DNA Hybridization Research Articles

Colorimetric detection of Staphylococcus aureus based on self-linkable and hollow organic-inorganic nanocomposites as light-driven oxidase-like nanozyme for cascade signal amplification

Facing increasingly serious bacterial infections and their threat to food safety and human health, exploring specific and sensitive bacterial strategies is indispensable. Nanozyme-based colorimetric biosensors with the superiorities of easy-to-read and catalytic signal amplification have attracted increasing interest. However, few investigations relate to the nanozymes with excellent light-driven oxidase-like activity. In this study, a sensitive colorimetric biosensor for Staphylococcus aureus (S. aureus) detection was constructed based on a light-driven oxidase-like nanozyme (PHCS@CuNcPOPTP) as well as the self-chain linking process. The hollow organic-inorganic nanocomposite (PHCS@CuNcPOPTP) was prepared by a one-step Friedel-Crafts alkylation reaction. The PHCS@CuNcPOPTP exhibited excellent and synergistically enhanced light-driven oxidase-like activity originating from its unique photosensitive properties. Subsequently, PHCS@CuNcPOPTP was served as a scaffold, loading with the rabbit anti-Staphylococcus aureus Rosenbach tropina antibody (bs-4582R, Ab2), DNA1, and DNA2, respectively, to construct signal probes (PHCS@CuNcPOPTP@Au-Ab2/DNA1, PHCS@CuNcPOPTP@Au-DNA1, and PHCS@CuNcPOPTP@Au-DNA2). By the repetitive DNA hybridization among signal probes, a large amount of PHCS@CuNcPOPTP-DNA dendrimers were formed and utilized to trigger the chromogenic reaction without the participation of high-concentration H2O2, resulting in the cascaded catalytic amplification and the lower background signal. As expected, the suggested sensing platform presented ultrasensitive bacterial detection with a remarkably broad linear range (101 to 108 CFU/mL) and a limit of detection (LOD, 3.40 CFU/mL).

DNA extraction optimization and authentication of Vaccinium berries and their products by high-resolution DNA melting analysis

Food adulteration has been an issue in the food industry for many decades. The market for natural and healthy products has been expanding and therefore the value of raw ingredients harvested from natural sources has increased, and, in some cases, it has led to adulteration of such high-valued products. Berry fruits and products from different species of the genus Vaccinium have been gaining worldwide popularity because of their nutraceutical benefits. However, there are increasing reports of adulteration or misidentification of high-value wild berries with their cultivated counterparts. During recent years, DNA-based methods for the authentication of commercial products have gained popularity, especially regarding species identification. Based on the availability of their chloroplast genome information, we developed DNA markers to differentiate lingonberry from cranberry as well as to discriminate European bilberry from North American blueberry. By using Bar-HRM analysis (DNA barcoding combined with High Resolution Melting), the markers were tested on plant DNA as well as DNA extracted from diverse berry products. The developed markers were able to discriminate between species and, moreover, detect potential adulteration in products made from these berry species. Subsequently, the Bar-HRM result was verified by amplicon sequencing. To conclude, the developed molecular markers represent a valuable tool for the berry food industry.

High-fidelity, hyper-accurate, and evolved mutants rewire atomic-level communication in CRISPR-Cas9.

The high-fidelity (HF1), hyper-accurate (Hypa), and evolved (Evo) variants of the CRISPR-associated protein 9 (Cas9) endonuclease are critical tools to mitigate off-target effects in the application of CRISPR-Cas9 technology. The mechanisms by which mutations in recognition subdomain 3 (Rec3) mediate specificity in these variants are poorly understood. Here, solution nuclear magnetic resonance and molecular dynamics simulations establish the structural and dynamic effects of high-specificity mutations in Rec3, and how they propagate the allosteric signal of Cas9. We reveal conserved structural changes and dynamic differences at regions of Rec3 that interface with the RNA:DNA hybrid, transducing chemical signals from Rec3 to the catalytic His-Asn-His (HNH) domain. The variants remodel the communication sourcing from the Rec3 α helix 37, previously shown to sense target DNA complementarity, either directly or allosterically. This mechanism increases communication between the DNA mismatch recognition helix and the HNH active site, shedding light on the structure and dynamics underlying Cas9 specificity and providing insight for future engineering principles.

Dynamic Interface-Assisted Rapid Self-Assembly of DNA Origami-Framed Anisotropic Nanoparticles.

The ordered arrangement of nanoparticles can generate unique physicochemical properties, rendering it a pivotal direction in the field of nanotechnology. DNA-based chemical encoding has emerged as an unparalleled strategy for orchestrating precise and controlled nanoparticle assemblies. Nonetheless, it is often time-consuming and has limited assembly efficiency. In this study, we developed a strategy for the rapid and ordered assembly of DNA origami-framed nanoparticles assisted by dynamic interfaces. By assembling Au nanoparticles (AuNPs) onto DNA origami with different sticky ends in various directions, we endowed them with anisotropic specific affinities. After assembling DNA origami-framed AuNPs onto supported lipid bilayers with freely diffusing single-stranded DNA via DNA hybridization, we found that DNA origami-framed AuNPs could form larger ordered assemblies than those in 3D solution within equivalent time frames. Furthermore, we also achieved rapid and ordered assembly of liposome nanoparticles by employing the aforementioned strategy. Our work provides a novel avenue for efficient and rapid assembly of nanoparticles across two-dimensional interfaces, which is expected to promote the application of ordered nanoparticle assemblies in sensor and biomimetic system construction.

TERRA and the alternative lengthening of telomeres: a dangerous affair.

Eukaryotic telomeres are transcribed into the long noncoding RNA TERRA. A fraction of TERRA remains associated with telomeres by forming RNA:DNA hybrids dubbed telR-loops. TERRA and telR-loops are essential to promote telomere elongation in human cancer cells that maintain telomeres through a homology-directed repair pathway known as alternative lengthening of telomeres or ALT. However, TERRA and telR-loops compromise telomere integrity and cell viability if their levels are not finely tuned. The study of telomere transcription in ALT cells will enormously expand our understanding of the ALT mechanism and of how genome integrity is maintained. Moreover, telomere transcription, TERRA and telR-loops are likely to become exceptionally suited targets for the development of novel anti-cancer therapies.

Programming crystallization kinetics of self-assembled DNA crystals with 5-methylcytosine modification

Self-assembled DNA crystals offer a precise chemical platform at the ångström-scale for DNA nanotechnology, holding enormous potential in material separation, catalysis, and DNA data storage. However, accurately controlling the crystallization kinetics of such DNA crystals remains challenging. Herein, we found that atomic-level 5-methylcytosine (5mC) modification can regulate the crystallization kinetics of DNA crystal by tuning the hybridization rates of DNA motifs. We discovered that by manipulating the axial and combination of 5mC modification on the sticky ends of DNA tensegrity triangle motifs, we can obtain a series of DNA crystals with controllable morphological features. Through DNA-PAINT and FRET-labeled DNA strand displacement experiments, we elucidate that atomic-level 5mC modification enhances the affinity constant of DNA hybridization at both the single-molecule and macroscopic scales. This enhancement can be harnessed for kinetic-driven control of the preferential growth direction of DNA crystals. The 5mC modification strategy can overcome the limitations of DNA sequence design imposed by limited nucleobase numbers in various DNA hybridization reactions. This strategy provides a new avenue for the manipulation of DNA crystal structure, valuable for the advancement of DNA and biomacromolecular crystallography.

Species Identification of Rehabilitated Critically Endangered Orangutans Through DNA Forensic: Implication for Conservation.

Rehabilitating and releasing orangutans back into the wild is one of the conservation strategies being pursued to conserve orangutans. However, the species determination between Sumatran, Tapanuli, and Bornean orangutans is essential for reintroduction to avoid outbreeding depression, which could lead to DNA hybridisation and increase the probability of recessive characters. Here, we reported on an investigation of three orangutans in which DNA forensic techniques were used to identify the species before release and reintroduction to their habitat. By applying DNA forensic, the orangutan was successfully confirmed with high probabilities (100%) by identifying two orangutan species, Pongo abelii and Pongo pygmaeus wurmbii. Based on ambiguous morphology, we found the possibility of orangutan species being misidentified in rehabilitation. This case report demonstrates the importance of molecular diagnostics to identify the orangutan species. We also provide workflow recommendations from genetic aspect for rehabilitated orangutans. These recommendations will enable decision-makers to consider genetics when assessing future management decisions, which will help ensure that the orangutan species is effectively conserved.

A Method Based on a Modified Fluorescence In Situ Hybridization (FISH) Approach for the Sensing of Staphylococcus aureus from Nasal Samples.

Staphylococcus aureus is a major source of bacteremia and develops several complications, causing high morbidity and mortality. Rapid identification and detection of these bacteria have become an important issue for biomedical applications. Herein, an optical method based on a modified fluorescence in situ hybridization (FISH) approach has been established using DNA hybridization technology for the swift detection of pathogenic S. aureus from clinical samples. The platform was constructed with single-stranded genomic DNA and microbial colony by directly immobilizing in agarose-polyvinyl alcohol (AG-PVA) hydrogel on the surface of a glass slide. The probe was based on an elongation factor encoding the tuf gene, which binds with equal affinity to single-stranded DNA targets as well as surface proteins on microbial cells. The probe was labeled with MFP488 fluorophore having excitation wavelength 501nm. The hybridization of the labeled probe with the target DNA and surface proteins was carried out under optimal FISH conditions, and the detection of bacteria was based on temporary field excitation of the labeled probe under a fluorescence microscope. Positive hybridization signals were detected by high fluorescence intensity. In comparison to genomic DNA, robust signals were observed with microbial cells, perhaps due to the moonlighting effect of the elongation factor Tu (Ef-Tu) expressed on the surface of bacterial cells. The applicability of the developed platform was tested on pediatric nasal samples, and results were verified with real-time qPCR. The designed platform is stable and sensitive, and after detailed optimization, a portable structure for on-site detection of pathogenic bacteria from clinical samples can be produced.

Anaerobic flora, Selenomonas ruminis sp. nov., and the bacteriocinogenic Ligilactobacillus salivarius strain MP3 from crossbred-lactating goats

This study aimed to examine the distribution of anaerobic bacteria in the rumen fluid of Thai crossbred goats and to screen potential probiotic strains capable of producing antimicrobial compounds and inhibiting bacteria that cause milk fat depression. Thirty-four strains of bacteria from the rumen fluid were divided into 13 groups within 12 genera based on 16S rRNA gene sequences. The RF1-5 and RF5-12 were identified as Streptococcus luteliensis and Bacillus licheniformis, respectively, and demonstrated non-ropy exopolysaccharide. Furthermore, mPRGC5T was closely related to Selenomonas caprae JCM 33725 T (97.8% similarity) based on 16S rRNA gene sequences. It exhibited low average nucleotide identity, digital DNA–DNA hybridization, and average amino acid identity values with related type strains ranging from 84.9 to 86.0%, 21.3 to 21.8%, and 73.8 to 76.1%, respectively. The genotypic and phenotypic characteristics of mPRGC5T strongly support this strain as a new species of the genus Selenomonas for which the name Selenomonas ruminis mPRGC5T was proposed. The type strain is mPRGC5T (= JCM 33724 T = KCTC 25177 T). Ligilactobacillus salivarius MP3 showed antibacterial activity against Cutibacterium acnes subsp. acnes DSM 1897 T and Kocuria rhizophila MIII. The enterolysin A cluster gene was identified in its genome. The auto-aggregation of L. salivarius MP3 was 93.6 ± 0.2%. Additionally, co-aggregation of L. salivarius MP3 with C. acnes DSM 1897 T and K. rhizophila MIII had 92.2 ± 3.4% and 87.3 ± 4.5%, respectively. The adhesion capacity of strain MP3 was 76.11 ± 2.2%. Probiogenomic analysis revealed that L. salivarius MP3 was nonhazardous to animal supplementation and included acid- and bile-tolerant ability. However, strain MP3 contained three antibiotic resistance genes. Thus, the supplementation of L. salivarius MP3 could increase the milk fat content by suppressing C. acnes DSM 1897 T with antibiotic resistance gene horizontal transfer awareness.

A novel universal fluorescence detection platform based on target binding-mediated primer exchange reaction strategy for sensitive and accurate detection of multiple biomolecules

This study introduces a universal fluorescent detection platform based on the binding-mediated primer exchange reaction strategy, designed for highly sensitive and accurate detection of multiple biomolecules. This method uses an intact DNA hybridization probe as the initial target recognition site, forming a stable probe-target complex upon binding to the target. This complex drives the primer exchange reaction to amplify the signal, and then to achieve signal output through fluorescence resonance energy transfer (FRET). The reaction process is initiated directly by the catalytic target binding medium, ensuring method specificity. The versatile platform, equipped with various recognition elements such as antisense nucleic acids, biotin, and split aptamers, demonstrates exceptional universality in detecting a range of biomolecules, including virus nucleic acid fragments, streptavidin, and ATP. The method exhibits strong linear relationships with detection limits of 1.02 pM for virus nucleic acid fragments, 1.08 nM for streptavidin, and 15.7 μM for ATP, respectively. Moreover, the method displays excellent selectivity and outstanding performance in complex biological samples. This promising biosensing platform is believed to find numerous applications spanning bioanalysis, disease diagnosis, and biomedicine.

Plug-and-Play Module for Reversible and Continuous Control of DNA Strand Displacement Kinetics.

Regulatory modules for controlling the kinetics of toehold-mediated strand displacement (TMSD) play critical roles in designing dynamic and dissipative DNA chemical reaction networks (CRNs) but are hardwired into sequence designs. Herein, we introduce antitoehold (At), a plug-and-play module for reversible and continuous tuning of TMSD kinetics by temporarily occupying the toehold domain via a metastable duplex and base stacking. We demonstrate that kinetic control can be readily activated or deactivated in real time for any TMSD by simply adding At or anti-At. Continuous tuning of TMSD kinetics can also be achieved by altering the concentration of At. Moreover, the simple addition of At could readily reprogram existing TMSDs into a pulse-generation DNA CRN with continuous tunability. Our At approach also offers a new way for engineering continuously tunable DNA hybridization probes, which may find practical uses for discriminating clinically important mutations. Because of the simplicity, we anticipate that At will find wide applications for engineering DNA CRNs with diverse dynamic and dissipative behaviors, and DNA hybridization probes with tunable affinity and selectivity.

Polyvalent Nanobody Structure Designed for Boosting SARS-CoV-2 Inhibition.

Coronavirus transmission and mutations have brought intensive challenges on pandemic control and disease treatment. Developing robust and versatile antiviral drugs for viral neutralization is highly desired. Here, we created a new polyvalent nanobody (Nb) structure that shows the effective inhibition of SARS-CoV-2 infections. Our polyvalent Nb structure, called "PNS", is achieved by first conjugating single-stranded DNA (ssDNA) and the receptor-binding domain (RBD)-targeting Nb with retained binding ability to SARS-CoV-2 spike protein and then coalescing the ssDNA-Nb conjugates around a gold nanoparticle (AuNP) via DNA hybridization with a desired Nb density that offers spatial pattern-matching with that of the Nb binding sites on the trimeric spike. The surface plasmon resonance (SPR) assays show that the PNS binds the SARS-CoV-2 trimeric spike proteins with a ∼1000-fold improvement in affinity than that of monomeric Nbs. Furthermore, our viral entry inhibition assays using the PNS against SARS-CoV-2 WA/2020 and two recent variants of interest (BQ1.1 and XBB) show an over 400-fold enhancement in viral inhibition compared to free Nbs. Our PNS strategy built on a new DNA-protein conjugation chemistry provides a facile approach to developing robust virus inhibitors by using a corresponding virus-targeting Nb with a desired Nb density.

Chiral-Induced Spin Selectivity Modulated Time-Correlated Single-Photon Counting for DNA Hybridization Detection.

The chiral-induced spin selectivity (CISS) effect can distinguish between the spin of electrons as they pass through chiral molecules by backscattering one of the spin components. Herein, we explore the role of the CISS effect in time-correlated single-photon counting measurements to detect DNA hybridization. We observe that the average lifetime of optical excited states of quantum dots attached to double-stranded DNA (dsDNA) varies with directions of the applied magnetic field. Specifically, the difference in the nonradiative average decay lifetime for the two orientations of the applied magnetic field is 2.21 ns in the case of hybridized strands, which is 130 times higher than that observed with quantum dots attached to single-strand DNA. Additionally, we investigate the application of Fourier transform infrared (FTIR) spectroscopy for detecting double-stranded DNA in the presence of a magnetic field, establishing a theoretical framework to substantiate the experimental evidence of magnetic field-dependent FTIR spectroscopy for dsDNA.

Antibody-Protein-Aptamer Electrochemical Biosensor based on Highly Efficient Proximity-Induced DNA Hybridization on Tetrahedral DNA Nanostructure for Sensitive Detection of Insulin-like Growth Factor-1.

Herein, an antibody-protein-aptamer electrochemical biosensor was designed by highly efficient proximity-induced DNA hybridization on a tetrahedral DNA nanostructure (TDN) for ultrasensitive detection of human insulin-like growth factor-1 (IGF-1). Impressively, the IGF-1 antibody immobilized on the top vertex of the TDN could effectively capture the target protein with less steric effect, and the ferrocene-labeled signal probe (SP) bound on the bottom vertex of the TDN was close to the electrode surface for generating a strong initial signal. In the presence of target protein IGF-1 and an aptamer strand, an antibody-protein-aptamer sandwich could be formed on the top vertex of TDN, which would trigger proximity-induced DNA hybridization to release the SP on the bottom vertex of TDN; therefore, the signal response would decrease dramatically, enhancing the sensitivity of the biosensor. As a result, the linear range of the proposed biosensor for target IGF-1 was 1 fM to 1 nM with the limit of detection down to 0.47 fM, which was much lower than that of the traditional TDN designs on electrochemical biosensors. Surprisingly, the use of this approach offered an innovative approach for the sensitive detection of biomarkers and illness diagnosis.

Description of a new genus of the Pectobacteriaceae family isolated from water in coastal brackish wetlands of the French Camargue region, Prodigiosinella gen. nov., including the new species Prodigiosinella aquatilis sp. nov

The Pectobacteriaceae family comprises plant pathogens able to provoke diverse diseases, including plant maceration due to the production of pectinases disrupting the plant cell wall. To better understand their diversity, a survey of pectinolytic bacteria was performed in brackish lakes of the French region La Camargue near the Mediterranean Sea. The genome of six atypical isolates was sequenced; their size is around 4.8 to 5.0 Mb, including a plasmid of 59 to 61 kb; their G+C values range from 49.1 to 49.3 mol%. Phylogenetic analyses indicated that the novel strains form a new clade of Pectobacteriaceae that branches at the basis of the group encompassing the genera Lonsdalea, Musicola, and Dickeya. Based on phenotypic, genomic and phylogenetic characteristics, we propose the creation of a new genus with the name Prodigiosinella gen. nov. Both the phenotypic and phylogenetic analyses separated the strains into two distinct subgroups, G1 and G2. The type strain LS101T (CFBP 8826T = LMG 32072T) and strain CE70 (CFBP 9054 = LMG 32867) are representative G1 and G2 members, respectively. Three genomic methods were used to analyze DNA–DNA relatedness: digital DNA–DNA hybridization (isDDH), average nucleotide identity (ANI), and genome alignment fraction (AF). They revealed a close relationship between genomes of the two groups, supporting their appurtenance to a same species for which we propose the name Prodigiosinella aquatilis sp. nov. Four strains previously designated as Serratia sp. (ATCC 39006), Brenneria “ulupoensis” (K61) or Erwinia sp. (MK01 and MK09) belong to the new genus Prodigiosinella.

Bacterial Flora in Screw-Fixed Superstructures with Different Sealing Materials: A Comparative Clinical Trial.

A screw-fixed superstructure is predominantly selected for implant prostheses because of the concern regarding developing peri-implantitis, although its infection route remains unclear. Focusing on microleakage from access holes, the present study clinically investigated the bacterial flora in access holes with different sealing materials. We examined 38 sites in 19 patients with two adjacent screw-fixed superstructures. Composite resin was used in the control group, and zinc-containing glass ionomer cement was used in the test group. Bacteria were collected from the access holes 28 days after superstructure placement and were subjected to DNA hybridization analysis. The same patient comparisons of the bacterial counts showed a significant decrease in 14 bacterial species for the red, yellow, and purple complexes in the test group (p < 0.05). In addition, the same patient comparisons of the bacterial ratios showed a significant decrease in six bacterial species for the orange, green, yellow, and purple complexes in the test group (p < 0.05). Furthermore, the same patient comparisons of the implant positivity rates showed a significant decrease in the six bacterial species for the orange, yellow, and purple complexes in the test group. The results of this study indicate that zinc-containing glass ionomer cement is effective as a sealing material for access holes.

Peptoniphilus genitalis sp. nov. and Mobiluncus massiliensis sp. nov.: Novel Bacteria Isolated from the Vaginal Microbiome

The strains Marseille-Q7072T (= CSUR Q7072T = CECT 30604 T) and Marseille-Q7826T (= CSUR Q7826T = CECT 30727 T) were isolated from vaginal samples. As MALDI-TOF mass spectrometry failed to identify them, their genomes were directly sequenced to determine their taxogenomic identities. Both strains are anaerobic without any oxidase and catalase activity. C16:0 is the most abundant fatty acid for both strains. Strain Marseille-Q7072T is non-spore-forming, non-motile, Gram-stain-positive, and coccus-shaped, while strain Marseille-Q7826T is non-spore-forming, motile, Gram-stain-variable, and curved rod-shaped. The genomic comparison of the Marseille-Q7072T and Marseille-Q7826T strains showed that all digital DNA–DNA hybridisation (dDDH) and mean orthologous nucleotide identity (OrthoANI) values were below published species thresholds (70% and 95–96%, respectively) with other closely related species with standing in nomenclature. Thus, we conclude that both strains are new bacterial species. Strain Marseille-Q7072T is a new member of the Bacillota phylum, for which the name Peptoniphilus genitalis sp. nov. is proposed, while the Marseille-Q7826T strain is a new member of the Actinomycetota phylum, for which the name Mobiluncus massiliensis sp. nov. is proposed.

Pseudidiomarina fusca sp. nov., Isolated from the Surface Seawater of the Western Pacific Ocean.

The Gram-negative marine bacterium GXY010T, which has been isolated from the surface seawater of the western Pacific Ocean, is aerobic, non-motile and non-flagellated. Strain GXY010T exhibits growth across a temperature range of 10-42 °C (optimal at 37 °C), pH tolerance from 7.0 to 11.0 (optimal at 7.5) and a NaCl concentration ranging from 1.0 to 15.0% (w/v, optimal at 5.0%). Ubiquinone-8 (Q-8) was the predominant isoprenoid quinone in strain GXY010T. The dominant fatty acids (>10%) of strain GXY010T were iso-C15:0 (14.65%), summed feature 9 (iso-C17:1ω9c and/or 10-methyl C16:0) (12.41%), iso-C17:0 (10.85%) and summed feature 3 (C16:1ω7c and/or C16:1ω6c) (10.41%). Phosphatidylethanolamine (PE), phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), unidentifiable glycolipid (GL) and four non-identifiable aminolipids (AL1-AL4) were the predominant polar lipids of strain GXY010T. The genomic DNA G+C content was identified as a result of 48.0% for strain GXY010T. The strain GXY010T genome consisted of 2,766,857 bp, with 2664 Open Reading Frames (ORFs), including 2586 Coding sequences (CDSs) and 78 RNAs. Strain GXY010T showed Average Nucleotide Identity (ANI) values of 73.4% and 70.6% and DNA-DNA hybridization (DDH) values of 19.2% and 14.5% with reference species Pseudidiomarina tainanensis MCCC 1A02633T (=PIN1T) and Pseudidiomarina taiwanensis MCCC 1A00163T (=PIT1T). From the results of the polyphasic analysis, a newly named species, Pseudidiomarina fusca sp. nov. within the genus Pseudidiomarina, was proposed. The type strain of Pseudidiomarina fusca is GXY010T (=JCM 35760T = MCCC M28199T = KCTC 92693T).

Amplification-free quantitative detection of genomic DNA using lateral flow strips for milk authentication

With the globalization and complexity of the food supply chain, the market is becoming increasingly competitive and food fraudulent activities are intensifying. The current state of food detection faced two primary challenges. Firstly, existing testing methods were predominantly laboratory-based, requiring complex procedures and precision instruments. Secondly, there was a lack of accurate and efficient quantitative detection methods. Taking cow's milk as an example, this study introduced a novel method for nucleic acid quantification in dairy products, based on lateral flow strips (LFS). The core idea of this method is to design single-stranded DNA (ssDNA) probes to hybridize with mitochondrial genes, which are abundant, stable, and species-specific in dairy products, as detection targets. Drawing inspiration from the principles of nucleic acid amplification, this research innovatively established a new DNA hybridization method, named LAMP-Like Hybridization (HybLAMP-Like). Leveraging the denaturation and DNA polymerization functions of the bst enzyme, efficient binding of the probe and template strand was achieved. This method eliminated the need for nucleic acid amplification, simplifying the procedure and mitigating aerosol contamination, thereby ensuring the accuracy of the detection results. The method exhibited exceptional sensitivity, capable of detecting extremely low to 12.5 ng in visual inspection and 3.125 ng when using a reader. In terms of practicality, it could achieve visual detection of cow's milk content as low as 1% in adulterated dairy products. When combined with a portable LFS reader, it also enabled precise quantitative analysis of milk adulteration.

Transient states during the annealing of mismatched and bulged oligonucleotides.

Oligonucleotide hybridization is crucial in various biological, prebiotic and nanotechnological processes, including gene regulation, non-enzymatic primer extension and DNA nanodevice assembly. Although extensive research has focused on the thermodynamics and kinetics of nucleic acid hybridization, the behavior of complex mixtures and the outcome of competition for target binding remain less well understood. In this study, we investigate the impact of mismatches and bulges in a 12bp DNA or RNA duplex on its association (kon) and dissociation (koff) kinetics. We find that such defects have relatively small effects on the association kinetics, while the dissociation kinetics vary in a position-dependent manner by up to 6 orders of magnitude. Building upon this observation, we explored a competition scenario involving multiple oligonucleotides, and observed a transient low specificity of probe hybridization to fully versus partially complementary targets in solution. We characterize these long-lived metastable states and their evolution toward equilibrium, and show that sufficiently long-lived mis-paired duplexes can serve as substrates for prebiotically relevant chemical copying reactions. Our results suggest that transient low accuracy states may spontaneously emerge within all complex nucleic acid systems comprising a large enough number of competing strands, with potential repercussions for gene regulation in the realm of modern biology and the prebiotic preservation of genetic information.