps to eliminate false positive signals in imaging and screening applications.

Triplexes with 8-Aza-2'-deoxyisoguanosine replacing protonated dC: probing third strand stability with a fluorescent nucleobase targeting duplex DNA

The fluorescent 8-aza-2'-deoxyisoguanosine (4) as well as the parent 2'-deoxyisoguanosine (1) were used as protonated dCH(+) surrogates in the third strand of oligonucleotide triplexes. Stable triplexes were formed by Hoogsteen base pairing. In contrast to dC, triplexes containing nucleoside 1 or 4 in place of dCH(+) are already formed under neutral conditions or even at alkaline pH values. Triplex melting can be monitored separately from duplex dissociation in cases in which the third strand contains the fluorescent nucleoside 4. Third-strand binding of oligonucleotides with 4, opposite to dG, was selective as demonstrated by hybridisation experiments studying mismatch discrimination. Third-strand binding is more efficient when the stability of the DNA duplex is reduced by mismatches, giving third-strand binding more flexibility.