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Uracil-DNA glycosylase (UDG), an enzyme for repairing uracil-containing DNA damage, is crucial for maintaining genomic stability. Simple and fast quantification of UDG activity is essential for biological assay and clinical diagnosis, since its aberrant level is associated with DNA damage and various diseases. Herein, we developed a fully integrated "sample in-signal out" distance-based paper analytical device (dPAD) for visual quantification of UDG using a flow-controlled uracil-rich DNA hydrogel (URDH). The uracil base sites contained in the DNA hydrogel are mis-incorporated with dUTP by rolling circle amplification (RCA), which simplifies the preparation process of the functionalized hydrogel. In the presence of UDG, the uracil in URDH can be recognized and removed to induce the permeability change of URDH, resulting in the visible distance signal along the paper channel. Using dPAD, as low as 6.4 × 10 -4 U/mL of UDG (within 80 min) is visually identified without any instruments and complicated operations. This integrated dPAD is advantageous for its simplicity, cost effectiveness, and ease of use. We envision that it has the great potential for point-of-care testing (POCT) in DNA damage testing, personalized healthcare assessment, and biomedical applications., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Point of care (PoC) nucleic acid amplification tests (NAATs) are a cornerstone of public health, providing the earliest and most accurate diagnostic method for many communicable diseases in the same location where the patient receives treatment. Communicable diseases, such as human immunodeficiency virus (HIV), disproportionately impact low-resource communities where NAATs are often unobtainable due to the resource-intensive enzymes that drive the tests. Enzyme-free nucleic acid detection methods, such as hybridization chain reaction (HCR), use DNA secondary structures for self-driven amplification schemes, producing large DNA nanostructures, capable of single-molecule detection in cellulo . These thermodynamically driven DNA-based tests have struggled to penetrate the PoC diagnostic field due to their inadequate limits of detection or complex workflows. Here, we present a proof-of-concept NAAT that combines HCR-based amplification of a target nucleic acid sequence with paper-based nucleic acid filtration and enrichment capable of detecting sub-pM levels of synthetic DNA. We reconstruct the favorable hybridization conditions of an in cellulo reaction in vitro by incubating HCR in an evaporating, microvolume environment containing poly(ethylene glycol) as a crowding agent. We demonstrate that the kinetics and thermodynamics of DNA-DNA and DNA-RNA hybridization is enhanced by the dynamic evaporating environment and inclusion of crowding agents, bringing HCR closer to meeting PoC NAAT needs.

Deoxyribonuclease I (DNase I) is a biomarker which has important applications in various biological processes. Thus, it is highly important to develop a user-friendly method for the detection of DNase I. Here, we present a paper-based distance sensor for the rapid detection of DNase I based on changes in the viscosity of DNA mucus. The viscosity of DNA mucus varies with different concentrations of DNase I, showing different water flow lengths on the pH test papers, this makes the quantification of DNase I possible. This method has a wide linear range (0.01-10 U/mL), excellent sensitivity, remarkable specificity and excellent reproducibility. The detection limit reaches 0.003 U/mL. Additionally, it can be well applied to detection of DNase I inhibitors, assay of DNase I in human serum and quality evaluation of nucleic acid scavengers. In general, this study offers a brief, convenient, label-free, and economical method to construct paper-based distance sensors using DNA mucus, which is very promising in the detection of DNase I in various applications., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier B.V. All rights reserved.)

Nucleic acid amplification testing has great potential for point-of-need diagnostic testing with high detection sensitivity and specificity. Current sample preparation is limited by a tedious workflow requiring multiple steps, reagents and instrumentation, hampering nucleic acid testing at point of need. In this study, we present the use of mixed cellulose ester (MCE) paper for DNA binding by ionic interaction under molecular crowding conditions and fluid transport by wicking. The poly(ethylene) glycol-based (PEG) reagent simultaneously provides the high pH for alkaline lysis and crowding effects for ionic binding of the DNA under high salt conditions. In this study, we introduce Paper-based Abridged Solid-Phase Extraction with Alkaline Poly(ethylene) Glycol Lysis (PASAP). The anionic mixed cellulose ester (MCE) paper is used as solid phase and allows for fluid transport by wicking, eliminating the need for pipetting skills and the use of a magnet to retain beads. Following the release of DNA from the cells due to the lytic activity of the PASAP solution, the DNA binds to the anionic surface of the MCE paper, concentrating at the bottom while the sample matrix is transported towards the top by wicking. The paper was washed by dipping it in 40% isopropanol for 10 s. After air-drying for 30 s, the bottom section of the paper (3 mm × 4 mm) was snapped off using the cap of a PCR tube and immersed in the colourimetric loop-mediated isothermal amplification (cLAMP) solution for direct amplification and colourimetric detection. The total sample processing was completed in 15 min and ready for amplification. cLAMP enabled the detection of 102 CFU/mL of Escherichia coli (E. coli) from culture media and the detection of E. coli in milk < 103 CFU/mL (10 CFU) after incubation at 68 °C for 60 min, demonstrating applicability of the method to complex biological samples. [ABSTRACT FROM AUTHOR]

The main aim of this work was to validate the detection of saliva samples from denim, cotton, and polyester fabrics aged up to six months, applying rapid immunochromatographic tests resulting in the analysis of nuclear and mitochondrial DNA recovered. A comparison was also carried out between two saliva detection tests, Laboratory and Crime Scene. 50 μl saliva samples (three per time and test) were deposited on denim, cotton, and polyester fabrics. After 1, 3, 7, 14, 21, 30, 60, 90, 150, and 180 days of storage at room temperature, the samples were recovered by swabbing and detected by SERATEC ® Amylase (Laboratory) test and SERATEC ® SALIVA CS (Crime Scene) test (SERATEC ® , Göttingen, Germany). DNA was isolated from the swab extraction buffer applying a silica-based methodology, and quantified based on fluorescent and human-specific quantifications. Then, it was submitted to STR profiling and mtDNA sequencing. According to our results, saliva stains up to six months after deposition remain valid specimens. The intensity of the bands varied among fabric type and time. Total DNA was successfully recovered from all tested samples, though with the limitations of obtaining partial nuclear DNA profiles from the oldest samples. In contrast, complete characterization of mtDNA was achieved from all samples. Lab and CS tests performed similar on the detection of saliva, as well as, DNA yield and profiling. Future research will be able to expand these results, analyzing the stability of other body fluids and the sensitivity of rapid immunochromatographic tests to detect them., (© 2023. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

Small extracellular vesicle–derived microRNAs (sEV-miRNAs) have emerged as promising noninvasive biomarkers for early cancer diagnosis. Herein, we developed a molecular probe based on three-dimensional (3D) multiarmed DNA tetrahedral jumpers (mDNA-Js)-assisted DNAzyme activated by Na+, combined with a disposable paper-based electrode modified with a Zr-MOF–rGO–Au NP nanocomplex (ZrGA) to fabricate a novel biosensor for sEV-miRNAs Assay. Zr-MOF tightly wrapped by rGO was prepared via a one-step method, and it effectively aids electron transfer and maximizes the effective reaction area. In addition, the mechanically rigid, and nanoscale-addressable mDNA-Js assembled from the bottom up ensure the distance and orientation between fixed biological probes as well as avoid probe entanglement, considerably improving the efficiency of molecular hybridization. The fabricated bioplatform achieved the sensitive detection of sEV-miR-21 with a detection limit of 34.6 aM and a dynamic range from100 aM to 0.2 µM. In clinical blood sample tests, the proposed bioplatform showed results highly consistent with those of qRT-PCRs and the signal increased proportionally with the NSCLC staging. The proposed biosensor with a portable wireless USB-type analyzer is promising for the fast, easy, low-cost, and highly sensitive detection of various nucleic acids and their mutation derivatives, making it ideal for POC biosensing. [ABSTRACT FROM AUTHOR]

Innovative chiral capillary silica monoliths (CSMs) were developed based on DNA nanoflowers (DNFs). Baseline separation of enantiomers such as atenolol, tyrosine, histidine, and nefopam was achieved by using DNF-modified CSMs, and the obtained resolution value was higher than 1.78. To further explore the effect of DNFs on enantioseparation, different types of chiral columns including DNA strand containing the complementary sequence of the template (DCT)-modified CSMs, DNF 2 -modified CSMs, and DNF 3 -modified CSMs were prepared as well. It was observed that DNF-modified CSMs displayed better chiral separation ability compared with DCT-based columns. The intra-day and inter-day repeatability of model analytes' retention time and resolution kept desirable relative standard deviation values of less than 8.28%. DNF 2 /DNF 3 -modified CSMs were able to achieve baseline separation of atenolol, propranolol, 2'-deoxyadenosine, and nefopam enantiomers. Molecular docking simulations were performed to investigate enantioselectivity mechanisms of DNA sequences for enantiomers. To indicate the successful construction of DNFs and DNF-modified CSMs, various charaterization approaches including scanning electron microscopy, agarose gel electrophoresis, dynamic light scattering analysis, electroosmotic flow, and Fourier-transform infrared spectroscopy were utilized. Moreover, the enantioseparation performance of DNF-modified CSMs was characterized in terms of sample volume, applied voltage, and buffer concentration. This work paves the way to applying DNF-based capillary electrochromatography microsystems for chiral separation., (© 2024. The Author(s), under exclusive licence to Springer-Verlag GmbH Austria, part of Springer Nature.)

Nucleotide-based molecules called DNA and RNA are essential for several biological processes that affect both normal and cancerous cells. They contain the critical genetic material needed for normal cell growth and functioning. The DNA structure patterns that make up the genetic code affect cells' growth, behavior, and control. Different DNA structure patterns indicate different physiological effects in the cell. Knowledge of these patterns is necessary to identify the molecular origins of cancer and other disorders. Analyzing these patterns can help in the early detection of diseases, which is essential for the effectiveness of cancer research and therapy. The novelty of this study is to examine the patterns of dinucleotide structure in many genomic regions, including the non-coding region sequence (N-CDS), coding region sequence (CDS), and whole raw DNA sequence (W.R. sequence). It provides an in-depth discussion of dinucleotide patterns related to these diverse genetic environments and contains malignant and non-malignant DNA sequences. The Markovian modeling that predicts dinucleotide probabilities also reduces feature complexity and minimizes computational costs compared to the approaches of Kernelized Logistic Regression (KLR) and Support Vector Machine (SVM). This technique is effectively evaluated in essential case studies, as indicated by accuracy metrics and 10-fold cross-validation. The classifier and feature reduction, which are generated by Markovian probability, operate well together and can help predict cancer. Our findings successfully distinguish DNA sequences related to cancer from those diagnostics of non-cancerous diseases by analyzing the W.R. DNA sequence as well as its CDS and N-CDS regions., (© 2024. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

Simple Summary: Blood clots are formed when blood vessels are injured. They help stop bleeding and heal wounds, but can also cause serious problems if they block blood flow or break off and travel to other organs. This study investigates how blood clots differ in people with cancer compared to healthy or non-cancerous individuals. This study found that cancer patients have higher levels of histones in their blood, which make their clots stiffer and resistant to lysis. Further, clots formed in cancer patients have higher viscoelastic properties, and hence are harder to break down. These findings suggest that cancer patients have abnormal clotting properties that may increase their risk of developing thrombosis, and evaluating these properties can be helpful in detecting cancer. Background: Blood viscoelasticity and plasma protein levels can play an important role in the diagnosis and prognosis of cancer. However, the role of histones and DNA in modulating blood clot properties remains to be investigated. This study investigates the differences in blood viscoelasticity and plasma protein levels among cancer patients, individuals with other diseases, and healthy individuals. Methods: Blood samples were collected from 101 participants, including 45 cancer patients, 22 healthy individuals, and 34 individuals with other diseases. Rheological properties of clots formed in vitro by reconstituted elements of fibrinogen or plasma were analyzed with an Anton Paar Rheometer, USA. Plasma protein levels of D-dimer, TPA, EPCR, fibrinogen, and histone H3 were measured through ELISA. Blood clots were formed with or without DNA and histones (H3) by adding thrombin and calcium to plasma samples, and were evaluated for viscoelasticity, permeability, and degradation. Results: Cancer patients show higher blood viscoelasticity and plasma D-dimer levels compared to healthy individuals and individuals with other diseases. Our in vitro analysis showed that the addition of histone to the plasma results in a significant decrease in viscoelasticity and mean fiber thickness of the clot formed thereafter. In parallel studies, using plasma from patients, DNA and histones were detected in fibrin clots and were associated with less degradation by t-PA. Moreover, our results show that the presence of DNA and histones not only increases clots' permeability, but also makes them more prone to degradation. Conclusions: Plasma histones and DNA affect the structure of the clot formed and induce defective fibrinolysis. Moreover, the increased viscoelastic properties of plasma from cancer patients can be used as potential biomarkers in cancer prognosis. [ABSTRACT FROM AUTHOR]

Synthetic signaling receptors enable programmable cellular responses coupling with customized inputs. However, engineering a designer force-sensing receptor to rewire mechanotransduction remains largely unexplored. Herein, we introduce nongenetically engineered artificial mechanoreceptors (AMRs) capable of reprogramming non-mechanoresponsive receptor tyrosine kinases (RTKs) to sense user-defined force cues, enabling de novo-designed mechanotransduction. AMR is a modular DNA-protein chimera comprising a mechanosensing-and-transmitting DNA nanodevice grafted on natural RTKs via aptameric anchors. AMR senses intercellular tensile force via an allosteric DNA mechano-switch with tunable piconewton-sensitive force tolerance, actuating a force-triggered dynamic DNA assembly to manipulate RTK dimerization and activate intracellular signaling. By swapping the force-reception ligands, we demonstrate the AMR-mediated activation of c-Met, a representative RTK, in response to the cellular tensile forces mediated by cell-adhesion proteins (integrin, E-cadherin) or membrane protein endocytosis (CI-M6PR). Moreover, AMR also allows the reprogramming of FGFR1, another RTK, to customize mechanobiological function, for example, adhesion-mediated neural stem cell maintenance., (© 2024. The Author(s), under exclusive licence to Springer Nature America, Inc.)

Unlike proteins, which have a wealth of validated structural data, experimentally or computationally validated DNA origami datasets are limited. Here we present a graph neural network that can predict the three-dimensional conformation of DNA origami assemblies both rapidly and accurately. We develop a hybrid data-driven and physics-informed approach for model training, designed to minimize not only the data-driven loss but also the physics-informed loss. By employing an ensemble strategy, the model can successfully infer the shape of monomeric DNA origami structures almost in real time. Further refinement of the model in an unsupervised manner enables the analysis of supramolecular assemblies consisting of tens to hundreds of DNA blocks. The proposed model enables an automated inverse design of DNA origami structures for given target shapes. Our approach facilitates the real-time virtual prototyping of DNA origami, broadening its design space., (© 2024. The Author(s), under exclusive licence to Springer Nature Limited.)

• A cost-effective and eco-friendly polyDOPA@paper was prepared for DNA extraction. • The adsorption capacity of polyDOPA@paper for DNA was 20.7 μg cm−2. • An automated extraction system was designed to ensure results consistency. • The DNA extraction platform averts the need for specialized training of operators. • The platform combined with qPCR realized the detection of E. coli in milk samples. The success of polymerase chain reaction (PCR) depends on the quality of deoxyribonucleic acid (DNA) templates. This study developed a cost-effective and eco-friendly DNA extraction system utilizing poly(3,4-dihydroxyphenylalanine)-modified cellulose paper (polyDOPA@paper). PolyDOPA@paper was prepared by oxidatively self-polymerizing DOPA under weak alkaline conditions and utilizing the adhesive property of polyDOPA on different materials. Compared to the uncoated cellulose paper, polyDOPA coating significantly enhances DNA adsorption owing to its abundant amino, carboxyl, and hydroxyl moieties. The DNA extraction mechanism using polyDOPA@paper was discussed. The maximum adsorption capacity of polyDOPA@paper for DNA was 20.7 μg cm−2. Moreover, an automated extraction system was designed and fabricated using 3D printing technology. The device simplifies the operation and ensures the reproducibility and consistency of the results. More importantly, it eliminates the need for specialized training of operators. The feasibility of the polyDOPA@paper-based automated extraction system was evaluated by quantitatively detecting Escherichia coli in spiked milk samples via a real-time PCR. The detection limit was 102 cfu mL−1. The results suggest that the system would have significant potential in detecting pathogens. [ABSTRACT FROM AUTHOR]

Latent fingerprints on plastic substrates can be visualized by using sequential treatments to enhance the contrast between the fingerprint residues and underlying substrate; however, the extent to which these processes affect subsequent DNA analysis is mostly unknown. Latent fingerprints deposited on black plastic by one donor were visualized with single-process fingerprint powders (i.e., white powder, bichromatic powder, or bichromatic magnetic powder) or sequential treatments (i.e., laser → reflected ultraviolet imaging system (RUVIS) → CA fuming → RUVIS → Rhodamine 6G, Ardrox, and MBD (RAM) or CA fuming → RAM/laser → bichromatic magnetic powder). Samples were examined after the addition of each treatment. DNA was collected using cotton swabs, extracted, quantified, and amplified. DNA yields, peak heights, number of alleles obtained, and percentage of DNA profiles eligible for CODIS upload were examined. Latent fingerprints processed with the laser and up to three sequential treatments generated DNA profiles with significantly higher peaks heights than those of the untreated samples. Fingerprints processed with the laser and up to two sequential treatments generated DNA profiles with significantly more alleles. All methods beginning with laser enhancement generated more CODIS-eligible profiles. Additional research is needed to determine the extent to which initial laser enhancement impacts the success of downstream DNA profiling results. Although DNA profile development is not guaranteed due to the variable quantities of DNA contained within latent fingerprints, the selection of an appropriate latent fingerprint visualization method could maximize both fingerprint detection and the generation of CODIS-eligible DNA profiles., (© 2024 The Authors. Journal of Forensic Sciences published by Wiley Periodicals LLC on behalf of American Academy of Forensic Sciences.)

The formation of highly organized metal-DNA structures has significant implications in bioinorganic chemistry, molecular biology and material science due to their unique properties and potential applications. In this study, we report on the conversion of single-stranded polydeoxycytidine (dC 15 ) into a Pd-DNA supramolecular structure using the [Pd(Aqa)] complex (Aqa=8-amino-4-hydroxyquinoline-2-carboxylic acid) through a self-assembly process. The resulting Pd-DNA assembly closely resembles a natural double helix, with continuous [Pd(Aqa)(C)] (C=cytosine) units serving as palladium-mediated base pairs, forming interbase hydrogen bonds and intrastrand stacking interactions. Notably, the design of the [Pd(Aqa)] complex favours the interaction with cytosine, distinguishing it from our previously reported [Pd(Cheld)] complex (Cheld=chelidamic acid). This finding opens possibilities for creating heteroleptic Pd-DNA hybrids where different complexes specifically bind to nucleobases. We confirmed the Pd-DNA supramolecular structural assembly and selective binding of the complexes using NMR spectroscopy, circular dichroism, mass spectrometry, isothermal titration calorimetry, and DFT calculations., (© 2024 The Authors. Angewandte Chemie International Edition published by Wiley-VCH GmbH.)

The exponential growth of global data has outpaced the storage capacities of current technologies, necessitating innovative storage strategies. DNA, as a natural medium for preserving genetic information, has emerged as a highly promising candidate for next-generation storage medium. Storing data in DNA offers several advantages, including ultrahigh physical density and exceptional durability. Facilitated by significant advancements in various technologies, such as DNA synthesis, DNA sequencing, and DNA nanotechnology, remarkable progress has been made in the field of DNA data storage over the past decade. However, several challenges still need to be addressed to realize practical applications of DNA data storage. In this review, the processes and strategies of in vitro DNA data storage are first introduced, highlighting recent advancements. Next, a brief overview of in vivo DNA data storage is provided, with a focus on the various writing strategies developed to date. At last, the challenges encountered in each step of DNA data storage are summarized and promising techniques are discussed that hold great promise in overcoming these obstacles., (© 2023 Wiley-VCH GmbH.)

Synthetic genomics is a novel field of chemical biology where the chemically modified genetic alphabets have been considered in central dogma of life. Tweaking of chemical compositions of natural nucleotide bases could be developed as novel building blocks of DNA/RNA. The modified bases (dP, dZ, dS, and dB etc.) have been demonstrated to be adaptable for replication, transcription and follow Darwinism law of evolution. With advancement of chemical biology especially nucleotide chemistry, synthetic genetic codes have been discovered and Hachimoji nucleotides are the most important and significant one among them. These additional nucleotide bases can form orthogonal base-pairing, and also follow Darwinian evolution and other structural features. In the Hachimoji base pairing, synthetic building blocks are formed using eight modified nucleotide (DNA/RNA) letters (hence the name "Hachimoji"). Their structural conformations, like polyelectrolyte backbones and stereo-regular building blocks favor thermodynamic stability and confirm Schrodinger aperiodic crystal. From the structural genomics aspect, these synthetic bases could be incorporated into the central dogma of life. Researchers have shown Hachimoji building blocks were transcribed to its RNA counterpart as a functional fluorescent Hachimoji aptamer. Apart from several unnatural nucleotide base pairs maneuvered into its in vitro and in vivo applications, this review describes future perspective towards the development and therapeutic utilization of the genetic codes, a primary objective of synthetic and chemical biology., (© 2023 John Wiley & Sons Ltd.)

We present avidity sequencing, a sequencing chemistry that separately optimizes the processes of stepping along a DNA template and that of identifying each nucleotide within the template. Nucleotide identification uses multivalent nucleotide ligands on dye-labeled cores to form polymerase-polymer-nucleotide complexes bound to clonal copies of DNA targets. These polymer-nucleotide substrates, termed avidites, decrease the required concentration of reporting nucleotides from micromolar to nanomolar and yield negligible dissociation rates. Avidity sequencing achieves high accuracy, with 96.2% and 85.4% of base calls having an average of one error per 1,000 and 10,000 base pairs, respectively. We show that the average error rate of avidity sequencing remained stable following a long homopolymer., (© 2023. The Author(s).)

Food is consumed by humans, which is indispensable to human life. Therefore, considerable attention of the whole society has been paid to food safety. Over the last few years, dramatic social development has brought new challenges to food safety, making developing new and quick methods for on-site food safety testing an important necessity. As a result, DNA-fueled molecular machines, characterized by high efficiency, accuracy, and sensitivity in testing, have come into the spotlight, based on which sensors can be constructed to detect toxic and harmful substances in food products. This study reviewed recent research on several DNA-fueled molecular machines, including DNA tweezers, DNA walkers, and DNA origami, for rapidly detecting toxic and harmful substances. Based on the above studies, the sensitivity and timeliness of several DNA molecular machines were summarized and compared, and the development prospect of DNA fuel molecular machines in the field of food safety detection was prospected., (© 2024 Institute of Food Technologists®.)

Proteins typically exert their biological functions by interacting with other biomolecules or ligands. The study of ligand-protein interactions is crucial in elucidating the biological mechanisms of proteins. Most existing studies have focused on analyzing ligand-protein interactions, and they ignore the additional situational of inserted and modified residues. Besides, the resources often support only a single ligand type and cannot obtain satisfied results in analyzing novel complexes. Therefore, it is important to develop a general analytical tool to extract the binding residues of ligand-protein interactions in complexes fully. In this study, we propose a ligand-protein interaction binding residue extractor (PDB-BRE), which can be used to automatically extract interacting ligand or protein-binding residues from complex three-dimensional (3D) structures based on the RCSB Protein Data Bank (RCSB PDB). PDB-BRE offers a notable advantage in its comprehensive support for analyzing six distinct types of ligands, including proteins, peptides, DNA, RNA, mixed DNA and RNA entities, and non-polymeric entities. Moreover, it takes into account the consideration of inserted and modified residues within complexes. Compared to other state-of-the-art methods, PDB-BRE is more suitable for massively parallel batch analysis, and can be directly applied for downstream tasks, such as predicting binding residues of novel complexes. PDB-BRE is freely available at http://bliulab.net/PDB-BRE., (© 2023 Wiley Periodicals LLC.)

By using the thin‐film transistor (TFT) technology, the oligo nucleotides array has been proved to be achieved in‐situ on a throughput matrix backplane of 16*16, with oligonucleotide lengths reaching 150mers, and the yield of each oligo has surpassed tens of fmol per pixel. This TFT‐based methods effectively balance the synthesis throughput with the loading capacity and offer a significantly lower cost for higher quality DNA for various applications in molecular biology. [ABSTRACT FROM AUTHOR]

This paper proposes an innovative image encryption algorithm that leverages partial face recognition and DNA diffusion, building upon advancements in chaotic image encryption and face recognition technologies. The key is generated using the secure SHA-512 algorithm, while the chaotic sequence for the encryption algorithm is derived from the Chen system. This paper begins by employing facial recognition technology to identify and focus on specific facial regions within an image. Subsequently, DNA diffusion is applied to encrypt the recognized face segment via a diffusion-scrambling encryption process. Following this, the entire image undergoes diffusion utilizing the devised diffusion rules. Finally, a uniform scrambling operation based on Fisher-Yeats is performed on the entire image. The experimental results and safety analysis show that the information entropy can exceed 7.9973, the average correlation can be less than 0.0023, the pixel number change rate can reach 99.6052%, and the unified average change intensity can reach 33.4644%, all of which are very close to the ideal values. [ABSTRACT FROM AUTHOR]

Due to the high blood glucose and low oxygen environment in diabetes wounds, complex pathological problems arise, such as failure to upregulate healing factors, biological barriers generation, microvascular lesions, and skin neuropathy. Inspired by nature and traditional Chinese paper‐cutting technology, polypeptide deoxyribonucleic acid (DNA) hydrogel microneedles (MNs) (P‐DNA gel MNs) are prepared. The obtained P‐DNA gel MNs possess optimized structure and large deformability, providing excellent clamping, stability, skin penetration, large deformation, tissue adhesion, and antibacterial properties. By incorporating extracellular vesicles (EVs) extracted under hypoxia (H‐EVs‐hypoxia), P‐DNA gel MNs can regulate tissue microenvironment, scavenge free radicals, and reduce inflammation. Notably, P‐DNA gel MNs integration system activates immune regulation and beneficial pathways, promoting neurogenesis and angiogenesis, reducing pathological pain, and achieving high‐quality healing. Overall, P‐DNA gel MNs system presents a fundamental mechanism for clinical transformation in treating diabetes wounds. [ABSTRACT FROM AUTHOR]

Nowadays, it is difficult to imagine a powerful algorithm of cryptography that can continue cryptanalyzing and attacking without the use of unconventional techniques. Although some of the substitution algorithms are old, such as Vigenere, Alberti, and Trithemius ciphers, they are considered powerful and cannot be broken. In this paper we produce the novelty algorithm, by using of biological computation as an unconventional search tool combined with an uninhibited analysis method is the vertical probabilistic model, that makes attacking and analyzing these ciphers possible and very easy to transform the problem from a complex to a linear one, which is a novelty achievement. The letters of the encoded message are processed in the form of segments of equal length, to report the available hardware components. Each letter codon represents a region of the memory strand, and the letters calculated for it are symbolized within the probabilistic model so that each pair has a triple encoding: the first is given as a memory strand encoding and the others are its complement in the sticker encoding; These encodings differ from one region to another. The solution space is calculated and then the parallel search process begins. Some memory complexities are excluded even though they are within the solution paths formed, because the natural language does not contain its sequences. The precision of the solution and the time consuming of access to it depend on the length of the processed text, and the precision of the solution is often inversely proportional to the speed of access to it. As an average of the time spent to reach the solution, a text with a length of 200 cipher characters needs approximately 15 minutes to give 98% of the correct components of the specific hardware. The aim of the paper is to transform OTP substitution analysis from a NP problem to a O(nm) problem, which makes it easier to find solutions to it easily with the available capabilities and to develop methods that are harnessed to attack difficult and powerful ciphers that differ in class and type from the OTP polyalphabetic substitution ciphers. [ABSTRACT FROM AUTHOR]

While dried blood spots are a convenient source of genetic material, they are usually associated with a lower DNA yield than from a native sample. The study evaluated the DNA yield from dried blood samples prepared on glass fibre and cellulose membranes and investigated the reasons for the yield reduction. The extraction of total DNA from membrane-dried blood samples was optimized by spin-column extraction method. It was shown that preliminary short-term (20 min) solubilization of a dried matrix in an aqueous medium, followed by standard extraction protocols for the mixture of the eluate with membranes, provides the highest DNA yield. The yield of DNA from a glass fibre membrane was 40–50% lower compared to a native sample, but on average, two times higher than from a conventional cellulose membrane (filter paper). The reduction of DNA yield when using a dried sample was found to be due to partial retention of nucleic acids by the membrane material during the lysis stage. [ABSTRACT FROM AUTHOR]

With the exponential growth of digital data, there is a pressing need for innovative storage media and techniques. DNA molecules, due to their stability, storage capacity, and density, offer a promising solution for information storage. However, DNA storage also faces numerous challenges, such as complex biochemical constraints and encoding efficiency. This paper presents Explorer , a high-efficiency DNA coding algorithm based on the De Bruijn graph, which leverages its capability to characterize local sequences. Explorer enables coding under various biochemical constraints, such as homopolymers, GC content, and undesired motifs. This paper also introduces Codeformer , a fast decoding algorithm based on the transformer architecture, to further enhance decoding efficiency. Numerical experiments indicate that, compared with other advanced algorithms, Explorer not only achieves stable encoding and decoding under various biochemical constraints but also increases the encoding efficiency and bit rate by ¿10%. Additionally, Codeformer demonstrates the ability to efficiently decode large quantities of DNA sequences. Under different parameter settings, its decoding efficiency exceeds that of traditional algorithms by more than two-fold. When Codeformer is combined with Reed–Solomon code, its decoding accuracy exceeds 99%, making it a good choice for high-speed decoding applications. These advancements are expected to contribute to the development of DNA-based data storage systems and the broader exploration of DNA as a novel information storage medium. [ABSTRACT FROM AUTHOR]

With the continuous development of information technology, ensuring information security has become an important issue. As a widely used multimedia tool, images often face the risk of leakage. Therefore, this paper proposes an image encryption algorithm based on 2D-SAHM chaotic system and a new DNA operation rule. The algorithm first constructs a new chaotic system 2D-SAHM, which has better chaotic characteristics and can generate more random chaotic sequences than the traditional low-dimensional chaotic system. And then, on the basis of this system, the algorithm scrambles and diffuses the image. In the scrambling stage, the whole image is converted into a one-dimensional pixel matrix and divided into several sub-images by double Joseph scrambling. In the diffusion stage, to solve the problem that traditional DNA encryption relies too much on chaotic sequences, this paper proposes a new DNA operation rule. This rule determines the operation symbol of DNA by the type of amino acid, which improves the randomness of the algorithm. The final simulation results and performance analysis show that the algorithm has high security and strong anti-interference ability. [ABSTRACT FROM AUTHOR]

With the urge to secure and protect digital assets, there is a need to emphasize the immediacy of taking measures to ensure robust security due to the enhancement of cyber security. Different advanced methods, like encryption schemes, are vulnerable to putting constraints on attacks. To encode the digital data and utilize the unique properties of DNA, like stability and durability, synthetic DNA sequences are offered as a promising alternative by DNA encoding schemes. This study enlightens the exploration of DNA's potential for encoding in evolving cyber security. Based on the systematic literature review, this paper provides a discussion on the challenges, pros, and directions for future work. We analyzed the current trends and new innovations in methodology, security attacks, the implementation of tools, and different metrics to measure. Various tools, such as Mathematica, MATLAB, NIST test suite, and Coludsim, were employed to evaluate the performance of the proposed method and obtain results. By identifying the strengths and limitations of proposed methods, the study highlights research challenges and offers future scope for investigation. [ABSTRACT FROM AUTHOR]

Bones and teeth represent a common finding in ancient DNA studies and in forensic casework, even after a long burial. Genetic typing is the gold standard for the personal identification of skeletal remains, but there are two main factors involved in the successful DNA typing of such samples: (1) the set-up of an efficient DNA extraction method; (2) the identification of the most suitable skeletal element for the downstream genetic analyses. In this paper, a protocol based on the processing of 0.5 g of bone powder decalcified using Na2EDTA proved to be suitable for a semi-automated DNA extraction workflow using the Maxwell® FSC DNA IQ™ Casework Kit (Promega, Madison, WI, USA). The performance of this method in terms of DNA recovery and quality was compared with a full demineralisation extraction protocol based on Qiagen technology and kits. No statistically significant differences were scored according to the DNA recovery and DNA degradation index (p-values ≥ 0.176; r ≥ 0.907). This new DNA extraction protocol was applied to 88 bone samples (41 femurs, 19 petrous bones, 12 metacarpals and 16 molars) allegedly belonging to 27 World War II Italian soldiers found in a mass grave on the isle of Cres (Croatia). The results of the qPCR performed by the Quantifiler Human DNA Quantification kit showed values above the lowest Limit of Quantification (lLOQ; 23 pg/µL) for all petrous bones, whereas other bone types showed, in most cases, lower amounts of DNA. Replicate STR-CE analyses showed successful typing (that is, >12 markers) in all tests on the petrous bones, followed by the metacarpals (83.3%), femurs (52.2%) and teeth (20.0%). Full profiles (22/22 autosomal markers) were achieved mainly in the petrous bones (84.2%), followed by the metacarpals (41.7%). Stochastic amplification artefacts such as drop-outs or drop-ins occurred with a frequency of 1.9% in the petrous bones, whereas they were higher when the DNA recovered from other bone elements was amplified (up to 13.9% in the femurs). Overall, the results of this study confirm that petrous bone outperforms other bone elements in terms of the quantity and quality of the recovered DNA; for this reason, if available, it should always be preferred for genetic testing. In addition, our results highlight the need for accurate planning of the DVI operation, which should be carried out by a multi-disciplinary team, and the tricky issue of identifying other suitable skeletal elements for genetic testing. Overall, the results presented in this paper support the need to adopt preanalytical strategies positively related to the successful genetic testing of aged skeletal remains in order to reduce costs and the time of analysis. [ABSTRACT FROM AUTHOR]

The apurinic/apyrimidinic (AP) site is an important intermediate in the DNA base excision repair (BER) pathway, having the potential of being a biomarker for DNA damage. AP sites could lead to the stalling of polymerases, the misincorporation of bases and DNA strand breaks, which might affect physiological function of cells. However, the abundance of AP sites in genomic DNA is very low (less than 2 AP sites/10 6  nts), which requires a sensitive and accurate method to meet its detection requirements. Here, we described an ultrasensitive quantification method based on a hydrazine-s-triazine reagent (i-Pr 2 N) labeling for AP sites combining with high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). The limit of detection reached an ultralow level (40 amol), realizing the most sensitive MS-based quantification for the AP site. To guarantee the accuracy of the quantitative results, the labeling reaction was carried out directly on DNA strands instead of labeling after DNA enzymatic digestion to reduce artifacts that might be produced during the enzymatic process of DNA strands. And selective detection was realized by MS to avoid introducing the false-positive signals from other aldehyde species, which could also react with i-Pr 2 N. Genomic DNA samples from different mammalian cell lines were successfully analyzed using this method. There were 0.4-0.8 AP sites per 10 6 nucleotides, and the values would increase 16.1 and 2.75 times when cells were treated with genotoxic substances methyl methanesulfonate and 5-fluorouracil, respectively. This method has good potential in the analysis of a small number of cell samples and clinical samples, is expected to be useful for evaluating the damage level of DNA bases, the genotoxicity of compounds and the drug resistance of cancer cells, and provides a new tool for cell function research and clinical precise treatment., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Advances in gene therapy, exemplified by mRNA vaccines against COVID-19, highlight the importance of lipid nanoparticles (LNPs) for nucleic acid delivery despite challenging storage conditions. Substituting mRNA with pDNA in LNPs may enhance stability and efficacy, yet maintaining LNP stability poses challenges, particularly during freeze-drying. Cryoprotectants offer potential to mitigate destabilization, improving LNP properties and in vivo performance. Here, we evaluated the effects of different concentrations of various cryoprotectants on the freeze-drying process of pDNA-loaded LNPs, assessing their physicochemical characteristics and transfection efficiency. Stability was examined under various storage conditions, confirming biological efficacy post-storage. Our results highlight the role of cryoprotectants in optimizing freeze-drying for the extended shelf life of nucleic acid-loaded LNPs. Trehalose emerged as an efficient cryoprotectant, maintaining LNP stability after the freeze-drying process for up to 2 years, with diameters and transfection efficiency comparable to fresh formulations. These findings demonstrate the optimized concentration of cryoprotectants to sustain LNP stability despite freeze-drying and prolonged storage, providing valuable insights for nucleic acid-based therapies., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier B.V.)

To identify compounds inhibiting the activity of the Early Growth Response (EGR)-1 DNA-binding domain, thirty-seven pyrazolines were prepared and their EGR-1 DNA-binding activities were measured. Pharmacophores were derived based on quantitative structure-activity relationship calculations. As compound 2, 1-(5-(4-methoxyphenyl)-4,5-dihydro-1H-pyrazol-3-yl)naphthalen-2-ol, showed the best inhibitory effects against the activity of the EGR-1 DNA-binding domain, the binding mode between compound 2 and EGR-1 was elucidated using in silico docking. The pharmacophores were matched to the binding modes. Electrophoretic mobility shift assays confirmed that compound 2 dose-dependently inhibited TNFα-induced EGR-1-DNA complex formation in HaCaT cells. Reverse transcription-polymerase chain reaction demonstrated that compound 2 effectively reduced the mRNA expression of EGR-1-regulated inflammatory genes, including thymic stromal lymphopoietin (TSLP), interleukin (IL)-1β, IL-6, and IL-31, in TNFα-stimulated HaCaT cells. Therefore, compound 2 could be developed as an agent that inhibits the activity of the EGR-1 DNA-binding domain., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Label-free optical deoxyribonucleic acid (DNA) sensing with arrayed plasmonic nanostructures (plasmonic crystals) is a promising technology for biomedical diagnosis and bioanalytical science. Plasmonic biosensors can detect target biomolecules by utilizing the shift in plasmonic resonance caused by changes in the surrounding refractive index (RI) attributed to the capture of target biomolecules using a recognizer. Conventional explanations for the sensitivity of plasmonic crystals are based on bulk (BRIS) and surface RI sensitivities (SRIS) for basic plasmonic nanoparticles despite their unique properties such as surface lattice resonances (SLRs), wherein localized surface plasmons (LSPs) cooperatively oscillate with their pitch. Therefore, investigating the sensitivity of SLRs is imperative for improving sensing performance. In this study, the sensitivity of adenomatous polyposis coli (APC) gene-related DNA hybridization detection of complementary plasmonic crystals composed of nanodisks (PNDs) on or under plasmonic nanoholes (PNHs) was investigated considering the SLR properties. The BRIS was measured using the conventional definition of the peak wavelength shift per unit RI increment (nm/RIU) followed by the SRIS measurement using the layer-by-layer method. The BRIS and SRIS measurements reflect the practical sensitivity for DNA detection. PNHs had higher sensitivity than PNDs, with a limit of detection of 0.30 nM. Further, only the SLR-based mode responded to localized RI changes because of DNA hybridization, whereas both the LSPs- and SLR-based modes responded to uniform RI changes caused by layer-by-layer coating. Our investigation will open up possibilities and opportunities for plasmonic crystal biosensors., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests:Tatsuro Endo reports financial support was provided by Japan Society for the Promotion of Science. If there are other authors, they declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Hg 2+ is a highly toxic heavy metal ion that poses serious risks to human health and the environment. Due to its tendency to accumulate, it can easily enter the human body through the food chain, making it crucial to develop detection sensors that mimic real environmental conditions. To achieve this, our study employed a surface-enhanced Raman scattering (SERS) sensor using two strategies. First, we designed a highly selective probe by optimizing the probe and reporter DNA strands to bind Hg 2+ within a thymine-thymine mismatch. Second, we used the double coffee ring effect to concentrate the optimized probe DNA. These two strategies greatly enhanced the SERS signal, resulting in a sensor with exceptional sensitivity, a low detection limit of 208.71 fM, and superior selectivity for Hg 2+ . The practical application of the sensor was demonstrated by successfully detecting Hg 2+ in drinking water, tap water, canned tuna, and tuna sashimi. Additionally, the experimental results were presented in a pizza-shaped SERS mapping image, allowing users to estimate Hg 2+ concentrations through color, providing a user-friendly and intuitive method for data comprehension and analysis. Our study presents a promising approach for sensitive and reliable Hg 2+ detection, with potential implications for environmental monitoring and food safety., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests:Jinsung Park reports financial support was provided by National Research Foundation of South Korea (NRF). Joohyung Park reports financial support was provided by National Research Foundation of South Korea (NRF). Juneseok You reports financial support was provided by Korea University. If there are other authors, they declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier B.V.)

With the developing resistance to traditional antiparasitic medications, the purpose of this study was to efficiently develop a series of six noble flavanoidal tetrazinane-6'-one derivatives by a one-pot reaction pathway. FT-IR, 1 HNMR, 13 CNMR, and Mass spectra were employed for the structural elucidation of the synthesized compounds (7-12). Clinostomum complanatum, a parasite infection model that has been well-established, demonstrated that all the synthesized compounds are potent antiparasitic agents. DNA is the main target for various medicinal compounds. As a result, thestudy of how small molecules attach to DNA has received a lot of attention. In the present study, we have performed various biophysical techniques to determine the mode of binding of synthesized compounds (7-12) with calf thymus DNA (ct-DNA). It was observed from the UV-visible absorbance and fluorescence spectra that all synthesized compounds (7-12) form complexes with the ct-DNA. The value of binding constant (K b ) was obtained to be in the range of 4.36---24.50 × 10 3 M - 1 at 298 K. Competitive displacement assay with ethidium bromide (EB), CD spectral analysis, viscosity measurements, and in silico molecular docking confirmed that ligands (7-12) incorporate with ct-DNA through groove binding only. Molecular docking studies were performed for all synthesized compounds with the calf thymus DNA and it was found that all the newly synthesized compounds strongly bind with the chain B of DNA in the minor groove with the value of binding energy in the range of -8.54 to -9.04 kcal per mole and several hydrogen bonding interactions., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Polycyclic aromatic hydrocarbons (PAHs) are potent inhibitors of DNA that can induce genetic damage, abnormal gene expression, and metabolic disorders upon interfacing with biological macromolecules. However, the mechanism of their interactions with DNA remains elusive. Therefore, this study selected three representative PAHs, including phenanthrene (Phen), pyrene (Pyre), and benzo[a]pyrene (B[a]P), and explored their binding mechanisms with the double-strand DNA (dsDNA) from different species, including 1J1V (Escherichia coli), 6J5B (Arabidopsis thaliana), and 6Q1V (Homo sapiens). The results revealed that binding between PAHs and dsDNA occurred in the groove via van der Waals forces and π-π stacking, with the carboxyl oxygen atom of the thymine (T)-base within dsDNA being the key binding site. This result was further confirmed by the spectroscopic experiments, where significant changes in the peak of the T-base were observed after PAHs-dsDNA binding. More interestingly, the total binding energies of Pyre with the three dsDNA were -138.800 kJ/mol (Pyre-1J1V), -105.523 kJ/mol (Pyre-6J5B), and -127.567 kJ/mol (Pyre-6Q1V), respectively, all of which were higher than those of Phen and B[a]P. This suggests that that Pyre has the strongest dsDNA binding ability. Additionally, analysis of the thermodynamic parameters indicated that the interactions between the three PAHs and dsDNA were exothermic reactions. In contrast, the Pyre-dsDNA interaction predominantly involved van der Waals forces and hydrogen bonding due to the enthalpy change (∆H) < 0 and entropy change (∆S) < 0, while the Phen-dsDNA and B[a]P-dsDNA interactions predominantly involved hydrophobic forces due to ∆H > 0 and ∆S > 0. Furthermore, Pyre caused local distortion of dsDNA, which was more pronounced under atomic force microscopy (AFM). In summary, this study has unveiled a new phenomenon of binding between PAHs and dsDNA. This sheds light on the carcinogenic potential and environmental impacts of PAHs pollution., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interest or personal relationships that could have appeared to influence that work reported in this paper., (Copyright © 2024. Published by Elsevier B.V.)

Slalom chromatography (SC) re-emerged in 2024 due to the availability of low adsorption ultra-high pressure liquid chromatography (UHPLC) packed columns/instruments and large modalities being investigated in the context of cell and gene therapies. The physico-chemical principles of SC retention combined with hydrodynamic chromatography (HDC) exclusion have been recently reported. In SC, DNA macromolecules are retarded because: (1) they can be stretched to lengths comparable to the particle diameter, and (2) their elastic relaxation time is long enough to maintain them in non-equilibrium extended conformations under regular UHPLC shear flow conditions. Here, a quantitative HDC-SC retention model is consolidated. A general plate height model accounting for the band broadening of long DNA biopolymers along packed beds is also derived for supporting method development and predicting speed-resolution performance in SC. For illustration, the chromatographic speed-resolution properties in SC are predicted for the separation of specific critical pairs (4.0/4.5, 10/11, and 25/27 kbp) of linear dsDNA polymers. The calculations are performed for two available custom-made particle sizes, d p = 1.7 and 2.5μm, at a constant pressure of 10,000 psi. The predictions are directly validated from experimental data acquired using low adsorption MaxPeak TM 4.6 mm i.d. Columns packed with 1.7μm BEH TM 45 Å (15 cm long column) and 2.5μm BEH 125 Å (30 cm long column) Particles, and by injecting six linear dsDNAs (λ DNA-Hind III Digest). The LC system is very low dispersion ACQUITY TM UPLC TM I-class PLUS System, and the mobile phase is a 100 mM phosphate buffer at pH 8. Maximum resolution is always achieved when the average extended lengths of linear dsDNAs are equal to a critical length, which is proportional to the particle diameter and to the square root of the applied shear rate. Most advantageously, the experimental results reveal that the relaxation times of linear dsDNAs observed under shear flow conditions are two orders of magnitude shorter than those expected in the absence of flow: this enables the detection of the longest linear dsDNAs up to 25 kbp without irremediable loss in column performance. Finally, the retention-efficiency model elaborated in this work can be used to rapidly anticipate and develop methods (selection of particle size, column length, and operating pressure) for any targeted DNA and time-resolution constraints., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Author. Published by Elsevier B.V. All rights reserved.)

Trimethine cyanine dyes are widely used as probes for the detection, study and quantification of biomolecules. In particular, cationic trimethine cyanines noncovalently interact with DNA with growing fluorescence. However, their use is often limited by the tendency to self-association - to the formation of aggregates. Disubstituted trimethine cyanines with hydrophobic substituents are especially prone to aggregation. In this work, we studied the interaction of a number of substituted trimethine cyanines with DNA (in aqueous buffer solutions) and showed that their aggregation strongly interfered with their use as fluorescent probes for DNA. To eliminate this drawback, preliminary heating of dye solutions with DNA to 60-70 °C was used, followed by cooling to room temperature. Compared to the experiments without heating, an increase in the dye fluorescence intensity was observed due to the partial thermal decomposition of the aggregates and the interaction of the resulting monomers with DNA. To decompose aggregates, another method was also used - protonation of the dyes with amino substituents in buffer solutions with pH 5.0, which also led to growing the dye fluorescence intensity in the presence of DNA. Complexes of the dyes with DNA were modeled using molecular docking. Effective binding constants of the dyes to DNA and detection limits when using the dyes as probes for DNA (LOD and LOQ) were determined. It is shown that dye 3 with heating in neutral buffer and dye 1 in acidic buffer may be recommended as sensitive probes for DNA. It is concluded that the method of preliminary heating may be applied to dyes prone to aggregation, for improving their properties as biomolecular probes. Another possible means to reduce the interfering effects of dye aggregates is to use easily protonated dyes (with amino substituents) in slightly acidic media., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

The primary goals of this study were to investigate the formation of abasic sites (AP sites) induced by methyl methanesulfonate (MMS) and hydrogen peroxide (H 2 O 2 ), and to characterize specific types of these pro-mutagenic DNA lesions in calf thymus DNA (CT-DNA), and BEAS-2B human lung normal cell line. Furthermore, these profiles were compared with those observed in leukocytes derived from healthy controls (HC), breast cancer patients (BCP) before treatment, and 5-year survivors. Results indicated that both H 2 O 2 and MMS induced the concentration- and time-dependent formation of AP sites in CT-DNA. To characterize the specific types of AP sites induced by H 2 O 2 or MMS, we performed AP site cleavage assay using putrescine, T7 exonuclease (T7 Exo), and exonuclease III (Exo III). Results showed that the AP sites induced by H 2 O 2 in CT-DNA were predominantly 5'-and 3'-nicked AP sites and no intact AP sites were detected. By contrast, the majority of AP sites generated by MMS in CT-DNA are not excisable and are classified as residual and intact AP sites. Similar approaches were performed in human BEAS-2B cells and comparable observations were confirmed in the cell-based model. Further investigation indicated that the profile of the AP sites observed in Taiwanese HC is identical to that of BEAS-2B cells treated with H 2 O 2 whereas the pattern of AP sites detected in BCP is similar to that of CT-DNA exposed to H 2 O 2 , suggesting that these AP sites were produced primarily through reactive oxygen species (ROS) generation. More than 70 % of the AP sites in leukocytes derived from BCP were 5'-nicked and residual AP sites. Furthermore, the characteristics of the AP sites detected in 5-year survivors are comparable with the ones in HC by using putrescine cleavage assay. Overall, we speculate that deficiency in the DNA repair cascade may play a role in mediating the formation of specific types of AP sites detected in BCP., Competing Interests: Declaration of Competing Interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Po-Hsiung Lin reports financial support was provided by National Science and Technology Council. If there are other authors, they declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Interactions of biological molecules in organisms are considered to be primary factors for the lifecycle of that organism. Various important biological functions are dependent on such interactions and among different kinds of interactions, the protein DNA interactions are very important for the processes of transcription, regulation of gene expression, DNA repairing and packaging. Thus, keeping the knowledge of such interactions and the sites of those interactions is necessary to study the mechanism of various biological processes. As experimental identification through biological assays is quite resource-demanding, costly and error-prone, scientists opt for the computational methods for efficient and accurate identification of such DNA-protein interaction sites. Thus, herein, we propose a novel and accurate method namely DeepDBS for the identification of DNA-binding sites in proteins, using primary amino acid sequences of proteins under study. From protein sequences, deep representations were computed through a one-dimensional convolution neural network (1D-CNN), recurrent neural network (RNN) and long short-term memory (LSTM) network and were further used to train a Random Forest classifier. Random Forest with LSTM-based features outperformed the other models, as well as the existing state-of-the-art methods with an accuracy score of 0.99 for self-consistency test, 10-fold cross-validation, 5-fold cross-validation, and jackknife validation while 0.92 for independent dataset testing. It is concluded based on results that the DeepDBS can help accurate and efficient identification of DNA binding sites (DBS) in proteins., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Research on self-assembled deoxyribonucleic acid (DNA) nanostructures with different shapes, sizes, and functions has recently made rapid progress owing to its biocompatibility, programmability, and stability. Among these, triangular unit-based DNA nanostructures, which are typically multi-arm DNA tiles, have been widely applied because of their unique structural rigidity, spatial flexibility, and cell permeability. Triangular unit-based DNA nanostructures are folded from multiple single-stranded DNA using the principle of complementary base pairing. Its shape and size can be determined using pre-set scaffold strands, segmented base complementary regions, and sequence lengths. The resulting DNA nanostructures retain the desired sequence length to serve as binding sites for other molecules and obtain satisfactory results in molecular recognition, spatial orientation, and target acquisition. Therefore, extensive research on triangular unit-based DNA nanostructures has shown that they can be used as powerful tools in the biosensing field to improve specificity, sensitivity, and accuracy. Over the past few decades, various design strategies and assembly techniques have been established to improve the stability, complexity, functionality, and practical applications of triangular unit-based DNA nanostructures in biosensing. In this review, we introduce the structural design strategies and principles of typical triangular unit-based DNA nanostructures, including triangular, tetrahedral, star, and net-shaped DNA. We then summarize the functional properties of triangular unit-based DNA nanostructures and their applications in biosensing. Finally, we critically discuss the existing challenges and future trends., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier Inc.)

According to the principle of Locard "Every contact leaves a trace", when touching a surface, a bi-directional transfer of self and non-self-DNA residing on the hands and touched objects can occur. Metals are commonly encountered in forensic evidence and, during hand contact with these surfaces, a transfer of metal particles could occur together with the transfer of human DNA. This study proposes a proof-concept approach for the original detection of metal particles and touch DNA to track the activity performed by a donor and particularly to assess the metallic substrate touched before the contact with a subsequent surface. To this scope, a scenario of contact events was simulated by three volunteers, who participated in fingerprint deposition firstly on copper and then on plastic and glass surfaces. Twenty-four stubs were collected on the hands of volunteers and the secondary surfaces and then analyzed by environmental scanning electron microscopy (ESEM). DNA was quantified only from copper and plastic surfaces. Ten additional volunteers followed the same protocol of deposition on copper and then on plastic surfaces to evaluate DNA transfer only. On 20 touch DNA samples, the copper surface yielded significantly lower DNA amounts, ranging from 0.001 to 0.129 ng/μl, compared to the secondary touched plastic surface, ranging from 0.007 to 0.362 ng/μl. ESEM-EDS analysis showed that copper particles could be abundantly detected on the hands of the volunteers after contact with the copper surface. Particles containing silicates with copper were shown on plastic, while they were only found in 1/3 of samples on glass. Our proof-of-concept study has shown that ESEM-EDS analysis has the potential to detect copper particles transferred to the hands of volunteers during contact with a copper metallic surface and deposited on secondarily touched items. The results suggest that this original ESEM-DNA parallel approach could potentially allow the tracking of DNA transfer and metal particles at a crime scene, although this represents only a first step and further research on a wider casuistry could help to address the interpretation of results given activity level propositions., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

In this study, we utilised hex-star phosphorene as the main detecting material to identify the nucleobases. Nucleobases, being crucial carriers of hereditary information are identified through specific hydrogen bonding and steric interactions such as adenine pairing with thymine (or) uracil and guanine pairing with cytosine. The stable hex-star phosphorene possesses negative formation energy of -5.194 eV. The hex-star phosphorene exhibits a semiconductor nature with an energy band gap of 1.658 eV, which is deployed as the adsorbing substrate for nucleobases. Based on the Mulliken charge analysis, adsorption energy, relative band gap variation, and the detection efficiency of hex-star phosphorene towards nucleobases are examined. The outcome confirms the physisorption of nucleobases on hex-star phosphorene and strongly supports that hex-star phosphorene can be used as sequencing material for DNA and RNA., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Constructing label-free bivariate fluorescence biosensor would be intriguing and desired for the recognizable and accurate detection of two specific DNA segments, yet the design of functional DNA structures with low overlapped interference might be challenging. Herein in this work, a double-faced Janus DNA nanoarchitecture (JDNA) with bi-responsive recognition regions on opposite sides was assembled, which consisted of two substrate strands and two template strands for loading green-/red-emissive Ag nanoclusters (gAgNC and rAgNC) as bivariate signaling reporters. Of note, the hybridized double helix in the middle rationally oriented two flank faces and stabilized the rigid conformation of JDNA, while the template sequences of bicolor clusters were blocked to minimize non-specific background leakage. Upon inputting two targets, the discernible hairpins lost their hairpin structures due to forming two dsDNA complexes. They were executed to simultaneously invade JDNA for activating two individual target-recycled strand displacement (TRSD) events, guiding signal transduction and efficient amplification. Consequently, the clustering templates were unlocked via the tailored conformation switch of JDNA, in which gAgNC and rAgNC were in situ synthesized in two diagonal positions, thereby significantly emitting bi-responsive signal without cross interference. Benefited from the logic integration of double-faced JDNA and TRSD, a label-free, sensitive and specific bivariate fluorescence approach was developed, which would open a new avenue for the potential application in biosensing and bioanalysis., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

The abuse of kanamycin (KAN) poses an increasing threat to human health by contaminating agricultural and animal husbandry products, drinking water, and more. Therefore, the sensitive detection of trace KAN residues in real samples is crucial for monitoring agricultural pollution, ensuring food safety, and diagnosing diseases. However, traditional assay techniques for KAN rely on bulky instruments and complicated operations with unsatisfactory detection limits. Herein, we developed a novel label-free aptasensor to achieve ultrasensitive detection of KAN by constructing mesoporous DNA-cobalt@carbon nanofibers (DNA-Co@C-NFs) as the recognizer. Leveraging the extended π-conjugation structure, prominent surface area, and abundant pores, the Co@C-NFs can effectively load aptamer strands via π-π stacking interactions, serving as KAN capturer and reporter. Due to the change in DNA configuration upon binding KAN, this aptasensor presented an ultralow detection limit and ultra-wide linear range, along with favorable precision and selectivity. Using real tap water, milk, and human serum samples, the aptasensor accurately reported trace KAN levels. As a result, this convenient and rapid autosensing technique holds promise for onsite testing of other antibiotic residues in agriculture, food safety, and clinical diagnosis., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Organophosphorus compounds are widely distributed and highly toxic to the environment and living organisms. The current detection of organophosphorus compounds is based on a single-mode method, which makes it challenging to achieve good portability, accuracy, and sensitivity simultaneously. This study designed a multifunctional microfluidic chip to develop a dual-mode biosensor employing a DNA hydrogel as a carrier and aptamers as recognition probes for the colorimetric/electrochemical detection of malathion, an organophosphorus compound. The biosensor balanced portability and stability by combining a microfluidic chip and target-triggered DNA hydrogel-sensing technologies. Moreover, the biosensor based on target-triggered DNA hydrogel modified microfluidic developed in this study exhibited a dual-mode response to malathion, providing both colorimetric and electrochemical signals. The colorimetric mode enables rapid visualization and qualitative detection and, when combined with a smartphone, allows on-site quantitative analysis with a detection limit of 56 nM. The electrochemical mode offers a broad linear range (0.01-3000 μM) and high sensitivity (a limit of detection of 5 nM). The two modes could validate each other and improve the accuracy of detection. The colorimetric/electrochemical dual-mode biosensor based on target-triggered DNA hydrogel modified microfluidic chip offers a portable, simple, accurate, and sensitive strategy for detecting harmful environmental and food substances., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)