Detection Of Deoxyribonucleic Acid Research Articles

A highly sensitivity electrochemistry biosensor for E. coli DNA detection based on hollow and porous dCuO@rGO composite

A highly sensitive DNA (deoxyribonucleic acid) sensor was prepared by using dCuO particles (derived from HKUST-1), electrochemical-reduced graphene oxide (rGO) and chitosan (CS) composite modified glassy carbon electrode (CS/dCuO@rGO/GCE). The morphology and nanostructure features of dCuO have been characterized with the HRTEM and SEM techniques. Electrochemical impedance spectroscopy characterisation (EIS) test showed that dCuO@rGO composite with a straight line which displaying the faster electron transfer rate compared to the Rct value obtained on dCuO (267 Ω) and rGO (47 Ω), this high conductivity was according with cyclic voltammetry (CV) results. It was ascribed to the octahedral hollow, porosity dCuO accelerated the electrolyte permeation capacity, and rGO with large surface area enhancing the electro-active site. Besides, the electro-reduction formed hybrid material of dCuO@rGO with well-synergetic effect significantly promoted the conductivity property. Of noteworthy, FT-IR spectroscopy indicating the retained carboxyl groups of dCuO, which could serve as functional arm-linker for capturing 5′-NH2 modified probe DNA (S1) to build the bio-sensing electrode (S1-CS/dCuO@rGO/GCE). Differential pulse voltammetry (DPV) characterization showed this manufactured biosensor with super-highly sensitivity for colitoxin DNA detection. The specific ssDNA sequences were detected in the concentration range from 0.001 to 37.5 pM with lower detection limit value of 3.89 × 10−1 fM (S/N = 3). This biosensor also showed well discrimination ability to the non-complementary and mismatched DNA sequences.

Highly selective detection of deoxyribonucleic acid in living cells using RecA-green fluorescent protein-single-stranded deoxyribonucleic acid filament fluorescence resonance energy transfer probe.

A fluorescence resonance energy transfer (FRET) method was developed for double-stranded deoxyribonucleic acid (dsDNA) detection in living cells using the RecA-GFP (green fluorescent protein) fusion protein filament. In brief, the thiol-modified single-stranded DNA (ssDNA) was attached to gold nanoparticles (AuNPs); on the contrary, the prepared RecA-GFP fusion protein interacted with ssDNA. Due to the FRET between AuNPs and RecA-GFP, fluorescence of RecA-GFP fusion protein was quenched. In the presence of homologous dsDNA, homologous recombination occurred to release RecA-GFP fusion protein. Thus, the fluorescence of RecA-GFP was recovered. The dsDNA concentration was detected using fluorescence intensity of RecA-GFP. Under optimal conditions, this method could detect dsDNA activity as low as 0.015 optical density (OD) Escherichia coli cells, with a wide linear range from 0.05 to 0.9 OD cells, and the regression equation was ΔF = 342.7c + 78.9, with a linear relationship coefficient of 0.9920. Therefore, it provided a promising approach for the selective detection of dsDNA in living cells for early clinical diagnosis of genetic diseases.

Eu-MOF-Based Fluorescent Ratiometric Sensor by Detecting 3,4,5-Trihydroxybenzoic for Fingerprint Visualization on Porous Objects

Latent fingerprints (LFPs) at the crime scene are served as important clues to locate the trajectory of criminal behavior and portray the characteristics of the suspect. Therefore, visualizing LFPs is of considerable significance. In this work, the europium metal-organic framework (Eu-MOF) sensor was successfully constructed for sensitive detection of gallic acid (3,4,5-trihydroxybenzoic acid, GA) and visualization of the sweat LFPs. The boric-acid-modified Eu-MOF was prepared by using the simple one-pot solvothermal method using Eu as the metal ion center and 3,5-dicarboxybenzeneboronic acid (BBDC) as the organic ligand. The sensor showed desirable photoluminescent performance through the chelating of BBDC with Eu3+. The sensor exhibited the satisfactory linear relationship to GA in the range of 1 nM to 20 nM with a low detection limit of 0.34 nM under the optimized conditions. The prepared sensor with ideal selectivity to GA was successfully applied for visualizing LFPs on porous substrates with the high contrast and superior stability. Given the good performance of the sensor, all fingerprint images obtained from 1 200 samples presented clear friction ridges and met the identification criteria. Notably, the sensor had less impact on the subsequent deoxyribonucleic acid (DNA) detection, displaying a promising perspective for applications in extracting physical evidence of site investigation.

Intra- and interlaboratory reproducibility of the RIATOL qPCR HPV genotyping assay.

The implementation of cervical screening based on human papillomavirus (HPV) continues to progress rapidly across countries. Evidence has shown that assays detecting high-risk human papillomavirus (hrHPV) deoxyribonucleic acid (DNA) are more effective than cytology-based screening. Validation of new hrHPV DNA assays requires both noninferior clinical accuracy compared to a standard comparator for cervical precancer and good reproducibility. This study builds upon previous diagnostic accuracy assessments of the RIATOL HPV genotyping qPCR assay and aims to evaluate the international validation criteria for reproducibility. The intra- and interreproducibility of the RIATOL-qPCR assay were assessed using 550 remnant cervical cell material from the cytology archive of the National Reference Center for HPV in Belgium. Specimens were collected in the context of cervical cancer screening and tested in two different laboratories. The international reproducibility criteria include the lower bound of 95% confidence interval of the intra- and interlaboratory agreement regarding the detection of hrHPV DNA exceeding 87% with kappa ≥0.50. The RIATOL-qPCR assay demonstrated excellent intralaboratory reproducibility, achieving an overall agreement of 98.2 (95% CI 96.6-99.1%) and a kappa of 0.96. Interlaboratory testing showed an overall agreement of 98.5 (95% CI 97.1-99.4%) with a kappa of 0.97. The RIATOL-qPCR assay fulfills the third criterion for HPV test reproducibility requirement for use in cervical cancer screening.

CMOS Capacitive Sensor for DNA Detection in Undiluted Ionic Solution

Capacitive detection of affinity-bound biomolecules enables rapid and label-free bioassays suitable for point-of-care diagnostic applications. However, direct detection at high ionic strengths is severely limited by the Debye charge-screening effect of the electric double layer on the sensor surface, leading most studies to be performed at diluted ionic strengths. In this study, probe-target deoxyribonucleic acid (DNA) hybridization was successfully measured by modulating the electric field of the interdigitated sensing electrodes to reduce charge screening. The developed 8 × 8 complementary metal oxide semiconductor (CMOS) capacitive sensor array exhibited a sensitivity of 150 fF/log10[DNA] measured at 15 MHz from 10 aM to 100 pM with a response time of approximately 400 seconds. The array also exhibited a pH sensitivity of 354 fF/pH.

Enhanced detection sensitivity of Leptospira DNA using a post-deposition annealed carbon quantum dots integrated tapered optical fiber biosensor

Leptospirosis is an illness caused by a Leptospira bacterial infection, and it can be fatal if not correctly diagnosed and treated. This work explores the development of an optical biosensor that utilizes tapered optical fiber integrated with post-deposition annealed carbon quantum dots (CQDs) to improve Leptospira deoxyribonucleic acid (DNA) detection. A standard optical single-mode fiber was tapered before being deposited with CQDs. The surface properties of CQDs on the tapered optical fiber were then tuned using a simple, one-step annealing process. Leptospira probe DNA was covalently bonded to the annealed CQDs surface using several commercially available linkers. The detection was achieved through probe DNA fragments that were hybridized into different concentrations of complementary target DNA. The biosensor limit of detection remained at 1.0 fM, but a better sensitivity of 2.321 ± 0.048 nm/nM was obtained. The affinity towards Leptospira complementary DNA improved as the equilibrium dissociation constant value was lowered to 0.15 х 10−9 M compared to previous studies. In non-complementary DNA reactions, a minimal wavelength shift is detected, indicating the biosensor's high specificity, whereas studies using genomic DNAs from Leptospira and Clostridium difficile (as a control for genomic DNA) revealed similar observation. The integration of CQDs has achieved these remarkable biosensor traits, which hold great potential for developing a reliable leptospirosis diagnosis.

Pre-analytical Associated Factors of Foreign DNA Detection Beneath Deceased’s Fingernails

Objective: To assess the pre-analytical factors including hand-side, representative collection technique and individual forensic physician for foreign deoxyribonucleic acid (DNA) detection in specimen collected from deceased’s fingernails. Material and Methods: This cross-sectional study, of an initial 164 samples from the fingernails of both hands, of 82 deceased caseworks; from 2010 to 2018, at the Forensic Unit, Faculty of Medicine, Prince of Songkla University. The autosomal short tandem repeats profile fingernail DNA results, pre-analytical factors, and the deceased’s characteristics were obtained from the records. The fingernail DNA outcomes were evaluated and ranked into five groups, i.e., high-level profile, low-level profile, or residual profile; if foreign alleles of more than 11 alleles, 4 to 11 alleles, or less than 4 alleles were detected, respectively. The non-specific profile group consisted of foreign DNA being detected; however the peak signals were below the decisional threshold. The unidentified group consisted of no foreign DNA being detected. The full model underwent both directional stepwise model selection, and the resulting model with the lowest Akaike information criterion was selected as the final model. The final model was analyzed by ordinal logistic regression for significant associated factors: at a 95% confidence level. Results: The representative collection technique is an associated factor, via the use of fingernail swabs (adjusted odds ratio (ORa)=13.44, 95% confidence interval (CI)=2.89–62.45), and had a larger effect size than using fingernail cuttings (ORa=6.84, 95% CI=1.47–31.86). Conclusion: At post-mortem examination, for the collection of foreign DNA from fingernails, the use of fingernail swabs, as a collection technique, is of particular interest.

Zoophilic dermatophytes during coronavirus pandemic in Germany

During the coronavirus pandemic, significantly more pets were probably bought and kept. This study focuses on whether more zoophilic dermatophytes have subsequently been isolated and which species predominate. In the 1‑year period from March 2020 through February 2021, all zoophilic dermatophytes from all submissions to the Mölbis laboratory were recorded. Both the cultural and the molecular evidence of fungal detection from skin scrapings, hair roots, and, in single cases, from nails, were considered. For dermatophyte DNA(Deoxyribonucleic acid) detection, an in-house polymerase chain reaction (PCR)- enzyme-linked immunosorbent assay (ELISA) was used. In distinct cases, identification of dermatophytes was confirmed by sequencing of the internal transcribed spacer (ITS) region of the rDNA, and of the gene of the translation elongation factor (TEF)-1α. In 579 (2.56%) of 22,575 samples studied in the year 2020/2021, zoophilic dermatophytes were detectable with PCR-ELISA and/or by cultivation. In comparison, the proportion of zoophilic dermatophytes was 2.03% in the 1‑year period 2014/2015, and only 1.6% in 2018/2019. The 579 zoophilic dermatophytes were identified as follows: Trichophyton(T.) benhamiae 186 (32.1%), T.mentagrophytes 173 (29.9%), T.quinckeanum 110 (19.0%), Microsporum(M.) canis 78(13.5%), T.verrucosum 22(3.8%), Nannizzia(N.) persicolor 8(1.4%), T.erinacei 1(0.2%), and T.equinum 1(0.2%). T.benhamiae had the highest prevalence from June to September 2020, then again in December. T.quinckeanum is associated with asharp increase in the mice population in Germany in 2020; asignificant increase was found in the months September 2020 to January 2021. T.mentagrophytes had aconspicuous peak in September. Compered with that M. canis in November. Up to 50% of the dermatophytoses caused by T.mentagrophytes, T.quinckeanum, and M.canis affected children and adolescents, while in the case of T.benhamiae it was as much as two thirds. Tinea corporis was the most common, followed by tinea faciei and tinea capitis. M.canis infections affected the capillitium more frequently than the face. Zoophilic dermatophytes were increasingly isolated during the coronavirus pandemic in Germany when compared to previous year periods. In first place, the dermatophyte T.benhamiae from guinea pigs was found in children and adolescents. Asignificant proportion of dermatophytoses concerned adults. T.quinckeanum is an emerging pathogen in Germany with unprecedented high infection rates in 2020.

Nucleotide detection mechanism and comparison based on low-dimensional materials: A review.

The recent pandemic has led to the fabrication of new nucleic acid sensors that can detect infinitesimal limits immediately and effectively. Therefore, various techniques have been demonstrated using low-dimensional materials that exhibit ultrahigh detection and accuracy. Numerous detection approaches have been reported, and new methods for impulse sensing are being explored. All ongoing research converges at one unique point, that is, an impetus: the enhanced limit of detection of sensors. There are several reviews on the detection of viruses and other proteins related to disease control point of care; however, to the best of our knowledge, none summarizes the various nucleotide sensors and describes their limits of detection and mechanisms. To understand the far-reaching impact of this discipline, we briefly discussed conventional and nanomaterial-based sensors, and then proposed the feature prospects of these devices. Two types of sensing mechanisms were further divided into their sub-branches: polymerase chain reaction and photospectrometric-based sensors. The nanomaterial-based sensor was further subdivided into optical and electrical sensors. The optical sensors included fluorescence (FL), surface plasmon resonance (SPR), colorimetric, and surface-enhanced Raman scattering (SERS), while electrical sensors included electrochemical luminescence (ECL), microfluidic chip, and field-effect transistor (FET). A synopsis of sensing materials, mechanisms, detection limits, and ranges has been provided. The sensing mechanism and materials used were discussed for each category in terms of length, collectively forming a fusing platform to highlight the ultrahigh detection technique of nucleotide sensors. We discussed potential trends in improving the fabrication of nucleotide nanosensors based on low-dimensional materials. In this area, particular aspects, including sensitivity, detection mechanism, stability, and challenges, were addressed. The optimization of the sensing performance and selection of the best sensor were concluded. Recent trends in the atomic-scale simulation of the development of Deoxyribonucleic acid (DNA) sensors using 2D materials were highlighted. A critical overview of the challenges and opportunities of deoxyribonucleic acid sensors was explored, and progress made in deoxyribonucleic acid detection over the past decade with a family of deoxyribonucleic acid sensors was described. Areas in which further research is needed were included in the future scope.

Characterization of Rare Spontaneous Human Immunodeficiency Virus Viral Controllers Attending a National United Kingdom Clinical Service Using a Combination of Serology and Molecular Diagnostic Assays.

We report outcomes and novel characterization of a unique cohort of 42 individuals with persistently indeterminate human immunodeficiency virus (HIV) status, the majority of whom are HIV viral controllers. Eligible individuals had indeterminate or positive HIV serology, but persistently undetectable HIV ribonucleic acid (RNA) by commercial assays and were not taking antiretroviral therapy (ART). Routine investigations included HIV Western blot, HIV viral load, qualitative HIV-1 deoxyribonucleic acid (DNA), coinfection screen, and T-cell quantification. Research assays included T-cell activation, ART measurement, single-copy assays detecting HIV-1 RNA and DNA, and plasma cytokine quantification. Human immunodeficiency virus seropositivity was defined as ≥3 bands on Western blot; molecular positivity was defined as detection of HIV RNA or DNA. Human immunodeficiency virus infection was excluded in 10 of 42 referrals, remained unconfirmed in 2 of 42, and was confirmed in 30 of 42, who were identified as HIV elite controllers (ECs), normal CD4 T-cell counts (median 820/mL, range 805-1336), and normal CD4/CD8 ratio (median 1.8, range 1.2-1.9). Elite controllers had a median duration of elite control of 6 years (interquartile range = 4-14). Antiretroviral therapy was undetected in all 23 subjects tested. Two distinct categories of ECs were identified: molecular positive (n = 20) and molecular negative (n = 10). Human immunodeficiency virus status was resolved for 95% of referrals with the majority diagnosed as EC. The clinical significance of the 2 molecular categories among ECs requires further investigation.

Assessment of the Association of Chlamydia e pneumoniae Infection with Lung Cancer in a Moroccan Patients' Cohort.

Chlamydia pneumoniae (C. pneumoniae) is a respiratory pathogen associated with chronic inflammatory and its detection in human lung cancer suggests its involvement in cancerogenesis. Our study aimed to evaluate the association between C. pneumoniae infection and Lung Cancer disease in Moroccans patients and control cohorts, through a molecular investigation. The study comprised 42 lung cancer patients and 43 healthy controls. All participants provided demographics, Clinical, and Toxic behaviors datas, and a peripheral blood sample for testing, a Nested Polymerase Chain Reaction (PCR) was performed for C. pneumoniae Deoxyribonucleic acid (DNA) detection. Statistical analysis was performed using IBM®SPSS®software. Positive Nested PCR results for cases and controls were respectively 33.3% and 4.7%, there by significant difference between cases and controls infection was identified (p <0.05). Data analysis also showed that tobacco could act synergically with C. pneumoniae infection as a risk factor of lung cancer. In fact a significant difference between patients and controls was shown for tobacco and alcohol use (p < 0.05). C. pneumoniae infection is potentially associated with primary Lung cancer in the Moroccan population and has combined effects with Tabaco consumption.

Locus-Specific Detection of DNA Methylation: The Advance, Challenge, and Perspective of CRISPR-Cas Assisted Biosensors.

Deoxyribonucleic acid (DNA) methylation is one of the epigenetic characteristics that result in heritable and revisable phenotype changes but without sequence changes in DNA. Aberrant methylation occurring at a specific locuswasreported to be associated with cancers, insulin resistance, obesity, Alzheimer's disease, Parkinson's disease, etc. Therefore, locus-specific DNA methylation can serve as a valuable biomarker for disease diagnosis and therapy. Recently, Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas systems are applied to develop biosensors for DNA, ribonucleic acid, proteins, and small molecules detection. Because of their highly specific binding ability and signal amplification capacity, CRISPR-Cas assisted biosensor also serve as a potential tool for locus-specific detection of DNA methylation. In this perspective, based on the detection principle, a detailed classification and comprehensive discussion of recent works about the latest advances in locus-specific detection of DNA methylation using CRISPR-Cas systems are provided. Furthermore, current challenges and future perspectives of CRISPR-based locus-specific detection of DNA methylation are outlined.

Seroprevalence and Molecular Detection of Symptomatic and Asymptomatic Genital Herpes Simplex Virus 2 among HIV Positive Patients: A Cross-sectional Study

Introduction: Genital Herpes Simplex Virus (HSV) infection is the most common infection in Acquired Immunodeficiency Syndrome (AIDS) patients, occurring in 60-90% according to World Health Organisation (WHO) reports. Early detection of HSV-2 infection, the introduction of chemotherapy, and prophylaxis improve the lifespan of AIDS patients. Aim: To detect the HSV-2 seroprevalence that is Immunoglobulin G (IgG) and Immunoglobulin M (IgM) antibodies in Human Immunodeficiency Virus (HIV) positive serum and molecular detection of HSV-2 Deoxyribonucleic Acid (DNA) in symptomatic HSV-2 Patients. Materials and Methods: The descriptive cross-sectional study was conducted in the Guntur Government Hospital with the help of the Antiretroviral Therapy (ART) Centre and Department of Dermatology, Venereology and Leprosy (DVL) in GGH, Guntur, Andhra Pradesh, India. A total of 100 blood samples from HIV positive individuals were collected and for those with symptoms on the external genitalia, a biopsy specimen from the ulcer and fluid from vesicles were taken. All the cases in the study group are on ART and without any antiviral treatment. A blood sample was collected for IgG (Calbiotech kit), IgM detection (Merilisa kit), and biopsy from genital ulcer for gene detection by realtime Polymerase Chain Reaction (PCR) (HELINI Biomolecules, Chennai). Statistical analysis was done by mean and percentages with p-value by calculating Chi-square test, Fisher’s-Exact test to know significance of association between HSV-2 and HIV. Results: Among the total 100 HIV positive patients, it was observed that IgG seroprevalence of HSV-2 in HIV positive individuals is 78%, while it is 19% for IgM. In the present study, 19 symptomatic cases showed DNA of HSV-2 in PCR, out of which, 17 were from genital ulcers and two from vesicle fluid. Conclusion: As HSV-2 is a lifelong infection, serological testing provides the best method, to estimate its prevalence even in asymptomatic individuals.

Detection of Human Papillomavirus among Cervical Cancer Patients by Qualitative Polymerase Chain Reaction on Formalin- fixed, Paraffin-embedded Tissue: A Retrospective Observational Analysis

Introduction: Cervical cancer is second most commonly diagnosed and third most common cause for cancer death among women in the developing countries. It is now-established that Human Papillomavirus (HPV) infection is responsible for pathogenesis of cervical cancer. HPV Deoxyribonucleic Acid (DNA) detection is generally done on cytology specimens to triage women undergoing cervical cancer screening, but testing of Formalin-fixed, Paraffin- embedded tissue (FFPE) is not yet widely used. Aim: To study the detection of HPV by Qualitative PCR by extraction of DNA from FFPE. Materials and Methods: This retrospective observational analysis was carried out at Department of Pathology, Armed Forces Medical College, Pune, Maharashtra, India, managed at the centre from 2008 to 2015. The data analysis was done Aug 2013-Oct 2015 on 35 patients of cervical cancer which were reconfirmed by histopatholgical study of sections. Tissue blocks were obtained from the selected subjects and 3-5 micron sections were taken and prepared for Haematoxylin and Eosin (H&amp;E) staining. Qualitative PCR was run on DNA extracted from FFPE tissue for evaluation of HPV. The amplified DNA varied between 230-270 base pairs (bp) and was analysed for oncogenic HPV type 16, 18, 31, 33, 35, 45, 52b and 58 by gel electrophoresis. Data was tabulated in Microsoft excel and mean, frequency and percentages were calculated. Pearson’s Chi-square test was used to calculate the significance. Results: Out of the total 35 samples analysed (mean age: 51.08±10.6 years),15 cases were large cell non keratinising carcinoma, 12 cases of keratinising squamous cell carcinoma, 5 cases of carcinoma in-situ and 3 cases were adenocarcinoma. A total of 13 cases out of 35 showed the bands of HPV genomes, indicating either of the HPV strain. Conclusion: Although molecular diagnostics on FFPE tissue is need of hour, stringent protocols for timing of fixation, technical expertise for extraction of DNA or Ribonucleic Acid (RNA), careful handling of the sample and quality control is of paramount importance. Fragmentation is a problem in DNA extracted from FFPE tissue, so primers having small base pairs should be used to maximise the yield.

The Structural Profile of HPV 18 in Terms of Chromosomal and Nuclear Degenerative Changes and the Ratio of Nucleus/Cytoplasm on Liquid based Cervical Cells.

HPV 18 is one of the important oncogenic types. HPV 18 is generally evaluated together with HPV 16 and/or high-risk HPV types in light microscopic studies. The purpose of this study was to evaluate the impact of only HPV 18 on the nucleus/cytoplasm ratio, and chromosomal and nuclear degenerative changes in liquid-based samples. Eighty liquid-based cervical samples were used in this retrospective study. These smears were prepared by HPV Deoxyribonucleic Acid (DNA) detection and genotyping with the Cobas 4800 HPV system. Forty HPV 18 infected and forty smears with no infection agent were evaluated for chromosomal (nuclear budding, micronuclei), nuclear degenerative changes (membrane irregularity, nuclear enlargement, hyperchromasia, abnormal chromatin distribution, binucleation (BN), karyorrhexis (KR), karyolysis (KL), karyopyknosis (KP)), and cytologic findings (koilocyte (KC), cells with perinuclear PR) using light microscopy. Cellular diameters were evaluated using image analysis software. Statistical analysis was performed with Statistical Package for Social Sciences (SPSS) 19.0. p values < .05 were considered significant. The statistically significant difference between the presence of HPV 18 and karyorrectic cell, KC, nuclear membrane irregularity, enlargement, the mean nuclear width and height (p < 0.05). No cellular changes other than those mentioned were observed. The present study is significant in that, it reveals the relationship between only and particularly HPV 18 and nucleus/cytoplasm ratio, and chromosomal and nuclear degenerative changes in liquid-based cytology. HPV 18 affects KR, koilocytosis, nuclear membrane irregularity, enlargement, and nuclear diameters. Light microscopic analysis of these abnormalities increases the sensitivity and specificity of cytology in the evaluation of cellular pictures due to HPV 18.

Label-free DNA quantification using isothermal amplification on an exposed core optical fiber microfluidic platform.

Isothermal amplification technology has triggered a surge in research due to its compatibility with small and portable equipment, simplicity, and high efficiency, especially in light of the COVID-19 pandemic where reliable widescale testing is critical to outbreak management. In this paper, a label-free isothermal deoxyribonucleic acid (DNA) amplification method based on refractive index (RI) quantification is proposed and demonstrated for the first time by combining optical fiber sensing, microfluidics, and isothermal amplification. A highly RI-sensitive Mach-Zehnder (MZ) interference is formed by splicing a short length of an exposed-core fiber between two lengths of a single-mode fiber while the microfluidic liquid channel on the exposed side of the ECF is filled with target DNA and the amplification solution. Real-time quantitative measurement of the target DNA is then realized by monitoring the change in RI of the solution during the isothermal DNA amplification process. The experimental results show that the platform successfully realizes real-time label-free monitoring of isothermal amplification of 0.16 aM DNA samples. This method is a breakthrough for applications in the fields of DNA detection and quantification where simple operation, rapid detection, portability, small size, high selectivity, and high sensitivity are required.

Detection and Absolute Quantification Porcine DNA in Sausages Using Quantitative Polymerase Chain Reaction (qPCR) Method

Identification of adulteration of processed meat products with unwanted ingredients is a crucial issue. These meat products are prone to forgery and mix with porcine. Meat source authentication is important for Muslim consumers to whom comsumption of products containing pork and its derivatives in an products is prohibited. This present study aims at development of detection and quantification method of porcine DNA (Deoxyribo Nucleic Acid) in processed meat products, sausages. Two novel primer pairs were designed specifically targeting fragment of Displacement Loop (D-Loop) and cytochrome b (cyt b) of porcine mitochondrial DNA and to generate 139 bp and 143 bp amplicons, respectively. Detection and quantification were accomplished by Quantitative Polymerase Chain Reaction (qPCR). Porcine DNA standard curves and cycle threshold were used for quantification. The detection limit of porcine DNA was as little as 0.05 pg. Of all sausages tested (n=13), four of them contained porcine DNA as much 3.1 pg; 0.160 pg; 0.294 pg; and 0.110 pg in 0.001 mg of sausages for J, G, I, and L samples respectively. The specific qPCR assay method can be used for the detection of porcine DNA in minute amounts, which can be used for the halal authentication of food and pharmaceutical products.

Single Particle Inductively Coupled Plasma Mass Spectrometry-Based Homogeneous Detection of HBV DNA with Rolling Circle Amplification-Induced Gold Nanoparticle Agglomeration.

A highly sensitive and simple method based on rolling circle amplification (RCA) and single particle inductively coupled plasma mass spectrometry (spICP-MS) was proposed for the homogeneous detection of hepatitis B virus (HBV) deoxyribonucleic acid (DNA). In the presence of target DNA, long ssDNA possessing a large number of repeating sequence units was generated by RCA. DNA-labeled AuNP probes assembled into long chains based on complementary base pairing, further aggregating into large particles. Small Au NPs hardly produced pulse signals in spICP-MS; obvious pulse signals appeared in spICP-MS after the agglomeration of Au NPs caused by the addition of RCA products and spermidine. On the basis of this, the homogeneous detection of target DNA was realized by spICP-MS with high sensitivity. Under optimal conditions, the proposed method exhibited a good linear relationship between the frequency of the pulse signal of Au in spICP-MS and the concentration of target HBV DNA in the range of 10-2000 fmol L-1 (R = 0.997), the limit of detection was 5.1 fmol L-1, and the relative standard deviation was 3.7-6.8%. Recoveries of 94.2-108% were obtained for target DNA in spiked serum samples, demonstrating a good matrix tolerance ability for the method.

The diagnostic accuracy of TCT + HPV-DNA for cervical cancer: systematic review and meta-analysis.

BackgroundThis study sought to systematically analyze the clinical diagnostic value of tumor markers combined with ThinPrep cytologic test (TCT) and human papillomavirus (HPV) deoxyribonucleic acid (DNA) detection for cervical cancer and pre-cancerous lesions. However, there is a lot of controversy in the field of TCT + HPV-DNA. Many people have mixed opinions on the accuracy of TCT + HPV-DNA, and there is no unified opinion. Therefore, it is necessary to further confirm the significance of this combined detection method in the early diagnosis of cervical cancer by applying meta method.MethodsThe Cochrane Library, PubMed, Web of Science, Embase, Chinese Biomedical Literature Database (CBM) databases were searched to retrieve studies. To assess the methodological quality of each study and potential risk of bias, QUADAS-2 Guidelines were used to evaluate the quality of all articles that met the inclusion criteria and data extraction of the included articles were performed, and a meta-analysis was performed of the included studies using Review Manager 5.2 software.ResultsA total of 5 studies were included in the study, and a total of 2,778 patients were included in the study, and there was no significant publication bias observed. The meta-analysis showed that there was a statistical difference in terms of the accuracy of the tumor markers combined with TCT in the detection of cervical cancer. The results were as follows: the pooled sensitivity (SEN) was 0.86 (95% CI: 0.75–0.93); the combined specificity (SPE) was 0.79 (95% CI: 0.57–0.92); the diagnostic performance of combined with thin-layer liquid-based cytology and HPV DNA detection in the diagnosis accuracy of cervical cancer by summary receiver operating characteristic (SROC) curve analysis, result showed excellent diagnostic accuracy, with a combined area under the curve (AUC) of 0.90 (95% CI: 0.87–0.92).DiscussionTumor markers are important for the early diagnosis of cervical cancer. Combining the tumor markers with TCT and HPV DNA detection effectively improved the detection rate.

Theoretical simulation of DNA hybridization based on cascaded plasmonic V-shaped channel biosensor

A compact biosensor based on specially designed Cascaded V-shaped Channels (CVSChs) for the analysis and detection of Deoxyribonucleic Acid (DNA) hybridization is presented in this paper. The proposed biosensor employs a Gold (Au) nanowire in then CVSChs sensing region and provides more flexibility as far as tailoring the detection range and sensitivity as compared to the single V-shaped channel (VSC). It has been numerically demonstrated that the detection sensitivity of DNA hybridization is significantly dependent on the number of the V shaped channels. A two – dimensional Finite Difference Time Domain (FDTD) analysis with Perfectly Matched Layers (PMLs) is employed to evaluate the sensor performance with different structural parameters. Simulation results indicate that the proposed biosensor can achieve a high sensitivity of 2541 nm / RIU by optimizing the structural parameters. We demonstrate a proof-of-concept hybrid biosensor by monitoring the resonance shift due to the hybridization event. The proposed biosensor will have great impact on early stage detection of infected cells.