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The growth of liquid biopsy, i. e., the possibility of obtaining health information by analysing circulating species (nucleic acids, cells, proteins, and vesicles) in peripheric biofluids, is pushing the field of sensors and biosensors beyond the limit to provide decentralised solutions for nonspecialists. In particular, among all the circulating species that can be adopted in managing cancer evolution, both for diagnostic and prognostic applications, microRNAs have been highly studied and detected. The development of electrochemical devices is particularly relevant for liquid biopsy purposes, and the screen‐printed electrodes (SPEs) represent one of the building blocks for producing novel portable devices. In this work, we have taken miR‐2115‐3p as model target (it is related to lung cancer), and we have developed a biosensor by exploiting the use of a complementary DNA probe modified with methylene blue as redox mediator. In particular, the chosen sensing architecture was applied to serum measurements of the selected miRNA, obtaining a detection limit within the low nanomolar range; in addition, various platforms were interrogated, namely commercial and hand‐made SPEs, with the aim of providing the reader with some insights about the optimal platform to be used by considering both the cost and the analytical performance. [ABSTRACT FROM AUTHOR]

Many diseases in the human body are related to the overexpression of viscosity and sulfur dioxide. Therefore, it is essential to develop rapid and sensitive fluorescent probes to detect viscosity and sulfur dioxide. In the present work, we developed a dual-response fluorescent probe (ES) for efficient detection of viscosity and sulfur dioxide while targeting mitochondria well. The probe generates intramolecular charge transfer by pushing and pulling the electron–electron system, and the ICT effect is destroyed and the fluorescence quenched upon reaction with sulfite. The rotation of the molecule is inhibited in the high-viscosity system, producing a bright red light. In addition, the probe has good biocompatibility and can be used to detect sulfite in cells, zebrafish and mice, as well as upregulation of viscosity in LPS-induced inflammation models. We expect that the dual response fluorescent probe ES will be able to detect viscosity and sulfite efficiently, providing an effective means of detecting viscosity and sulfite-related diseases. [ABSTRACT FROM AUTHOR]

Deoxyribonucleic acid can reflect species, life trait characteristics, and the diversity of species in the environment. Preferably, detection technology should be able to discriminate soil microbial DNA pools in different ecosystems. However, current detection technologies cannot meet this challenge rapidly. Herein, BCK, as a functional material for new research and development, capable of quickly discriminating soil microbial DNA pools in different ecosystems and model organisms with different fluorescence signals, is used to remedy this limitation. In three typical ecosystems, namely forest, grassland, and cropland, BCK could distinguish the gross amount of DNA pools and the DNA pools per microbiomass by different fluorescence signals caused by sequence differences. Likewise, BCK could distinguish the two model species of prokaryotic Escherichia coli and eukaryotic yeast genomic DNA. Further structural comparison experiments revealed significantly different patterns and responses of the probe BCK to the three structures of DNA with the combination of double-strand DNA to the probe being the strongest, followed by single-strand and supercoil DNA. Considering that double-strand DNA is the genetic basis of most living organisms, BCK was applied to examine its effects on DNA replication. The results showed that BCK could bind to template DNA and inhibit the process of DNA replication in the polymerase chain reaction system. This method should guide future research to fill the knowledge gap in rapid DNA detection and help researchers to quickly reveal the impact of different ecosystems or different land use changes on the composition of soil microbial communities. [ABSTRACT FROM AUTHOR]

Background: In recent years, preimplantation genetic testing for aneuploidies (PGT-A) has become widespread in assisted reproduction. However, contrary to expectations, PGT-A does not significantly improve the clinical outcomes of assisted reproductive technologies. One of the underlying reasons is the discordance between the PGT-A results and the true chromosomal constitution of the blastocyst. In this case series, we re-examined the PGT-A results in trophectoderm (TE) re-biopsies and in the two isolated blastocyst compartments—the TE and the inner cell mass (ICM). Methods: This study enrolled 23 human blastocysts from 17 couples who were referred for assisted reproduction. The blastocysts were unsuitable for uterine transfer due to the chromosomal imbalance revealed by PGT-A using array comparative genomic hybridization (aCGH) (n = 11) or next-generation sequencing (NGS) (n = 12). The re-examination of the PGT results involved two steps: (1) a TE re-biopsy with subsequent aCGH and (2) blastocyst separation into the TE and the ICM with a subsequent cell-by-cell analysis of each isolated compartment by fluorescence in situ hybridization (FISH) with the DNA probes to chromosomes 13, 16, 18, 21, and 22 as well as to the PGT-A detected imbalanced chromosomes. Results: In 8 out of 23 cases, the PGT-A results were concordant with both the re-biopsy and the isolated TE and ICM analyses. The latter included the diagnoses of full non-mosaic aneuploidies (five cases of trisomies and two cases of monosomies). In one case, the results of PGT-A, aCGH on the TE re-biopsy, and FISH on the isolated TE showed Xp tetrasomy, which contrasted with the FISH results on the isolated ICM, where this chromosomal pathology was not detected. This case was classified as a confined mosaicism. In 4 out of 23 cases, the results were partially discordant. The latter included one case of trisomy 12, which was detected as non-mosaic by PGT-A and the re-biopsy and as mosaic by FISH on the isolated TE and ICM. This case was classified as a true mosaicism with a false negative PGT-A result. In 11 out of 23 cases, the re-examination results were not concordant with the PGT-A results. In one of these discordant cases, non-mosaic tetraploidy was detected by FISH in the isolated TE and ICM, whereas the PGT-A and the TE re-biopsy failed to detect any abnormality, which advocated for their false negative result. In two cases, the re-examination did not confirm full aneuploidies. In eight cases, full or partial mosaic aneuploidies as well as chaotic mosacism were not confirmed in the isolated TE nor the isolated ICM. Thus, in 47.8% of cases, the PGT-A results did not reflect the true chromosomal constitution of a blastocyst. Conclusions: The PGT results may have different prognostic value in the characterization of the chromosomal constitution of a blastocyst. The detected non-mosaic aneuploidies have the highest prognostic value. In stark contrast, most PGT-identified mosaic aneuploidies fail to characterize the true chromosomal constitution of a blastocyst. Once detected, a differential diagnosis is needed. [ABSTRACT FROM AUTHOR]

Toward the construction of robotic and cybernetic systems with molecular reactions, development of a reaction that can rapidly generate single-stranded DNA (ssDNA) molecules in response to an input signal is an essential demand. This study explored the cascading of DNA generation reactions employing DNA polymerase and nicking endonuclease to achieve significant amplification of ssDNA molecules serving as signals to direct and fuel the operation of DNA-based systems. The modular architecture allows for interconnection with other reactions through primer-binding sequence or template design, making it adaptable to various molecular robotic components. The research aims to contribute to the development of efficient and reliable amplification circuits for molecular robotics and cybernetics. The cascading reactions, implemented up to three layers, exhibit enhanced amplification rates and sensitivities at physiological temperatures, enabling stable hybridization with complementary sequences. The investigation reveals the potential of the proposed approach to bridge the molecular quantity gap and restore signals in molecular systems including molecular robots and related applications. The experimental validation demonstrates the feasibility of achieving up to 100,000-fold amplification in response to low concentrations of primers within two hours, driving the structural transformation of DNA probes and nanomotors, while suppressing non-specific leak amplification, thereby showcasing practical applicability. The study's findings address fundamental challenges in ssDNA amplification and opens avenues for creating intelligent systems composed of molecular components with increased sensitivity and responsiveness. [ABSTRACT FROM AUTHOR]

A method has been developed for manufacturing biological microchips on an aluminum substrate with hydrophilic cells from brush copolymers with the formation of a matrix of cells using photolithography. The surface of aluminum substrates was previously coated with a thin, durable, moderately hydrophobic layer of cross-linked polymer to prevent contact with the aluminum surface of the components used in the analysis of nucleic acids. Aluminum biochip substrates have high thermal conductivity and low heat capacity, which is important for the development of methods for multiplex PCR analysis on a chip. Oligonucleotide probes were covalently immobilized in the cells of the biochip. The preservation of the hybridization activity of the immobilized DNA probes was demonstrated in a hybridization analysis with a synthetic DNA target representing a section of the sequence of the seventh exon of the human ABO gene. The methods developed can be used in the development of a technology for parallel multiple rapid microanalysis of nucleic acids "lab on a chip" for the detection of human somatic and infectious diseases. [ABSTRACT FROM AUTHOR]

Loop-mediated isothermal amplification (LAMP) is a molecular diagnosis technology with the advantages of isothermal reaction conditions and high sensitivity. However, the LAMP reactions are prone to producing false-positive results and thus are usually less reliable. This study demonstrates a gold nanoparticle (AuNP)-assisted colorimetric LAMP technique for diagnosing SARS-CoV-2, which aims to overcome the false-positive results. The AuNPs were functionalized with E gene probes, specifically tailored to bind to the amplified E-gene LAMP product, using the freezing method. Varied salt concentration and AuNP/probe combinations were tested for the highest visual performance. The experiments were conducted on synthetic SARS-CoV-2 RNA (Omicron variant), as well as on clinical samples. The assay showed an exceptional sensitivity of 8.05 fg of LAMP amplicon mixture (0.537 fg/µL). The average reaction time was ~ 30 min. In conclusion, AuNP-assisted LAMP detection will not identify any potential unspecific amplification, which helps to improve the efficiency and reliability of LAMP assays in point-of-care applications. The freezing method to functionalize the AuNPs with probes simplifies the assay, which can be utilized in further diagnostic studies. [ABSTRACT FROM AUTHOR]

Hybrid parthenogenetic animals are an exceptionally interesting model for studying the mechanisms and evolution of sexual and asexual reproduction. A diploid parthenogenetic lizard Darevskia unisexualis is a result of an ancestral cross between a maternal species Darevskia raddei nairensis and a paternal species Darevskia valentini and presents a unique opportunity for a cytogenetic and computational analysis of a hybrid karyotype. Our previous results demonstrated a significant divergence between the pericentromeric DNA sequences of the parental Darevskia species; however, an in‐depth comparative study of their pericentromeres is still lacking. Here, using target sequencing of microdissected pericentromeric regions, we reveal and compare the repertoires of the pericentromeric tandem repeats of the parental Darevskia lizards. We found species‐specific sequences of the major pericentromeric tandem repeat CLsat, which allowed computational prediction and experimental validation of fluorescent DNA probes discriminating parental chromosomes within the hybrid karyotype of D. unisexualis. Moreover, we have implemented a generalizable computational method, based on the optimization of the Levenshtein distance between tandem repeat monomers, for finding species‐specific fluorescent probes for pericentromere staining. In total, we anticipate that our comparative analysis of Darevskia pericentromeric repeats, the species‐specific fluorescent probes that we found and the pipeline that we developed will form a basis for the future detailed cytogenomic studies of a wide range of natural and laboratory hybrids. Research Highlights: We computationally predicted and experimentally verified fluorescent DNA probes discriminating parental pericentromeric subgenomes in a hybrid parthenogenetic lizard Darevskia unisexualis. We implemented our prediction method as a species‐agnostic Nextflow pipeline. [ABSTRACT FROM AUTHOR]

DNA is a re-configurable, biological information-storage unit, and much remains to be learned about its heterogeneous structural dynamics. For example, while it is known that molecular dyes templated onto DNA exhibit increased photostability, the mechanism by which the structural dynamics of DNA affect the dye photophysics remains unknown. Here, we use femtosecond, two-dimensional electronic spectroscopy measurements of a cyanine dye, Cy5, to probe local conformations in samples of single-stranded DNA (ssDNA–Cy5), double-stranded DNA (dsDNA–Cy5), and Holliday junction DNA (HJ–DNA–Cy5). A line shape analysis of the 2D spectra reveals a strong excitation–emission correlation present in only the dsDNA–Cy5 complex, which is a signature of inhomogeneous broadening. Molecular dynamics simulations support the conclusion that this inhomogeneous broadening arises from a nearly degenerate conformer found only in the dsDNA–Cy5 complex. These insights will support future studies on DNA's structural heterogeneity. [ABSTRACT FROM AUTHOR]

ABSTRACTHoney adulteration has been on the rise with the increasing demand for high-quality honey. The ladders-shape melting temperature isothermal amplification (LMTIA) was a newly developed nucleic acid amplification technique, and the aim of this study was to establish a method combining the LMTIA with the proofreading enzyme-mediated probe cleavage (Proof-man probe) for detecting the thaumatin-like protein (TLP) genes of Brassica rapa var. oleifera in honey. The LMTIA primers was selected as a target to be designed, the temperature of the Proof-man LMTIA reaction was optimized, and the specificity, sensitivity, and applicability to the honey samples were determined. The results showed that the Proof-man LMTIA method was highly specific with a detection sensitivity of 30-40 copies genomic DNA/reaction at the optimal temperature of 60°C, and the amplification could be completed within 20 min. This method can detect the adulteration of low-price B. rapa honey into high-price honey.

Competence development is essential for bacterial transformation since it enables bacteria to take up free DNA from the surrounding environment. The regulation of teichoic acid biosynthesis is tightly controlled during pneumococcal competence; however, the mechanism governing this regulation and its impact on transformation remains poorly understood. We demonstrated that a defect in lipoteichoic acid ligase (TacL)-mediated lipoteichoic acids (LTAs) biosynthesis was associated with impaired pneumococcal transformation. Using a fragment of tacL regulatory probe as bait in a DNA pulldown assay, we successfully identified several regulatory proteins, including ComE. Electrophoretic mobility shift assays revealed that phosphomimetic ComE, but not wild-type ComE, exhibited specific binding to the probe. DNase I footprinting assays revealed the specific binding sequences encompassing around 30 base pairs located 31 base pairs upstream from the start codon of tacL. Expression of tacL was found to be upregulated in the DcomE strain, and the addition of exogenous competence-stimulating peptide repressed the tacL transcription in the wild-type strain but not the DcomE mutant, indicating that ComE exerted a negative regulatory effect on the transcription of tacL. Mutation in the JH2 region of tacL upstream regulatory sequence led to increased LTAs abundance and displayed higher transformation efficiency. Collectively, our work identified the regulatory mechanisms that control LTAs biosynthesis during competence and thereby unveiled a repression mechanism underlying pneumococcal transformation. [ABSTRACT FROM AUTHOR]

Bacterial infections are a leading cause of death globally. The detection of DNA sequences correlated to the causative pathogen has become a vital tool in medical diagnostics. In practice, PCR-based assays for the simultaneous detection of multiple pathogens currently rely on probe-based quantitative strategies that require expensive equipment but have limited sensitivity or multiplexing capabilities. Hence, novel approaches to address the limitations of the current gold standard methods are still in high demand. In this study, we propose a simple multiplex PCR/SERS assay for the simultaneous detection of four bacterial pathogens, namely P. aeruginosa, S. aureus, S. epidermidis, and M. smegmatis. Wherein, specific primers for amplifying each target gDNA were applied, followed by applying SERS nanotags functionalized with complementary DNA probes and Raman reporters for specific identification of the target bacterial pathogens. The PCR/SERS assay showed high specificity and sensitivity for genotyping bacterial pathogen gDNA, whereby as few as 100 copies of the target gDNA could be detected. With high sensitivity and the convenience of standard PCR amplification, the proposed assay shows great potential for the sensitive detection of multiple pathogen infections to aid clinical decision-making. [ABSTRACT FROM AUTHOR]

MiR-378 is abnormally expressed in various cancers, such as hepatocellular carcinoma, renal cell carcinoma, and nonsmall cell lung cancer. Here, we developed a label- and immobilization-free ratiometric homogeneous electrochemical strategy based on exonuclease III (Exo III) for the facile and rapid determination of miR-378. Two 3′-protruding hairpin DNA probes (HPs) are designed in this strategy. Doxorubicin (DOX) and potassium ferrocyanide (Fe2+) were used as label-free probes to produce a response signal (IDOX) and a reference signal (IFe2+) in the solution phase. When no target was present in the solution, the HP was stable, most of the DOX was intercalated in the stem of the HP, and the diffusion rate of DOX was significantly reduced, resulting in reduced electrochemical signal response. When miR-378 was present, double-cycle signal amplification triggered by Exo III cleavage was initiated, ultimately disrupting the hairpin structures of HP1 and HP2 and releasing a large amount of DOX into the solution, yielding a stronger electrochemical signal, which was low to 50 pM. This detection possesses excellent selectivity, demonstrating high application potential in biological systems, and offers simple and low-cost electrochemical detection for miR-378. [ABSTRACT FROM AUTHOR]

Our preliminary investigation has identified the potential of serum fucosylated extracellular vesicles (EVs) miR-4732-5p in the early diagnosis of lung adenocarcinoma (LUAD) by a fucose-captured strategy utilizing lentil lectin (LCA)-magnetic beads and subsequent screening of high throughput sequencing and validation of real-time quantitative polymerase chain reaction (RT-qPCR). Considering the relatively complicated procedure, expensive equipment, and stringent laboratory condition, we have constructed an electrochemical biosensor assay for the detection of miR-4732-5p. miR-4732-5p is extremely low in serum, down to the fM level, so it needs to be detected by highly sensitive electrochemical methods based on the Mg2+-dependent DNAzyme splitting nucleic acid lock (NAL) cycle and hybridization chain reaction (HCR) signal amplification. In this study, signal amplification is achieved through the dual amplification reactions using NAL cycle in combination with HCR. In addition, hybridized DNA strands bind to a large number of methylene blue (MB) molecules to enhance signaling. Based on the above strategy, we further enhance our signal amplification strategies to improve detection sensitivity and accuracy. The implementation of this assay proceeded as follows: initially, miR-4732-5p was combined with NAL, and then Mg2+-dependent DNAzyme splitted NAL to release auxiliary DNA (S1) strands, which were subsequently captured by the immobilized capture probe DNA (C1) strands on the electrode surface. Following this, abundant quantities of DNA1 (H1) and DNA2 (H2) tandems were generated by HCR, and S1 strands then hybridized with the H1 and H2 tandems through base complementary pairing. Finally, MB was bonded to the H1 and H2 tandems through π–π stacking interaction, leading to the generation of a signal current upon the detection of a potential capable of inducing a redox change of MB by the electrode. Furthermore, we evaluated the performance of our developed electrochemical biosensor assay. The results demonstrated that our assay is a reliable approach, characterized by its high sensitivity (with a detection limit of 2.6 × 10−17 M), excellent specificity, good accuracy, reproducibility, and stability. Additionally, it is cost-effective, requires simple operation, and is portable, making it suitable for the detection of serum fucosylated extracellular vesicles miR-4732-5p. Ultimately, this development has the potential to enhance the diagnostic efficiency for patients with early-stage LUAD. [ABSTRACT FROM AUTHOR]

Background: The electrophoretic mobility shift assay (EMSA) is a common technology to detect DNA-protein interactions. However, in most cases, the protein used in EMSA is obtained via prokaryotic expression, and rarely from plants. At the same time, the proteins expressed from prokaryotic systems usually cannot fold naturally and have no post translationally modification, which may affect the binding of proteins to DNA. Results: Here, we develop a technique to quickly isolate proteins of interest from host plants and then analyze them using fluorescent EMSA. This technology system is called: protein from plants fluorescent EMSA method (PPF-EMSA). In PPF-EMSA, a special transient transformation method is employed to transiently deliver genes into the plant, enabling efficient synthesis the encoded proteins. Then, the target protein is isolated using immunoprecipitation, and the DNA probes were labeled with cyanine 3 (Cy3). Both fluorescent EMSA and super-shift fluorescent EMSA can be performed using the proteins from plants. Three kinds of plants, Betula platyphylla, Populus. davidiana×P. bolleana and Arabidopsis thaliana, are used in this study. The proteins isolated from plants are in a natural state, can fold naturally and are posttranslationally modified, enabling true binding to their cognate DNAs. Conclusion: As transient transformation can be performed quickly and not depended on whether stable transformation is available or not, we believe this method will have a wide application, enabling isolation of proteins from host plant conveniently. [ABSTRACT FROM AUTHOR]

Nucleic Acid Lateral Flow Assays (NALFAs) are a promising solution for the point-of-care detection of viruses like SARS-CoV-2. However, they show some drawbacks, such as the great dependency on the use of antibodies and the need for post-amplification protocols that enable the preparation of amplicons for effective readings, as well as low sensitivity. Here, we developed amplicons of a specific SARS-CoV-2 gene tailed with single-strand DNA (ssDNA) sequences to hybridize with DNA probes immobilized on the NALFA strips, thus overcoming the aforementioned problems. Results have shown that tailed primers have not compromised the amplification efficiency and allowed the correct detection of the amplicons in the lateral flow strip. This approach has presented a limit of detection (LOD) of 25 RNA copies /reaction mix (1 copy/μL) and the test of cross-reactivity with other related viruses has not shown any cross-reactivity. Twenty clinical samples were evaluated by NALFA and simultaneously compared with the gold standard RT-qPCR protocol, originating equal results. Although the number of clinical specimens tested being relatively small, this indicates a sensitivity and specificity both of 100%. In short, an alternative NALFA was successfully implemented, rendering an accurate route for SARS-CoV-2 diagnosis, compatible with low-resource settings. [ABSTRACT FROM AUTHOR]

In order to realize portable pathogen diagnostics with easier quantitation, digitization and integration, we develop a ready‐to‐use electrochemical sensing strategy (Iso‐E‐Codelock) for real‐time detection of isothermal nucleic acid amplification. Bridged by a branched DNA as codelock, the isothermal amplicon is transduced into increased current of an electrochemical probe, holding multiple advantages of high sensitivity, high selectivity, signal‐on response, "zero" background and one‐pot operation. Through a self‐designed portable instrument (BioAlex PHE−T), the detection can be implemented on a multichannel microchip and output real‐time amplification curves just like an expensive commercial PCR machine. The microchip is a rebuilding‐free and disposable component. The branch codelock probe can be customized for different targets and designs. Such high performance and flexibility have been demonstrated utilizing four virus (SARS‐CoV‐2, African swine fever, FluA and FluB) genes as targets, and two branch (3‐way and 4‐way) DNAs as codelock probes. [ABSTRACT FROM AUTHOR]

This article discusses the development of a cubic DNA nanocage probe for the analysis of miRNA-10b in tumor-derived extracellular vesicles (EVs). The probe was able to enter EVs and react with miRNA-10b, allowing visualization of EV-mediated intercellular communication. The study highlights the importance of EVs in communication between cells and the potential of miRNA-10b as a biomarker for cancer diagnosis. The DNA nanocage probe offers a simple and effective approach for the detection and analysis of miRNAs in tumor-derived EVs. [Extracted from the article]

The mediator complex subunit 23 (MED23) gene encodes a protein that acts as a tail module mediator complex, a multi-subunit co-activator involved in several cellular activities. MED23 has been shown to have substantial roles in myogenesis and other molecular mechanisms. The functions of MED23 in the neurological system remain unclear and the clinical phenotype is not thoroughly described. Whole exome sequencing was used to identify a novel mutation in the MED23 gene. DNA capture probes using next-generation sequencing-based copy number variation analysis with Illumina array were performed. The clinical, demographic, neuroimaging, and electrophysiological data of the patients were collected, and similarly, the data of all reported cases in the literature were extracted to compare findings. Screening a total of 9,662 articles, we identified 22 main regulatory processes for the MED23 gene, including suppressive activity for carcinogenic processes. MED23 is also involved in the brain’s neurogenesis and functions. The identified cases mainly presented with intellectual disability (87.5%) and developmental delay (50%). Seizures were present in only 18.75% of the patients. Slow backgrounds and spike and sharp-wave complexes were reported on the electroencephalogram (EEG) of a few patients and delayed myelination, thin corpus callosum, and pontine hypoplasia on magnetic resonance imaging (MRI). The MED23 gene regulates several processes in which its understanding promotes considerable therapeutic potential for patients. It is crucial to consider genetic and laboratory testing, particularly when encountering potential carriers. Intellectual disability and developmental delay are the most notable clinical signs with heterogeneous features on EEG and MRI. [ABSTRACT FROM AUTHOR]

Simple Summary: Anopheles mosquitoes are the only vectors of human malaria, a deadly disease causing over 500,000 deaths annually, mainly in sub-Saharan Africa. Less than 10% of the roughly 500 Anopheles species are malaria vectors. Although malaria has been eliminated in Europe, Anopheles mosquito species remain a focus of research due to their potential to transmit malaria and other infectious diseases. Understanding the evolution of vectorial capacity can be enhanced by knowledge of the speciation and adaptation of malaria mosquitoes. Chromosomal inversions, such as large-scale genomic rearrangements, are believed to play a role in the ability of mosquitoes to diversify and adapt to human-created environments. However, genome mapping and the characterization of chromosomal inversions have only been conducted on a small fraction of malaria mosquito species. In this study, we mapped and characterized inversions that differentiate the European mosquito Anopheles atroparvus and the Eurasian mosquito An. messeae. Two small genomic blocks underwent a change in position and orientation on the X chromosome between the two species. The rearranged chromosomal regions are enriched with genes that play roles in regulating the immune system and mating behavior. These findings offer insight into the underlying molecular mechanisms behind the differences in susceptibility to infection and behavior between An. atroparvus and An. messeae. The Maculipennis subgroup of malaria mosquitoes includes both dominant malaria vectors and non-vectors in Eurasia. Understanding the genetic factors, particularly chromosomal inversions, that differentiate Anopheles species can provide valuable insights for vector control strategies. Although autosomal inversions between the species in this subgroup have been characterized based on the chromosomal banding patterns, the number and positions of rearrangements in the X chromosome remain unclear due to the divergent banding patterns. Here, we identified two large X chromosomal inversions, approximately 13 Mb and 10 Mb in size, using fluorescence in situ hybridization. The inversion breakpoint regions were mapped by hybridizing 53 gene markers with polytene chromosomes of An. messeae. The DNA probes were designed based on gene sequences from the annotated An. atroparvus genome. The two nested inversions resulted in five syntenic blocks. Only two small syntenic blocks, which encompass 181 annotated genes in the An. atroparvus genome, changed their position and orientation in the X chromosome. The analysis of the An. atroparvus genome revealed an enrichment of gene ontology terms associated with immune system and mating behavior in the rearranged syntenic blocks. Additionally, the enrichment of DNA transposons was found in sequences homologous to three of the four breakpoint regions. This study demonstrates the successful application of the physical genome mapping approach to identify rearrangements that differentiate species in insects with polytene chromosomes. [ABSTRACT FROM AUTHOR]

Three new phenanthridine peptide derivatives (19, 22, and 23) were synthesized to explore their potential as spectrophotometric probes for DNA and RNA. UV/Vis and circular dichroism (CD) spectra, mass spectroscopy, and computational analysis confirmed the presence of intramolecular interactions in all three compounds. Computational analysis revealed that compounds alternate between bent and open conformations, highlighting the latter's crucial influence on successful polynucleotide recognition. Substituting one glycine with lysine in two regioisomers (22, 23) resulted in stronger binding interactions with DNA and RNA than for a compound containing two glycines (19), thus emphasizing the importance of lysine. The regioisomer with lysine closer to the phenanthridine ring (23) exhibited a dual and selective fluorimetric response with non-alternating AT and ATT polynucleotides and induction of triplex formation from the AT duplex. The best binding constant (K) with a value of 2.5 × 107 M−1 was obtained for the interaction with AT and ATT polynucleotides. Furthermore, apart from distinguishing between different types of ds-DNA and ds-RNA, the same compound could recognize GC-rich DNA through distinct induced CD signals. [ABSTRACT FROM AUTHOR]

Medulloblastoma (MB) is a molecularly heterogeneous brain malignancy with large differences in clinical presentation. According to genomic studies, there are at least four distinct molecular subgroups of MB: sonic hedgehog (SHH), wingless/INT (WNT), Group 3, and Group 4. The treatment and outcomes depend on appropriate classification. It is difficult for the classification algorithms to identify these subgroups from an imbalanced MB genomic data set, where the distribution of samples among the MB subgroups may not be equal. To overcome this problem, we used singular value decomposition (SVD) and group lasso techniques to find DNA methylation probe features that maximize the separation between the different imbalanced MB subgroups. We used multinomial regression as a classification method to classify the four different molecular subgroups of MB using the reduced DNA methylation data. Coordinate descent is used to solve our loss function associated with the group lasso, which promotes sparsity. By using SVD, we were able to reduce the 321,174 probe features to just 200 features. Less than 40 features were successfully selected after applying the group lasso, which we then used as predictors for our classification models. Our proposed method achieved an average overall accuracy of 99% based on fivefold cross-validation technique. Our approach produces improved classification performance compared with the state-of-the-art methods for classifying MB molecular subgroups. [ABSTRACT FROM AUTHOR]

This study investigates the feasibility of a simple electrochemical detection of Prostate Cancer Antigen 3 (PCA3) fragments extracted from patients' urine, using a thiolated single-strand DNA probe immobilized on a gold surface without using a redox probe. To enhance the PCA3 recognition process, we conducted a comparative analysis of the hybridization location using two thiolated DNA probes: Probe 1 targets the first 40 bases, while Probe 2 targets the fragment from bases 47 to 86. Hybridization with PCA3 followed, using square wave voltammetry. The limit of detection of the designed genosenors were of the order of (2.2 ng/mL), and (1.6 ng/mL) for Probes 1 and 2, respectively, and the subsequent sensitivities were of the order of (0.09 ± 0.01) µA−1 · µg−1 · mL and (0.10 ± 0.01) µA−1 · µg−1 · mL. Specificity tests were then conducted with the sensor functionalized with Probe 2, as it presents better analytical performances. The electrochemical results indicate that the designed sensor can clearly discriminate a complementary target from a non-complementary one. A further modeling of the calibration curves with the Power Law/Hill model indicates that the dissociation constant increases by one order of magnitude, confirming the ability of the designed sensor to perfectly discriminate complementary targets from non-complementary ones. [ABSTRACT FROM AUTHOR]

In this study, we innovatively synthesized bipyridine ruthenium cluster nanosheets (RuMOFNCs), a novel metal–organic framework material that exhibits both fluorescence and electrochemiluminescence. Gold nanoparticles (AuNPs) were anchored onto RuMOFNCs via bipyridine chelation, enhancing optical signals and creating sites for attaching biologically functional probes. We employed tetraferrocene-modified DNA probes, linked via gold–sulfur (Au–S) bonds, to construct a dual-mode fluorescence–electrochemiluminescence biosensor. This sensor, exploiting exonuclease III (Exo III)-mediated cyclic amplification, inhibits the electron transfer from RuMOFNC to tetraferrocene, resulting in amplified fluorescence and electrochemiluminescence signals. The sensor demonstrates exceptional sensitivity for detecting the BRAF gene, with fluorescence and electrochemiluminescence detection limits of 10.3 aM (range: 0.1 fM to 1 nM) and 3.1 aM (range: 1 aM to 10 pM), respectively. These capabilities are attributed to RuMOFNCs' luminescence properties, tetraferrocene's quenching effect, and the specificity of base pairing. This study's findings hold substantial promise for biomedical research and clinical diagnostics, particularly in precision medicine and early disease detection. [ABSTRACT FROM AUTHOR]

In this work, we developed a rapid and sensitive label-free ratiometric fluorescent (FL) probe for the detection of bleomycin (BLM). The probe consists of a DNA sequence (D6) and two fluorophore groups, 2-amino-5,6,7-trimethyl-1,8-naphthalene (ATMND) and SYBR Green I (SGI). The D6 sequence could be folded into a three-way junction structure containing a C–C mismatch position in the junction pocket. The unique "Y" structure not only could entrap ATMND in the mismatch pocket with high affinity, leading to FL quenching at 408 nm, but also embed SGI in the grooves of the double-stranded portion, resulting in FL enhancement at 530 nm. In the presence of BLM–Fe(II), the "Y" structure of D6 was destroyed due to the specific cleavage of the BLM recognition site, the 5′-GT-3′ site in D6. This caused the release of ATMND and SGI and thus the ratiometric signal change of FL enhancement by ATMND and FL quenching by SGI. Under optimal conditions, the ratiometric probe exhibited a linear correlation between the intensity ratio of F408/F530 and the concentration of BLM in the range of 0.5–1000 nM, with a detection limit of 0.2 nM. In addition, the probe was applied to detect BLM in human serum samples with satisfactory results, indicating its good clinical application potential. [ABSTRACT FROM AUTHOR]

Ochratoxin A (OTA) is a fungus-produced secondary metabolite, which causes food safety issues and exposures to health threats to humans. In this study, an electrochemical biosensor based on target-initiated detection was constructed to accurately and efficiently detect OTA. After the identification and specific hybridization of OTA and its aptamer, the primer exchange reaction (PER) was initiated to generate vast quantities of DNAzymes. The DNAzymes specifically cleave the hairpin modified with silver nanoclusters (AgNCs), allowing the released DNA–AgNC strands to attach to capture DNA probes (cDNA) on the electrode surface with detectable electrochemical signal transforms. The detection of this electrochemical biosensor can only be initiated after OTA is identified with the aptamer, which guarantees that the reaction products in the detection process can only be specifically generated, providing assurance for the ultimate generation of authentic and dependable detection results. The biosensor has the advantages of effortless operation, rapid reaction, and cost-effectiveness, and the OTA targets can be detected by this strategy up to 0.65 ng mL−1. Furthermore, the detection of diverse targets can be accomplished by simply replacing the aptamer, offering huge possibilities in the field of food security and environmental detection. [ABSTRACT FROM AUTHOR]

A molecular tool has been set up for the unambiguous molecular identification of the ambrosia beetle, Xyleborinus saxesenii (Ratzeburg, 1837) (Coleoptera Curculionidae Scolytinae), the cosmopolitan fruit‐tree pinhole borer, widely distributed in temperate regions of the five continents, where it infests a wide range of hardwoods and softwoods. The test was based on real‐time PCR with TaqMan probe technology and was developed on whole insect bodies (adults) as well as on frass produced by the beetle. The test was shown to meet the criteria established by EPPO for the harmonization of molecular diagnostic methods. In particular, the test gave good results in terms of analytical specificity (inclusivity and exclusivity) and analytical sensitivity, and was fully repeatable and reproducible. Since X. saxesenii is one of the most commonly intercepted ambrosia beetles during phytosanitary controls worldwide, this practical diagnostic tool will be useful for its rapid identification of the beetle in biological material (frass, body fragments). The test can be useful in countries where X. saxesenii is a quarantine species, as well as in the EPPO region. [ABSTRACT FROM AUTHOR]

Chromosome conformation capture techniques have revolutionized our understanding of chromatin architecture and dynamics at the genome-wide scale. In recent years, these methods have been applied to a diverse array of species, revealing fundamental principles of chromosomal organization. However, structural organization of the extrachromosomal entities, like viral genomes or plasmids, and their interactions with the host genome, remain relatively underexplored. In this work, we introduce an enhanced 4C-protocol tailored for probing plasmid DNA interactions. We design specific plasmid vector and optimize protocol to allow high detection rate of contacts between the plasmid and host DNA. [ABSTRACT FROM AUTHOR]

The document titled "The materials of the XVIII Ukrainian Conference of Young Scientists of IMBG of NAS of Ukraine" discusses a study on the association between genotypes and allelic variants of the I/D polymorphism of the ACE1 gene and the severity of COVID-19 in children from Ukraine. The study found no significant difference in genotypes and alleles between children with COVID-19 and the control group, but allele I was more common in patients with lung damage. Additionally, a statistically significant increase in the frequency of genotype I/I was found in children with a history of juvenile idiopathic arthritis and mild COVID-19. Another article in the document discusses the development of a continuous monitoring system integrated with an enzyme inhibition-based biosensor to detect heavy metal ions in water. The system showed high sensitivity, stability, and reproducibility, and has potential for analyzing heavy metals. [Extracted from the article]

The article discusses the development of acyclic nucleosides that can detect specific DNA sequences and distinguish between matched and mismatched base pairs. The researchers created new nucleosides that are flexible and can change their shape in response to changes in the opposing base of the DNA strand. These nucleosides emit light at longer wavelengths as the solvent becomes more polar. The study provides valuable information on designing and synthesizing fluorescent nucleosides for DNA detection and base discrimination. Additionally, the researchers developed a specific nucleoside, referred to as 1, which showed improved flexibility and base-discrimination ability compared to a previously reported nucleoside. This nucleoside can be used as a bioprobe to detect single-base alterations in DNA strands and study nucleic acid interactions. [Extracted from the article]

The grooves of DNA provide recognition sites for many nucleic acid binding proteins and anticancer drugs such as the covalently binding cisplatin. Here we report a crystal structure showing, for the first time, groove selectivity by an intercalating ruthenium complex. The complex Λ‐[Ru(phen)2phi]2+, where phi=9,10‐phenanthrenediimine, is bound to the DNA decamer duplex d(CCGGTACCGG)2. The structure shows that the metal complex is symmetrically bound in the major groove at the central TA/TA step, and asymmetrically bound in the minor groove at the adjacent GG/CC steps. A third type of binding links the strands, in which each terminal cytosine base stacks with one phen ligand. The overall binding stoichiometry is four Ru complexes per duplex. Complementary biophysical measurements confirm the binding preference for the Λ‐enantiomer and show a high affinity for TA/TA steps and, more generally, TA‐rich sequences. A striking enantiospecific elevation of melting temperatures is found for oligonucleotides which include the TATA box sequence. [ABSTRACT FROM AUTHOR]

Aptamer‐based probes are pivotal components in various sensing strategies, owing to their exceptional specificity and versatile programmable structure. Nevertheless, numerous aptamer‐based probes usually offer only a single function, limiting their capacity to meet the diverse requirements of multi‐faceted sensing systems. Here, we introduced supersandwich DNA probes (SSW‐DNA), designed and modified on the outer surface of nanochannels with hydrophobic inner walls, enabling dual functionality: qualitative detection for on‐site analysis and quantitative detection for precise analysis. The fragmented DNAs resulting from the target recognition, are subsequently identified through lateral flow assays, enabling robust on‐site qualitative detection of microcystin‐LR with an impressively low limit of detection (LOD) at 0.01 μg/L. Meanwhile, the nanochannels enable highly sensitive quantification of microcystin‐LR through the current analysis, achieving an exceptionally low LOD at 2.5×10−7 μg/L, with a broad dynamic range spanning from 1×10−6 to 1×102 μg/L. Furthermore, the process of target recognition introduces just a single potential error propagation, which reduces the overall risk of errors during the entire qualitative and quantitative detection process. This sensing strategy broadens the scope of applications for aptamer‐based composite probes, holding promising implications across diverse fields, such as medical diagnosis, food safety, and environmental protection. [ABSTRACT FROM AUTHOR]

The grooves of DNA provide recognition sites for many nucleic acid binding proteins and anticancer drugs such as the covalently binding cisplatin. Here we report a crystal structure showing, for the first time, groove selectivity by an intercalating ruthenium complex. The complex Λ‐[Ru(phen)2phi]2+, where phi=9,10‐phenanthrenediimine, is bound to the DNA decamer duplex d(CCGGTACCGG)2. The structure shows that the metal complex is symmetrically bound in the major groove at the central TA/TA step, and asymmetrically bound in the minor groove at the adjacent GG/CC steps. A third type of binding links the strands, in which each terminal cytosine base stacks with one phen ligand. The overall binding stoichiometry is four Ru complexes per duplex. Complementary biophysical measurements confirm the binding preference for the Λ‐enantiomer and show a high affinity for TA/TA steps and, more generally, TA‐rich sequences. A striking enantiospecific elevation of melting temperatures is found for oligonucleotides which include the TATA box sequence. [ABSTRACT FROM AUTHOR]

The grooves of DNA provide recognition sites for many nucleic acid binding proteins and anticancer drugs such as the covalently binding cisplatin. Here we report a crystal structure showing, for the first time, groove selectivity by an intercalating ruthenium complex. The complex Λ‐[Ru(phen)2phi]2+, where phi=9,10‐phenanthrenediimine, is bound to the DNA decamer duplex d(CCGGTACCGG)2. The structure shows that the metal complex is symmetrically bound in the major groove at the central TA/TA step, and asymmetrically bound in the minor groove at the adjacent GG/CC steps. A third type of binding links the strands, in which each terminal cytosine base stacks with one phen ligand. The overall binding stoichiometry is four Ru complexes per duplex. Complementary biophysical measurements confirm the binding preference for the Λ‐enantiomer and show a high affinity for TA/TA steps and, more generally, TA‐rich sequences. A striking enantiospecific elevation of melting temperatures is found for oligonucleotides which include the TATA box sequence. [ABSTRACT FROM AUTHOR]

The grooves of DNA provide recognition sites for many nucleic acid binding proteins and anticancer drugs such as the covalently binding cisplatin. Here we report a crystal structure showing, for the first time, groove selectivity by an intercalating ruthenium complex. The complex Λ‐[Ru(phen)2phi]2+, where phi=9,10‐phenanthrenediimine, is bound to the DNA decamer duplex d(CCGGTACCGG)2. The structure shows that the metal complex is symmetrically bound in the major groove at the central TA/TA step, and asymmetrically bound in the minor groove at the adjacent GG/CC steps. A third type of binding links the strands, in which each terminal cytosine base stacks with one phen ligand. The overall binding stoichiometry is four Ru complexes per duplex. Complementary biophysical measurements confirm the binding preference for the Λ‐enantiomer and show a high affinity for TA/TA steps and, more generally, TA‐rich sequences. A striking enantiospecific elevation of melting temperatures is found for oligonucleotides which include the TATA box sequence. [ABSTRACT FROM AUTHOR]

Messenger RNA (mRNA)-based therapy shows immense potential for broad biomedical applications. However, the development of safe and efficacious mRNA delivery vectors remains challenging due to delivery barriers and inefficient intracellular payload release. Herein, we presented a simple strategy to boost the mRNA intracellular release by incorporation of anionic poly(γ-glutamic acid) (PGA) into an ionizable lipid-based LNP/mRNA. We systematically investigated the impact of PGA incorporation on mRNA transfection both in vitro and in vivo. The molecular weights and formulation ratios of PGA greatly affected the transfection efficacy of LNP/mRNA. From in vitro study, the optimized LNP/mRNA/PGA was formulated by incorporation of PGA with the molecular weight of 80 kDa or 200 kDa and the charge ratio (N/P/C) of 25/1/1. The optimized formulation achieved around 3-fold mRNA expression in HeLa cells compared to the bare LNP/mRNA. The intracellular releasing study using specific DNA probe revealed that this enhancement of transfection efficacy was attributed to the elevated mRNA release into cytoplasm. Moreover, the optimized LNP/mRNA/PGA achieved up to 5-fold or 3-fold increase of luciferase mRNA expression in vivo after being injected into mice systematically or intramuscularly, respectively. In addition, the incorporation of PGA did not significantly alter the biodistribution profile of the complexes on both organ and cellular levels. Therefore, our work provides a simple strategy to boost mRNA delivery, which holds great promise to improve the efficacy of mRNA therapeutics for various biomedical applications. The process of designing and screening potent mRNA carriers is complicated and time-consuming, while the efficacy is not always satisfying due to the delivery barriers and inefficient mRNA release. This work presented an alternative strategy to boost the mRNA delivery efficacy by incorporating an anionic natural polymer poly(γ-glutamic acid) (PGA) into LNP/mRNA complexes. The optimized LNP/mRNA/PGA achieved up to 3-fold and 5-fold increase in transfection efficacy in vitro and in vivo , respectively. Intracellular releasing analysis revealed that the enhancement of transfection efficacy was mainly attributed to the elevated intracellular release of mRNA. In addition, the incorporation of PGA did not alter the biodistribution or the biosafety profile of the complexes. These findings indicate that PGA incorporation is a promising strategy to improve the efficacy of mRNA therapeutics. [Display omitted] [ABSTRACT FROM AUTHOR]

The widespread adoption of genetically modified (GM) crops has escalated concerns about their safety and ethical implications, underscoring the need for efficient GM crop detection methods. Conventional detection methods, such as polymerase chain reaction, can be costly, lab-bound, and time-consuming. To overcome these challenges, we have developed RapiSense, a cost-effective, portable, and sensitive biosensor platform. This sensor generates a measurable voltage shift (0.1–1 V) in the system's current-voltage characteristics, triggered by an increase in membrane's negative charge upon hybridization of DNA/RNA targets with a specific DNA probe. Probes designed to identify the herbicide resistance gene hygromycin phosphotransferase show a detection range from ∼1 nM to ∼10 μM and can discriminate between complementary, non-specific, and mismatched nucleotide targets. The incorporation of a small membrane sensor to detect fragmented RNA samples substantially improve the platform's sensitivity. In this study, RapiSense has been effectively used to detect specific DNA and fragmented RNA in transgenic variants of Arabidopsis, sweet potato, and rice, showcasing its potential for rapid, on-site GM crop screening. • Accelerated GM plant detection with anion exchange membrane-based nucleic acid sensor. • Improved sensitivity with small membrane sensor integration to detect fragmented RNA. • The RapiSense prototype device is easy-to-operate, portable, and time-efficient. [ABSTRACT FROM AUTHOR]

Comprehensive Summary: N6‐methyladenosine (m6A) plays an important role in embryogenesis, nuclear export, transcription splicing, and protein translation control. Herein, we demonstrate a copper‐free click chemistry‐mediated assembly of single quantum dot (QD) nanosensor for accurately monitoring locus‐specific m6A in cancer cells. The m6A‐sensitive endoribonuclease MazF can digest the unmethylated A‐RNA, and the intact m6A‐RNA then hybridizes with DNA probes a and b to produce a sandwich hybrid, initiating the click chemistry to generate probe a–b ligation product via first tandem ligation detection reaction (LDR) cycle. Subsequently, DNA probes c and d can hybridize with the probe a–b ligation product to generate the probe c–d ligation product via second LDR cycle. Both LDR cycles can be repeated through denaturation and annealing reaction to generate abundant biotin‐/fluorophore‐modified probe c–d ligation products that can easily assemble on the QD surface to induce distinct fluorescence resonance energy transfer (FRET) between QD and Cy5. This assay can be homogenously performed without the involvement of copper catalyst, m6A‐specific antibody, radioactive labeling, ligase enzyme, enzymatic reverse transcription, and next‐generation sequencing. Moreover, it can discriminate even 0.01% m6A level in complex samples and accurately measure cellular m6A‐RNA expression, providing a promising avenue for clinical diagnostics and biomedical research. [ABSTRACT FROM AUTHOR]

With the advancement of large-scale omics technologies, particularly transcriptomics data sets on drug and treatment response repositories available in public domain, toxicogenomics has emerged as a key field in safety pharmacology and chemical risk assessment. Traditional statistics-based bioinformatics analysis poses challenges in its application across multidimensional toxicogenomic data, including administration time, dosage, and gene expression levels. Motivated by the visual inspection workflow of field experts to augment their efficiency of screening significant genes to derive meaningful insights, together with the ability of deep neural architectures to learn the image signals, we developed DTox, a deep neural network-based in visio approach. Using the Percellome toxicogenomics database, instead of utilizing the numerical gene expression values of the transcripts (gene probes of the microarray) for dose-time combinations, DTox learned the image representation of 3D surface plots of distinct time and dosage data points to train the classifier on the experts' labels of gene probe significance. DTox outperformed statistical threshold-based bioinformatics and machine learning approaches based on numerical expression values. This result shows the ability of image-driven neural networks to overcome the limitations of classical numeric value-based approaches. Further, by augmenting the model with explainability modules, our study showed the potential to reveal the visual analysis process of human experts in toxicogenomics through the model weights. While the current work demonstrates the application of the DTox model in toxicogenomic studies, it can be further generalized as an in visio approach for multi-dimensional numeric data with applications in various fields in medical data sciences. [ABSTRACT FROM AUTHOR]

Biomacromolecular probes have been extensively employed in the detection of metal ions for their prominent biocompatibility, water solubility, high selectivity, and easy modification of fluorescent groups. In this study, a fluorescent probe FP was constructed. The probe FP exhibited high specificity recognition for Cu2+. With the combination of Cu2+, the probe was subjected to fluorescence quenching. The research suggested that the probe FP carried out the highly sensitive detection of Cu2+ with detection limits of 1.7 nM. The fluorescence quenching of fluorescamine was induced by Cu2+ perhaps due to the PET (photoinduced electron transfer) mechanism. The FP-Cu2+ complex shows weak fluorescence, which is likely due to the PET quenching effect from Cu2+ to fluorescamine fluorophore. Moreover, the probe FP can be employed for imaging Cu2+ in living cells. The new fluorescent probe developed in this study shows the advantages of good biocompatibility and low cytotoxicity. It can be adopted for the targeted detection of Cu2+ in cells, and it has promising applications in the mechanism research and diagnosis of Cu2+-associated diseases. [ABSTRACT FROM AUTHOR]

Graphene-based materials and DNA probes/nanostructures have emerged as building blocks for constructing powerful biosensors. Graphene-based materials possess exceptional properties, including two-dimensional atomically flat basal planes for biomolecule binding. DNA probes serve as excellent selective probes, exhibiting specific recognition capabilities toward diverse target analytes. Meanwhile, DNA nanostructures function as placement scaffolds, enabling the precise organization of molecular species at nanoscale and the positioning of complex biomolecular assays. The interplay of DNA probes/nanostructures and graphene-based materials has fostered the creation of intricate hybrid materials with user-defined architectures. This advancement has resulted in significant progress in developing novel biosensors for detecting DNA, RNA, small molecules, and proteins, as well as for DNA sequencing. Consequently, a profound understanding of the interactions between DNA and graphene-based materials is key to developing these biological devices. In this review, we systematically discussed the current comprehension of the interaction between DNA probes and graphene-based materials, and elucidated the latest advancements in DNA probe–graphene-based biosensors. Additionally, we concisely summarized recent research endeavors involving the deposition of DNA nanostructures on graphene-based materials and explored imminent biosensing applications by seamlessly integrating DNA nanostructures with graphene-based materials. Finally, we delineated the primary challenges and provided prospective insights into this rapidly developing field. We envision that this review will aid researchers in understanding the interactions between DNA and graphene-based materials, gaining deeper insight into the biosensing mechanisms of DNA–graphene-based biosensors, and designing novel biosensors for desired applications. [ABSTRACT FROM AUTHOR]

Infectious diseases are one of the world's leading causes of morbidity. Their rapid spread emphasizes the need for accurate and fast diagnostic methods for large-scale screening. Here, we describe a robust method for the detection of pathogens based on microscale thermophoresis (MST). The method involves the hybridization of a fluorescently labeled DNA probe to a target RNA and the assessment of thermophoretic migration of the resulting complex in solution within a 2 to 30-time window. We found that the thermophoretic migration of the nucleic acid-based probes is primarily determined by the fluorescent molecule used, rather than the nucleic acid sequence of the probe. Furthermore, a panel of uniformly labeled probes that bind to the same target RNA yields a more responsive detection pattern than a single probe, and moreover, can be used for the detection of specific pathogen variants. In addition, intercalating agents (ICA) can be used to alter migration directionality to improve detection sensitivity and resolving power by several orders of magnitude. We show that this approach can rapidly diagnose viral SARS-CoV2, influenza H1N1, artificial pathogen targets, and bacterial infections. Furthermore, it can be used for anti-microbial resistance testing within 2 h, demonstrating its diagnostic potential for early pathogen detection. [ABSTRACT FROM AUTHOR]

Comprehensive Summary: N6‐methyladenosine (m6A) plays an important role in embryogenesis, nuclear export, transcription splicing, and protein translation control. Herein, we demonstrate a copper‐free click chemistry‐mediated assembly of single quantum dot (QD) nanosensor for accurately monitoring locus‐specific m6A in cancer cells. The m6A‐sensitive endoribonuclease MazF can digest the unmethylated A‐RNA, and the intact m6A‐RNA then hybridizes with DNA probes a and b to produce a sandwich hybrid, initiating the click chemistry to generate probe a–b ligation product via first tandem ligation detection reaction (LDR) cycle. Subsequently, DNA probes c and d can hybridize with the probe a–b ligation product to generate the probe c–d ligation product via second LDR cycle. Both LDR cycles can be repeated through denaturation and annealing reaction to generate abundant biotin‐/fluorophore‐modified probe c–d ligation products that can easily assemble on the QD surface to induce distinct fluorescence resonance energy transfer (FRET) between QD and Cy5. This assay can be homogenously performed without the involvement of copper catalyst, m6A‐specific antibody, radioactive labeling, ligase enzyme, enzymatic reverse transcription, and next‐generation sequencing. Moreover, it can discriminate even 0.01% m6A level in complex samples and accurately measure cellular m6A‐RNA expression, providing a promising avenue for clinical diagnostics and biomedical research. [ABSTRACT FROM AUTHOR]

Peroxisome proliferator‐activated receptors (PPARs) are essential for cellular physiological processes. However, there is less research on the PPAR‐related genes in lung adenocarcinoma (LUAD). Open‐access data were get from the cancer genome atlas (TCGA) and gene expression omnibus (GEO) databases. All the analysis were conducted in the R software based on different R packages. In this study, we gauged the PPAR score employing a set of 72 PPAR‐associated genes and probed the biological impact of this score on lung adenocarcinoma (LUAD). Subsequently, we established a unique signature composed of eight PPAR‐related genes (ANGPTL4, ACSL3, ADIPOQ, FABP1, SLC27A1, ACOX2, PPARD and OLR1) to forecast the prognosis of LUAD. The signature's effectiveness in predicting survival was validated through the receiver operating characteristic curve in the TCGA‐LUAD cohort. As per the pathway enrichment analysis, several crucial oncogenic pathways and metabolic processes were enriched in high‐risk individuals. Further, we observed that these high‐risk patients exhibited heightened genomic instability. Additionally, compared to the low‐risk cohort, high‐risk patients demonstrated diminished immune components and function. Intriguingly, high‐risk patients exhibited a potential heightened sensitivity to immunotherapy and certain drugs, including Gefitinib, Afatinib, Erlotinib, IAP_5620, Sapitinib, LCL161, Lapatinib and AZD3759. The prognosis model based on eight PPAR‐related genes has satisfactory prognosis prediction efficiency. Meanwhile, our results can provide direction for future studies in the relevant aspects. [ABSTRACT FROM AUTHOR]

Protein-based microarrays are important tools for high-throughput medical diagnostics, offering versatile platforms for multiplex immunodetection. However, challenges arise in protein microarrays due to the heterogeneous nature of proteins and, thus, differences in their immobilization conditions. This article advocates DNA-directed immobilization (DDI) as a solution, emphasizing its rapid and cost-effective fabrication of biosensing platforms. Thiolated single-stranded DNA and its analogues, such as ZNA® and PNA probes, were used to immobilize model proteins (anti-CRP antibodies and SARS-CoV nucleoprotein). The study explores factors influencing DDI-based immunosensor performance, including the purity of protein-DNA conjugates and the stability of their duplexes with DNA and analogues. It also provides insight into backfilling agent type and probe surface density. The research reveals that single-component monolayers lack protection against protein adsorption, while mixing the probes with long-chain ligands may hinder DNA-protein conjugate anchoring. Conventional DNA probes offer slightly higher surface density, while ZNA® probes exhibit better binding efficiency. Despite no enhanced stability in different ionic strength media, the cost-effectiveness of DNA probes led to their preference. The findings contribute to advancing microarray technology, paving the way for new generations of DDI-based multiplex platforms for rapid and robust diagnostics. [ABSTRACT FROM AUTHOR]

Background/Objectives: Vulvovaginal candidosis (VVC) is a common condition among women, with current diagnostic methods relying on clinical evaluation and laboratory testing. These traditional methods are often limited by the need for specialized training, variable performance, and lengthy diagnostic processes, leading to delayed treatment and inappropriate antifungal use. This review evaluates the efficacy of molecular diagnostic tools for VVC and provides guidance on their application in clinical practice. Methods: A literature search was conducted using PubMed to identify studies evaluating rapid diagnostic tests specifically for vulvovaginal Candida isolates. Inclusion criteria focused on studies utilizing molecular diagnostics for the detection of Candida species in VVC. Articles discussing non-vaginal Candida infections, non-English studies, and animal or in vitro research were excluded. Results: Twenty-three studies met the inclusion criteria, predominantly evaluating nucleid acid amplification tests/polymerase chain reaction (NAAT/PCR) assays and DNA probes. PCR/NAAT assays demonstrated high sensitivity and specificity (>86%) for VVC diagnosis, outperforming conventional diagnostic methods. Comparatively, DNA probes, while simpler, exhibited lower sensitivity. The included studies were mostly observational, with only one randomized controlled trial. Emerging diagnostic technologies, including artificial intelligence and integrated testing models, show promise for improving diagnostic precision and clinical outcomes. Conclusions: Molecular diagnostics offer a significant improvement in VVC management, though traditional methods remain valuable in resource-limited settings.

To address the requirement of ultra-sensitive detection of trace mercury(II) (Hg2+) ions in the environment and food, we developed an electrochemical biosensor with super-sensitivity, extremely high selectivity, and reusability. This biosensor comprised two signal amplification components: a three-dimensional macroporous dealloyed (3DOMD) Au–Ag thin-film electrode and a multifunctional encoded Au@Pt nanocage (APNC). As a platform for immobilized capture DNA (cDNA), a 3DOMD Au–Ag thin film prepared by a dealloying method with an active surface area 4.8 times higher than that of 3D macroporous gold films generated by cyclic voltammetry (CV) with sulfuric acid was capable of increasing the sensing surface area while also strengthening the electron transport capacity of the sensing substrate due to its multilayered multi-porous framework. In the presence of Hg2+, probe DNA (pDNA) could be hybridized with the mismatched capture DNA (cDNA) through stable thymine–Hg2+–thymine (T–Hg2+–T) linkages, connecting thionine–APNC to the electrode surface and utilizing the large specific surface area to accomplish highly sensitive detection of Hg2+. With an extremely low Hg2+ detection limit of 2 pM and a detection range from 0.01 to 1000 nM, this technique opened up a new avenue for the ultrasensitive detection of a wider range of heavy metal ions or biomolecules. [ABSTRACT FROM AUTHOR]

Photoacoustic imaging(PAI) is a widely developing imaging modality that has seen tremendous evolvement in the last decade. PAI has gained the upper hand in the imaging field as it takes advantage of optical absorption and ultrasound detection that imparts higher resolution, rich contrast and elevated penetration depth. Unlike other imaging techniques, PAI does not use ionising radiation and is a better, cost-effective and healthier alternative to other imaging techniques. It offers greater specificity than conventional ultrasound imaging with the ability to detect haemoglobin, lipids, water and other light-absorbing chromophores. These properties of PAI have led to its extended applications in the biomedical field in the treatment of diseases such as cancer. This paper reviews how DNA probes have been used in PAI, the various techniques by which it has been modified, and their role in the process. We also focus on different nanocomposites containing DNA having PAI and photothermal therapy(PTT) properties for detection, diagnosis and therapy, its constituents and the role of DNA in it. [Display omitted] • DNA-based probes show high sensitivity, specificity and biocompatibility in photoacoustic imaging applications. • Different types of DNA-based probes, such as aptamers, molecular beacons, and hybridization chain reaction probes, have been designed. • The development of DNA-based probes for PAI holds great promise for noninvasive early disease detection and monitoring. • DNA technology allows for the detection of complex genetic disorders by targeting multiple genetic markers. • Development of sensitive and specific imaging methods enables the detection of minute changes in DNA expression and function. [ABSTRACT FROM AUTHOR]

The CRISPR/Cas12a system is accelerated by glutathione-mediated reduction of MnO2 nanosheets. By monitoring the trans-cleavage of the DNA probe, an electrochemical method for glutathione assay is fabricated, with the detection limit of 3.5 pM. It provides a promising tool for plasma analysis with satisfactory performance, indicating the broad application prospects of this glutathione assay. [ABSTRACT FROM AUTHOR]

The convenient construction of carbon-based electrochemical immunosensors with high performance is highly desirable for the efficient detection of tumor biomarkers. In this work, an electrochemical immunosensor was fabricated by integrating a biofunctionalized mesoporous silica nanochannel film with a carbon-based electrode, which can enable the sensitive determination of carcinoembryonic antigen (CEA) in serum. The commonly used carbonaceous electrode, glassy carbon electrode (GCE), was employed as the supporting electrode and was pre-treated through electrochemical polarization to achieve the stable binding of a vertically ordered mesoporous silica film with amino groups (NH2-VMSF) without the use of any adhesive layer. To fabricate the immunorecognition interface, antibodies were covalently immobilized after the amino groups on the outer surface of NH2-VMSF was derivatized to aldehyde groups. The presence of amino sites within the high-density nanochannels of NH2-VMSF can facilitate the migration of negatively charged redox probes (Fe(CN)63-/4-) to the supporting electrode through electrostatic adsorption, leading to the generation of electrochemical signals. In the presence of CEA, the formation of immunocomplexes on the recognitive interface can reduce the electrochemical signal of Fe(CN)63-/4- on the supporting electrode. Based on this principle, the sensitive electrochemical detection of CEA was achieved. CEA can be determined to range from 0.01 ng mL−1 to 100 ng mL−1 with a limit of detection of 6.3 pg mL−1. The fabricated immunosensor exhibited high selectivity, and the detection of CEA in fetal bovine serum was achieved. [ABSTRACT FROM AUTHOR]