Rapid DNA Research Articles

On-site forensic DNA analysis has been hampered by inadequate automation and the limited scope of genetic information profiling. Here, a modular fully integrated microfluidic system is presented paired with a portable trolley-case analyzer to enable truly automated, on-site forensic DNA profiling. The system consists of a disposable plastic chip for DNA extraction/amplification (DEA) and a universal glass capillary electrophoresis (CAE) chip. The sample-in-answer-out platform generates complete DNA profiling within 124min without any manual intervention in field environments. The automated system is successfully validated to directly process six types of forensic samples. Modular microfluidic cartridge interfaces are designed to support parallel analyses, including human identification via short tandem repeats (STRs), ancestry inference using insertion/deletion polymorphism (InDels), and paternity testing based on Y-chromosomal STRs (Y-STRs) and single nucleotide polymorphisms (Y-SNPs). Validation demonstrated a sensitivity of 0.5ng for 21-locus STR profiling, enabling non-expert users to obtain complete profiles with just 1min of hands-on operation. The DIP38 ancestry panel exhibited complete concordance with self-reported ethnicities. Crucially, the system allows for simultaneous Y-STR/Y-SNP detection in outdoor settings, facilitating assignment of the O-M122 haplogroup (ISOGG 2023). The development of this microsystem offer a fully automated solution for rapid on-site forensic DNA detection.

Surface enhanced Raman scattering tag enabled ultrasensitive molecular identification of Hippocampus trimaculatus based on DNA barcoding.

A High-Throughout PCR Test Strip Method for the Rapid Identification of Four Placentas.

Sensitive and rapid detection of human immunodeficiency virus (HIV) DNA is crucial for the effective prevention and treatment of acquired immunodeficiency syndrome (AIDS). The entropy-driven catalytic strand displacement reaction (SDR), an enzyme-free and hairpin-free DNA self-assembly amplification strategy, offers several advantages such as minimal nonspecific amplification, carrier-free operation, and simplified procedures, rendering it a promising approach for developing highly sensitive, rapid HIV DNA detection assays. In nucleic acid testing, longer target sequences typically yield more accurate detection results but require stronger driving forces, which can prolong reaction times. Introducing a second toehold in the SDR offers an additional driving force, presenting a potential solution to this limitation. Based on this concept, this study developed an analytical method that integrates the SDR with fluorescence resonance energy transfer (FRET) to amplify fluorescence signals, enabling the detection of a 33-base pair (bp) HIV DNA target. This method achieved a low detection limit of 0.0200 nM and a wide linear detection range of 0.05-10 nM. The successful detection of the 33 bp target demonstrates the potential of this dual-toehold SDR strategy for highly sensitive and specific HIV diagnostics.

Understanding the importance of ligand patterning in biological processes requires precise control over molecular positioning and spacing. While DNA origami structures offer nanoscale precision in biomolecule arrangement, their biological applications are limited by challenges related to their structural stability, scalability, and surface area. Here, we present a straightforward and rapid DNA origami stamping technique for transferring nanoscale oligonucleotide patterns onto surfaces, visualized using DNA-PAINT super-resolution microscopy to quantitatively assess the stamping efficiency and precision across different stamp types. Unlike traditional top-down methods that require specialized equipment, our technique provides an accessible, self-assembled platform for surface patterning, with versatility across various substrates via modifiable pattern-transfer oligonucleotides. We demonstrate reliable, efficient, and precise pattern transfer at single-molecule resolution, opening opportunities to study distance-dependent biological processes, including receptor activation, multivalent binding, and enzymatic cascades across broader spatial scales and different detection techniques. The use of the passivated surface limits nonspecific interactions with unpatterned areas and enables control over the interaction between the biological target and the patterned biomolecules. Our method advances surface patterning by combining DNA nanotechnology with single-molecule imaging techniques, expanding access to cost-effective analytical approaches and potentially enabling multiplexed detection and live measurements.

A Phase 2 Exploratory Trial Evaluating Computed Tomography-Based Midtreatment Nodal Response to Select for De-escalated Chemoradiation Therapy in the Definitive Management of p16+ Oropharyngeal Cancer.

Forensic science has revolutionized criminal investigations by integrating scientific methodologies to provide objective evidence, thereby enhancing the accuracy, efficiency, and reliability of justice systems worldwide. This comprehensive article delves into the historical evolution of forensic science, from ancient practices to modern innovations, and examines its multifaceted impacts on criminal investigations. Key positive contributions include improved suspect identification through DNA analysis, streamlined investigative processes via forensic intelligence, and the exoneration of wrongfully convicted individuals. However, challenges such as human error, bias, resource constraints, and the potential for misleading evidence leading to wrongful convictions are critically analyzed. Emerging technologies like next-generation sequencing, rapid DNA profiling, and artificial intelligence (AI) are highlighted for their transformative potential. The article also identifies significant research gaps, including the need for standardized validation protocols, addressing interdisciplinary disconnects, mitigating human factors in analysis, and ensuring sustainable development amid global disparities. Drawing from a wide array of scholarly sources, this review emphasizes the imperative for continued research to bolster forensic science's integrity and efficacy in supporting equitable criminal justice outcomes.

Abstract BACKGROUND Intraoperative profiling of CNS tumors remains challenging due to limitations in current diagnostic strategies. While intraoperative sequencing combined with epigenetic classification demonstrates high accuracy, existing workflows are time-consuming and labor-intensive. Here, we developed a high-speed intraoperative sequencing protocol that optimizes quality control (QC) steps without compromising data integrity and accelerates library preparation using transposase adapters. MATERIAL AND METHODS Our optimized workflow includes rapid DNA extraction using intraoperative sample size optimization, and real-time tissue lysis (chemical and mechanical), followed by DNA isolation and quantification using a Qubit fluorometer. Libraries were prepared using a rapid sequencing protocol with transposase adapters, replacing traditional ligation-based methods. Real-time data analysis incorporated AI-assisted base-calling and modification detection, which combined with tumor classification using a neural network-based algorithm trained for methylation profiling. A total of 144 patients were sequenced, including 8 runs using the rapid-UKER protocol and 15 runs with the ligation-based protocol. RESULTS The mean duration of the rapid-UKER protocol was 50.54 minutes (n=144 patients), with DNA isolation and quantification accounting for two-thirds of the time. Library preparation and sequencer loading were completed within 10 minutes in 87.5% of cases, compared to a mean of 28.5 minutes for the ligation-based method. Both protocols demonstrated comparable performance, achieving 92% correct tumor detection within 5 minutes of sequencing and accurate copy number variation (CNV) profiling within approximately 25 minutes. No significant differences in sequencing accuracy were observed between transposase and ligation-based adapters. CONCLUSION The rapid-UKER protocol enables accurate CNS tumor classification within 1 hour, significantly reducing library preparation time without compromising sequencing quality. Transposase adapters represent a robust and efficient alternative to traditional ligation-based workflows for intraoperative tumor profiling.

Quantum tunneling-based DNA sequencing promises to transform genomic analysis by improving long-read accuracy and enabling high-throughput sequencing, particularly the precise measurement of electrical conductance and tunneling current signatures associated with individual nucleotides. However, key obstacles remain in achieving swift and precise nucleotide identification, such as variation in molecular conductance, noise interference in tunneling current signals, and the complexity of overlapping signal patterns. Here, we employed a quantum transport approach combined with a supervised machine learning (ML) model to accurately classify DNA molecules based on their transmission, conductance, and current readouts, emphasizing their relevance for single-molecule DNA sequencing. This approach significantly resolves overlapping issues with nucleotide classification accuracy as high as 100, 98, and 97% using current, transmission, and conductance readouts, respectively. Sensitivity analysis reveals that current-voltage characteristics are the most effective parameters for distinguishing different nucleotides. Our findings offer a guide for ML mapping of transmission, conductance, and current readouts, enabling rapid and high-precision DNA sequencing.

Rapid DNA release from arthropod specimens using the STEP buffer for molecular diagnostics

BackgroundSchistosomiasis in Africa is an ongoing public health problem that is caused by two major human species, Schistosoma mansoni and S. haematobium, which often cause concurrent infections. Due to the global goal of controlling or eliminating schistosomiasis as a public health problem, the issue of diagnostic sensitivity has become more critical in the assessment of program success. In that regard, the World Health Organization (WHO) has drawn attention to the need for field-applicable tests with high specificity and sensitivity.MethodsTo address this, we have evaluated the amplification of S. mansoni and S. haematobium cell-free repeat DNA by loop-mediated isothermal amplification (LAMP) from field-collected filtered urine samples from 30 school children in Zambia. We have used four DNA extraction techniques (Qiagen and LAMP-PURE (LP): column-based DNA extraction technique, Chelex, and heating: rapid DNA extraction technique) to determine their impact on LAMP sensitivity and specificity, along with cost analysis and person-time involvement for each approach.ResultsBoth Qiagen and LP extraction detected positive infections, but Qiagen extraction is more cost-effective than LP. DNA extraction by LP is the fastest (average 20 min.) compared to the other three methods, although it is the most expensive, including amplification ($9.35 compared to $4.90 for heating extraction and amplification). Chelex extraction is slower and simpler than LP and detects 20% more positive infections than heating. Heating extraction is very fast, inexpensive, and simple to perform. However, LAMP amplification for heating-extracted samples resulted in false negatives, possibly indicating the presence of inhibitor(s).ConclusionsWe have demonstrated the sensitivity, cost-effectiveness, and time requirement of LAMP with four different DNA extraction approaches for the detection of two schistosome parasite species from a single field-collected urine sample.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12879-025-11370-y.

Time-course physiological and transcriptomic study reveals cadmium effects on antioxidant, apoptosis, and immunity in the kidney of the freshwater snail Pomacea canaliculata.

Amoxicillin-loaded chitosan coated magnetic nanocarriers as a dual-platform for anaerobic bacterial preconcentration and gene-sensing in periodontal pathogen detection.

The primary concerns of this paper are to analyze the procedural status of rapid DNA test results obtained in mobile and stationary DNA laboratories. It identifies the benefits and restrictions of such studies and determines whether the results comply with the requirements for adequacy, admissibility, credibility, and sufficiency of evidence. Additionally, it proposes ways to improve the legal regulation concerning the procedural form for applying specific expertise in this area. To achieve this goal, the author employs a range of general scientific and special legal methods, including induction, deduction, analysis, synthesis, comparison, prognostic, comparative legal, and formal logical. The paper explores the procedural status of rapid DNA test results obtained in both mobile and stationary DNA laboratories. The paper discusses the differences between mobile and stationary laboratories, identifies peculiarities in the collection and processing of biosamples, and outlines problematic aspects of admitting such results as evidence. Emphasis is placed on the relevance of utilizing mobile technologies under martial law in Ukraine and the need to improve the legal regulation of their use. The latest legislative changes and case law on evaluating rapid research were also carefully analyzed.

Gummy stem blight (GSB), caused by three Stagonosporopsis species, S. citrulli, S. cucurbitacearum and S. caricae, is one of the most economically important diseases hindering watermelon production worldwide. Since there is no commercial resistance to GSB in watermelon cultivars, its management depends on cultural practices and preventative fungicides. Therefore, efficient methods for the detection of Stagonosporopsis species that could aid management decisions are required. To help achieve this, a loop-mediated isothermal amplification (LAMP) assay specific to S. citrulli (SCIT850) was developed under two detection formats: fluorescence quantification and endpoint colorimetric detection. The SCIT850 assay was determined to be specific to its target species and exhibited a consistent sensitivity of 1 pg of genomic DNA under both formats. The assay can be combined with a previously reported LAMP assay for the collective detection of the three Stagonosporopsis spp. (STAGY), which have comparable sensitivity to SCIT850 and can aid in species discrimination. A field diagnostic system for GSB-causing Stagonosporopsis was developed by coupling the SCIT850 and STAGY assays to quick DNA extraction protocols. Two DNA extraction methods were tested: one from leaves using cellulose dipsticks, and one from steel rods (typical of spore traps) using Chelex100. With the dipstick method, we detected pathogen DNA in inoculated asymptomatic, mildly infected, and severely infected plants, while with the Chelex100 we detected pathogen DNA from rods infested with as few as 500 spores. The SCIT850 and STAGY assays coupled with these quick sample processing methods could be adapted for field deployment, which would allow growers to make efficient and timely management decisions based on detection of the actual Stagonosporopsis species present in the field.

Convective PCR (cPCR) offers rapid and efficient DNA amplification in as little as 10min, presenting a promising alternative to traditional PCR. However, current palm-sized cPCR devices fail to achieve one-pot visual detection, limiting their utility for point-of-care testing. Here, we present a visual convective PCR (Vis-cPCR) assay that integrates reverse transcription, ultra-fast cPCR, nested invasive reactions, and gold nanoparticle probes (AuNPs)-based colorimetric detection into a single-tube, one-pot system. This assay eliminates the need for time-consuming nucleic acid extraction and purification by employing a room-temperature chemical lysis step, which rapidly releases viral RNA from pharyngeal swabs in just 2min and is fully compatible with downstream detection. The palm-sized cPCR device enables the entire process-including reverse transcription, DNA amplification, amplicon identification, and visual signal generation-to be completed in approximately 30min. The Vis-cPCR assay demonstrates high sensitivity (as low as 10 copies) and specificity for detecting a panel of viruses, including SARS-CoV-2, influenza A/B, western equine encephalitis virus, tick-borne encephalitis virus, chikungunya virus, and Zika virus. Validation using 30 clinical pharyngeal swab samples and 42 artificially prepared arboviral RNA samples showed 100% agreement with RT-qPCR results. By combining rapid sample preparation, ultra-fast amplification, and visual detection, Vis-cPCR represents a significant advancement in point-of-care diagnostics, offering a simple, cost-effective, and highly efficient tool for on-site pathogen screening in resource-limited settings and emergency situations.

To further activate devices based on DNA nanotechnology, we introduce an approach that notably enhances both the speed and force of DNA powered machines and artificial hinge machine. A microheater, with millisecond response, heats or recools DNA origami constructs, hybridizing or dehybridizing sticky ends. Because anything within 20 micrometers of the heater equilibrates to a programmed temperature change in milliseconds, sticky ends of a compound DNA origami machine can open and close synchronously and operate cooperatively, in phase, additively increasing the drive force compared to single pair of sticky ends DNA machine (the six-helix bundle DNA origami hinge machine). In our demonstrations, we fold and unfold two square origami with 10 pairs of complementary sticky ends to drive a bead on the end of a rod like origami to speeds exceeding 30 micrometers per second. Our device envisions the creation of complex, synchronized DNA machines.

Objective: This research aims to transform Disaster Victim Identification (DVI) by integrating advanced forensic technologies, including AI-driven biometrics, portable DNA sequencing, and drone-assisted geospatial analysis, to enhance accuracy, speed, and scalability in mass casualty events. Research Gaps: Traditional DVI methods, which rely on manual processes such as fingerprinting and dental records, face challenges in scalability, time efficiency, and degraded remains identification, particularly in large-scale disasters. The existing literature lacks comprehensive frameworks that combine multi-modal forensic tools with real-time data integration, leaving gaps in operational synergy and adaptability to diverse disaster scenarios. Methodology: This study employs a mixed-methods approach, combining field simulations of disaster scenarios with laboratory-based forensic analysis. We developed a novel DVI framework integrating AI facial recognition, rapid DNA profiling, and drone-based thermal imaging for victim localization. Data from 500 simulated cases across varied disaster types (earthquakes, floods, and conflicts) were analyzed, incorporating machine learning algorithms to optimize identification accuracy. Interdisciplinary collaboration with forensic experts, disaster response teams, and technology developers ensured practical applicability. Results: The proposed framework achieved a 92% identification accuracy within 48 hours, a 60% improvement over conventional methods. AI-driven biometrics reduced identification time by 45%, while portable DNA sequencing proved effective for degraded remains. Drone integration enhanced victim localization by 70% in remote areas. These findings demonstrate a scalable, technology-driven DVI model, offering a robust solution for future disaster response.

Infectious diseases poses a growing public health challenge. The COVID-19 pandemic has further emphasized the urgent need for rapid, accessible diagnostics. This study presents the development of an integrated, flexible point-of-care (POC) diagnostic system for the rapid detection of Corynebacterium diphtheriae, the pathogen responsible for diphtheria. The system comprises a microfluidic polymerase chain reaction (micro-PCR) device and an electrochemical DNA biosensor, both fabricated on flexible substrates. The micro-PCR platform offers rapid DNA amplification overcoming the time limitations of conventional thermocyclers. The biosensor utilizes specific molecular recognition and an electrochemical transducer to detect the amplified DNA fragment, providing a clear and direct indication of the pathogen’s presence. The combined system demonstrates the effective amplification and detection of a gene fragment from a toxic strain of C. diphtheriae, chosen due to its increasing incidence. The design leverages lab-on-a-chip (LOC) and microfluidic technologies to minimize reagent use, reduce cost, and support portability. Key challenges in microsystem design—such as flow control, material selection, and reagent compatibility—were addressed through optimized fabrication techniques and system integration. This work highlights the feasibility of using flexible, integrated microfluidic and biosensor platforms for the rapid, on-site detection of infectious agents. The modular and scalable nature of the system suggests potential for adaptation to a wide range of pathogens, supporting broader applications in global health diagnostics. The approach provides a promising foundation for next-generation POC diagnostic tools.

Mycoplasma spp. contamination is a major concern in laboratories handling cell cultures, and routine detection methods are usually time-consuming, laborious and lack sensitivity. This study presents a streamlined workflow integrating rapid thermal DNA extraction (99°C-1min) with a SYBR Green-based qPCR for Mycoplasma detection. High-coverage primers targeting an 86-bp region of the 16S rDNA were designed using 109 Mycoplasma spp. sequences from GeneBank. In silico analysis confirmed full primer annealing to major cell culture contaminants (M. arginini, M. hominis, M. orale, and M. hyorhinis). Upon thermal lysis and qPCR optimization, the yield of the protocol was equivalent to that of phenol-chloroform extraction plus qPCR, with a detection limit of 64 bacterial cells. Finally, the performance of the protocol was confirmed in cell cultures with known Mycoplasma spp. contamination, accurately reproducing the contamination status. Thus, the developed protocol provides a simple, rapid, cost-effective, and sensitive method for monitoring Mycoplasma spp. in cell cultures.