Detection of triple helix DNA formation of guanine-rich oligonucleotide in sodium ion abundant buffer by cross-checking FRET scheme

Dual single nucleotide polymorphisms typing of apolipoprotein E gene based on double restriction endonuclease with lambda exonuclease and triple helix molecular switch assistance

Single nucleotide polymorphisms (SNPs) are critical determinants of disease susceptibility, pathogenesis, and drug response, underscoring the need for their accurate monitoring in clinical practice. In this study, we propose a novel apolipoprotein E (APOE) genotyping method for the rapid and precise identification of six genotypes (ε2/ε2, ε3/ε3, ε4/ε4, ε2/ε3, ε2/ε4, and ε3/ε4). The method utilizes restriction endonucleases AflIII and HaeII to selectively cleave the rs429358 and rs7412 sites, thereby generating distinct double-stranded DNA fragments. These fragments are subsequently processed by Lambda exonuclease to produce single-stranded DNA, which binds to a triple-helix molecular switch (THMS) and induces its conformational transition into a hairpin structure, resulting in a fluorescence change. The optimized assay exhibits a linear detection range of 5-1000 copies with a minimum detection limit of 2 copies for the rs429358 site, and a range of 10-1000 copies with a minimum detection limit of 6 copies for the rs7412 site. Furthermore, the method was validated using clinical samples from 10 Alzheimer's disease patients, achieving complete concordance with sequencing results, which underlines the high specificity and sensitivity of the method and demonstrates its potential as a valuable tool for the early diagnosis and personalized treatment of Alzheimer's disease.

Dynamics Studies of DNA with Non-canonical Structure Using NMR Spectroscopy

The non-canonical structures of nucleic acids are essential for their diverse functions during various biological processes. These non-canonical structures can undergo conformational exchange among multiple structural states. Data on their dynamics can illustrate conformational transitions that play important roles in folding, stability, and biological function. Here, we discuss several examples of the non-canonical structures of DNA focusing on their dynamic characterization by NMR spectroscopy: (1) G-quadruplex structures and their complexes with target proteins; (2) i-motif structures and their complexes with proteins; (3) triplex structures; (4) left-handed Z-DNAs and their complexes with various Z-DNA binding proteins. This review provides insight into how the dynamic features of non-canonical DNA structures contribute to essential biological processes.

A simple fluorescent strategy based on triple-helix molecular switch for sensitive detection of chloramphenicol

A simple fluorescent strategy based on the formation of triple-helix molecular switch (THMS) between a signal transduction probe (STP) and an aptamer (Apt) was constructed for the determination of chloramphenicol (CAP). A weak fluorescence intensity was observed for STP solution due to the proximity of fluorophore and quencher through intramolecular DNA hybridization, causing the fluorescence quenching. The fluorescence intensity of the system was significantly enhanced after the addition of Apt. It was attributed to the formation of THMS between the Apt and STP through the Watson-Crick and Hoogsteen base pairing, resulting in the restoration of fluorescence because of the long distance between the fluorophore and quencher of STP. The fluorescence intensity of the system decreased due to the release of STP caused by the specific binding between Apt and CAP. The quantitative analysis of CAP could be achieved based on the decreased fluorescence intensity. The parameters affecting the performance of THMS including the Apt arm length, pH of buffer solution, Mg²⁺ concentration and the formation time of THMS were investigated in detail. Under the optimal conditions (Apt arm length of 9 bases, pH of 6.5, 2.5 × 10³ μmol L^-1 Mg²⁺, THMS formation time of 30 min), the decreased fluorescence intensity and the concentration of chloramphenicol were linear in the range of 5.0 × 10^-3-2.0 × 10^-1 μmol L^-1 with the correlation coefficient of 0.9963. The limit of detection was 1.2 nmol L^-1. Subsequently, the developed method was applied to the analysis of chloramphenicol in honey sample, and the recovery was between 84.5% and 103.0% with relative standard deviation less than 4.6%.

Conformational changes of non-B DNA

In contrast to B-DNA that has a right-handed double helical structure with Watson-Crick base pairing under the ordinary physiological conditions, repetitive DNA sequences under certain conditions have the potential to fold into non-B DNA structures such as hairpin, triplex, cruciform, left-handed Z-form, tetraplex, A-motif, etc. Since the non-B DNA-forming sequences induce the genetic instability and consequently can cause human diseases, the molecular mechanism for their genetic instability has been extensively investigated. On the contrary, non-B DNA can be widely used for application in biotechnology because many DNA breakage hotspots are mapped in or near the sequences that have the potential to adopt non-B DNA structures. In addition, they are regarded as a fascinating material for the nanotechnology using non-B DNAs because they do not produce any toxic byproducts and are robust enough for the repetitive working cycle. This being the case, an understanding on the mechanism and dynamics of their structural changes is important. In this critical review, we describe the latest studies on the conformational dynamics of non-B DNAs, with a focus on G-quadruplex, i-motif, Z-DNA, A-motif, hairpin and triplex (189 references).