Displaying publications 1 - 20 of 81 in total

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  1. Fulltext Ruthenium(II) Polypyridyl Complexes as FRET Donors: Structure- and Sequence-Selective DNA-Binding and Anticancer Properties
    Elgar CE, Yusoh NA, Tiley PR, Kolozsvári N, Bennett LG, Gamble A, et al.
    J Am Chem Soc, 2023 Jan 18;145(2):1236-1246.
    PMID: 36607895 DOI: 10.1021/jacs.2c11111
    Ruthenium(II) polypyridyl complexes (RPCs) that emit from metal-to-ligand charge transfer (MLCT) states have been developed as DNA probes and are being examined as potential anticancer agents. Here, we report that MLCT-emissive RPCs that bind DNA undergo Förster resonance energy transfer (FRET) with Cy5.5-labeled DNA, forming mega-Stokes shift FRET pairs. Based on this discovery, we developed a simple and rapid FRET binding assay to examine DNA-binding interactions of RPCs with diverse photophysical properties, including non-"light switch" complexes [Ru(dppz)2(5,5'dmb)]2+ and [Ru(PIP)2(5,5'dmb)]2+ (dppz = dipyridophenazine, 5,5'dmb = 5,5'-dimethyl-2,2'-bipyridine, PIP = 2-phenyl-imidazo[4,5-f][1,10]phenanthroline). Binding affinities toward duplex, G-quadruplex, three-way junction, and mismatch DNA were determined, and derived FRET donor-acceptor proximities provide information on potential binding sites. Molecules characterized by this method demonstrate encouraging anticancer properties, including synergy with the PARP inhibitor Olaparib, and mechanistic studies indicate that [Ru(PIP)2(5,5'dmb)]2+ acts to block DNA replication fork progression.
    Matched MeSH terms: DNA/chemistry
  2. Fulltext Chemical reaction of soybean flavonoids with DNA: a computational study using the implicit solvent model
    Abdallah HH, Mavri J, Repič M, Lee VS, Wahab HA
    Int J Mol Sci, 2012;13(2):1269-83.
    PMID: 22408390 DOI: 10.3390/ijms13021269
    Genistein, daidzein, glycitein and quercetin are flavonoids present in soybean and other vegetables in high amounts. These flavonoids can be metabolically converted to more active forms, which may react with guanine in the DNA to form complexes and can lead to DNA depurination. We assumed two ultimate carcinogen forms of each of these flavonoids, diol epoxide form and diketone form. Density functional theory (DFT) and Hartree-Fock (HF) methods were used to study the reaction thermodynamics between active forms of flavonoids and DNA guanine. Solvent reaction field method of Tomasi and co-workers and the Langevin dipoles method of Florian and Warshel were used to calculate the hydration free energies. Activation free energy for each reaction was estimated using the linear free energy relation. Our calculations show that diol epoxide forms of flavonoids are more reactive than the corresponding diketone forms and are hence more likely flavonoid ultimate carcinogens. Genistein, daidzein and glycitein show comparable reactivity while quercetin is less reactive toward DNA.
    Matched MeSH terms: DNA/chemistry*
  3. Fulltext Electronic Properties of DNA-Based Schottky Barrier Diodes in Response to Alpha Particles
    Al-Ta'ii HM, Periasamy V, Amin YM
    Sensors (Basel), 2015;15(5):11836-53.
    PMID: 26007733 DOI: 10.3390/s150511836
    Detection of nuclear radiation such as alpha particles has become an important field of research in recent history due to nuclear threats and accidents. In this context; deoxyribonucleic acid (DNA) acting as an organic semiconducting material could be utilized in a metal/semiconductor Schottky junction for detecting alpha particles. In this work we demonstrate for the first time the effect of alpha irradiation on an Al/DNA/p-Si/Al Schottky diode by investigating its current-voltage characteristics. The diodes were exposed for different periods (0-20 min) of irradiation. Various diode parameters such as ideality factor, barrier height, series resistance, Richardson constant and saturation current were then determined using conventional, Cheung and Cheung's and Norde methods. Generally, ideality factor or n values were observed to be greater than unity, which indicates the influence of some other current transport mechanism besides thermionic processes. Results indicated ideality factor variation between 9.97 and 9.57 for irradiation times between the ranges 0 to 20 min. Increase in the series resistance with increase in irradiation time was also observed when calculated using conventional and Cheung and Cheung's methods. These responses demonstrate that changes in the electrical characteristics of the metal-semiconductor-metal diode could be further utilized as sensing elements to detect alpha particles.
    Matched MeSH terms: DNA/chemistry*
  4. Protein adaptors assemble functional proteins on DNA scaffolds
    Ngo TA, Dinh H, Nguyen TM, Liew FF, Nakata E, Morii T
    Chem Commun (Camb), 2019 Oct 15;55(83):12428-12446.
    PMID: 31576822 DOI: 10.1039/c9cc04661e
    DNA is an attractive molecular building block to construct nanoscale structures for a variety of applications. In addition to their structure and function, modification the DNA nanostructures by other molecules opens almost unlimited possibilities for producing functional DNA-based architectures. Among the molecules to functionalize DNA nanostructures, proteins are one of the most attractive candidates due to their vast functional variations. DNA nanostructures loaded with various types of proteins hold promise for applications in the life and material sciences. When loading proteins of interest on DNA nanostructures, the nanostructures by themselves act as scaffolds to specifically control the location and number of protein molecules. The methods to arrange proteins of interest on DNA scaffolds at high yields while retaining their activity are still the most demanding task in constructing usable protein-modified DNA nanostructures. Here, we provide an overview of the existing methods applied for assembling proteins of interest on DNA scaffolds. The assembling methods were categorized into two main classes, noncovalent and covalent conjugation, with both showing pros and cons. The recent advance of DNA-binding adaptor mediated assembly of proteins on the DNA scaffolds is highlighted and discussed in connection with the future perspectives of protein assembled DNA nanoarchitectures.
    Matched MeSH terms: DNA/chemistry
  5. Silver(I)-mediated base pairing in parallel-stranded DNA involving the luminescent cytosine analog 1,3-diaza-2-oxophenoxazine
    Schönrath I, Tsvetkov VB, Zatsepin TS, Aralov AV, Müller J
    J Biol Inorg Chem, 2019 08;24(5):693-702.
    PMID: 31263954 DOI: 10.1007/s00775-019-01682-1
    1,3-Diaza-2-oxophenoxazine (X) has been introduced as a ligand in silver(I)-mediated base pairing in a parallel DNA duplex. This fluorescent cytosine analog is capable of forming stabilizing X-Ag(I)-X and X-Ag(I)-C base pairs in DNA duplexes, as confirmed by temperature-dependent UV spectroscopy and luminescence spectroscopy. DFT calculations of the silver(I)-mediated base pairs suggest the presence of a synergistic hydrogen bond. Molecular dynamics (MD) simulations of entire DNA duplexes nicely underline the geometrical flexibility of these base pairs, with the synergistic hydrogen bond facing either the major or the minor groove. Upon silver(I) binding to the X:X or X:C base pairs, the luminescence emission maximum experiences a red shift from 448 to 460 nm upon excitation at 370 nm. Importantly, the luminescence of the 1,3-diaza-2-oxophenoxazine ligand is not quenched significantly upon binding a silver(I) ion. In fact, the luminescence intensity even increases upon formation of a X-Ag(I)-C base pair, which is expected to be beneficial for the development of biosensors. As a consequence, the silver(I)-mediated phenoxazinone base pairs represent the first strongly fluorescent metal-mediated base pairs.
    Matched MeSH terms: DNA/chemistry*
  6. Fulltext Engineering artificial machines from designable DNA materials for biomedical applications
    Qi H, Huang G, Han Y, Zhang X, Li Y, Pingguan-Murphy B, et al.
    Tissue Eng Part B Rev, 2015 Jun;21(3):288-97.
    PMID: 25547514 DOI: 10.1089/ten.TEB.2014.0494
    Deoxyribonucleic acid (DNA) emerges as building bricks for the fabrication of nanostructure with complete artificial architecture and geometry. The amazing ability of DNA in building two- and three-dimensional structures raises the possibility of developing smart nanomachines with versatile controllability for various applications. Here, we overviewed the recent progresses in engineering DNA machines for specific bioengineering and biomedical applications.
    Matched MeSH terms: DNA/chemistry*
  7. Fulltext DNA tetrominoes: the construction of DNA nanostructures using self-organised heterogeneous deoxyribonucleic acids shapes
    Ong HS, Rahim MS, Firdaus-Raih M, Ramlan EI
    PLoS One, 2015;10(8):e0134520.
    PMID: 26258940 DOI: 10.1371/journal.pone.0134520
    The unique programmability of nucleic acids offers alternative in constructing excitable and functional nanostructures. This work introduces an autonomous protocol to construct DNA Tetris shapes (L-Shape, B-Shape, T-Shape and I-Shape) using modular DNA blocks. The protocol exploits the rich number of sequence combinations available from the nucleic acid alphabets, thus allowing for diversity to be applied in designing various DNA nanostructures. Instead of a deterministic set of sequences corresponding to a particular design, the protocol promotes a large pool of DNA shapes that can assemble to conform to any desired structures. By utilising evolutionary programming in the design stage, DNA blocks are subjected to processes such as sequence insertion, deletion and base shifting in order to enrich the diversity of the resulting shapes based on a set of cascading filters. The optimisation algorithm allows mutation to be exerted indefinitely on the candidate sequences until these sequences complied with all the four fitness criteria. Generated candidates from the protocol are in agreement with the filter cascades and thermodynamic simulation. Further validation using gel electrophoresis indicated the formation of the designed shapes. Thus, supporting the plausibility of constructing DNA nanostructures in a more hierarchical, modular, and interchangeable manner.
    Matched MeSH terms: DNA/chemistry*
  8. Correlation between polar surface area and bioferroelectricity in DNA and RNA nucleobases
    Yam SC, Zain SM, Sanghiran Lee V, Chew KH
    Eur Phys J E Soft Matter, 2018 Jul 18;41(7):86.
    PMID: 30014219 DOI: 10.1140/epje/i2018-11696-5
    We have performed computational molecular modelling to study the polarization switching and hysteresis loop behaviours of DNA and RNA nucleobases using the PM3 semi-empirical quantum mechanical approaches. All the nucleobases: adenine (A), thymine (T), guanine (G), cytosine (C), and uracil (U) were modelled. Our study indicates that all the nucleobases exhibit a zero-field polarization due to the presence of polar atoms or molecules such as amidogen and carbonyl. The shape of polarization P versus an applied electric field E hysteresis loop is square, implying typical ferroelectrics behaviour. The total energy U as a function of an applied electric field E exhibits a butterfly-like loop. The presence of zero-field polarization and ferroelectrics hysteresis loop behaviours in nucleobases may support the hypothesis of the existence of bioferroelectricity in DNA and RNA. We also found an interesting relationship between the minimum electric field required for switching [Formula: see text] and the ratio of the topological polar surface area (TPSA) to the total surface area (TSA) of a nucleobase. In particular, the [Formula: see text] of a nucleobase is inversely proportional to the TPSA/TSA ratio. This work may provide useful information for understanding the possible existence of ferroelectricity in biomaterials.
    Matched MeSH terms: DNA/chemistry*
  9. DNA-templated silver nanocluster for live-intracellular FOXP3 detection
    Lee SY, Fazlina N, Tye GJ
    Anal Biochem, 2019 09 15;581:113352.
    PMID: 31260647 DOI: 10.1016/j.ab.2019.113352
    DNA-templated silver nanocluster (AgNC), a new promising fluorescence probe has gained importance in biosensing and bioimaging in recent years. We employed a label-free AgNC to detect an intracellular transcription factor known as forkhead box p3 (FOXP3), which is the master regulator of regulatory T cells (Tregs) suppressive function. We developed an optimized method for the detection of messenger ribonucleic acid (mRNA) of FOXP3 by hybridizing AgNC and G-rich to the target FOXP3 mRNA of a MCF-7 cells. MCF-7 cells are chosen as a model as it readily expresses FOXP3. The hybridized samples were examined with UV illuminator and further verified with fluorescence spectroscopy, fluorescence microscope and flow cytometry. The successful hybridization of a three-way junction with AgNC, G-rich and mRNA FOXP3 target generated an improved fluorescence intensity with a spectral shift. We have successfully delivered the green fluorescing AgNC and G-rich into MCF-7 cells, producing a shift to red fluorescing cells corroborated by flow cytometry results. In summary, our approach enables the detection of intracellular FOXP3 nucleic acid and holds considerable potential in establishing a non-lethal intracellular detection system which would be crucial for the isolation of regulatory T-cells (Tregs) when combined with other cell surface markers.
    Matched MeSH terms: DNA/chemistry*
  10. A biological inspired fuzzy adaptive window median filter (FAWMF) for enhancing DNA signal processing
    Ahmad M, Jung LT, Bhuiyan AA
    Comput Methods Programs Biomed, 2017 Oct;149:11-17.
    PMID: 28802326 DOI: 10.1016/j.cmpb.2017.06.021
    BACKGROUND AND OBJECTIVE: Digital signal processing techniques commonly employ fixed length window filters to process the signal contents. DNA signals differ in characteristics from common digital signals since they carry nucleotides as contents. The nucleotides own genetic code context and fuzzy behaviors due to their special structure and order in DNA strand. Employing conventional fixed length window filters for DNA signal processing produce spectral leakage and hence results in signal noise. A biological context aware adaptive window filter is required to process the DNA signals.

    METHODS: This paper introduces a biological inspired fuzzy adaptive window median filter (FAWMF) which computes the fuzzy membership strength of nucleotides in each slide of window and filters nucleotides based on median filtering with a combination of s-shaped and z-shaped filters. Since coding regions cause 3-base periodicity by an unbalanced nucleotides' distribution producing a relatively high bias for nucleotides' usage, such fundamental characteristic of nucleotides has been exploited in FAWMF to suppress the signal noise.

    RESULTS: Along with adaptive response of FAWMF, a strong correlation between median nucleotides and the Π shaped filter was observed which produced enhanced discrimination between coding and non-coding regions contrary to fixed length conventional window filters. The proposed FAWMF attains a significant enhancement in coding regions identification i.e. 40% to 125% as compared to other conventional window filters tested over more than 250 benchmarked and randomly taken DNA datasets of different organisms.

    CONCLUSION: This study proves that conventional fixed length window filters applied to DNA signals do not achieve significant results since the nucleotides carry genetic code context. The proposed FAWMF algorithm is adaptive and outperforms significantly to process DNA signal contents. The algorithm applied to variety of DNA datasets produced noteworthy discrimination between coding and non-coding regions contrary to fixed window length conventional filters.

    Matched MeSH terms: DNA/chemistry*
  11. DNA Morphology: Global Alteration of DNA Topological States Induced by Chemotherapeutic Agents and Its Implication in Cancer
    Ahammed KS, Pachal S, Majumdar P, Dutta S
    Chembiochem, 2023 Apr 17;24(8):e202200715.
    PMID: 36747378 DOI: 10.1002/cbic.202200715
    The dynamic topological states of chromosomal DNA regulate many cellular fundamental processes universally in all three domains of life, that is, bacteria, archaea, and eukaryotes. DNA-binding proteins maintain the regional and global supercoiling of the chromosome and thereby regulate the chromatin architecture that ultimately influences the gene expression network and other DNA-centric molecular events in various microenvironments and growth phases. DNA-binding small molecules are pivotal weapons for treating a wide range of cancers. Recent advances in single-molecule biophysical tools have uncovered the fact that many DNA-binding ligands not only alter the regional DNA supercoiling but also modulate the overall morphology of DNA. Here we provide insight into recent advances in atomic force microscopy (AFM) acquired DNA structural change induced by therapeutically important mono- and bis-intercalating anticancer agents as well as DNA-adduct-forming anticancer drugs. We also emphasize the growing evidence of the mechanistic relevance of changes in DNA topology in the anticancer cellular responses of DNA-targeting chemotherapeutic agents.
    Matched MeSH terms: DNA/chemistry
  12. Fulltext Investigation of the dynamical structures of double-chain deoxyribonucleic acid model in biological sciences
    Yousaf MZ, Abbas M, Nazir T, Abdullah FA, Birhanu A, Emadifar H
    Sci Rep, 2024 Mar 17;14(1):6410.
    PMID: 38494490 DOI: 10.1038/s41598-024-55786-z
    The present research investigates the double-chain deoxyribonucleic acid model, which is important for the transfer and retention of genetic material in biological domains. This model is composed of two lengthy uniformly elastic filaments, that stand in for a pair of polynucleotide chains of the deoxyribonucleic acid molecule joined by hydrogen bonds among the bottom combination, demonstrating the hydrogen bonds formed within the chain's base pairs. The modified extended Fan sub equation method effectively used to explain the exact travelling wave solutions for the double-chain deoxyribonucleic acid model. Compared to the earlier, now in use methods, the previously described modified extended Fan sub equation method provide more innovative, comprehensive solutions and are relatively straightforward to implement. This method transforms a non-linear partial differential equation into an ODE by using a travelling wave transformation. Additionally, the study yields both single and mixed non-degenerate Jacobi elliptic function type solutions. The complexiton, kink wave, dark or anti-bell, V, anti-Z and singular wave shapes soliton solutions are a few of the creative solutions that have been constructed utilizing modified extended Fan sub equation method that can offer details on the transversal and longitudinal moves inside the DNA helix by freely chosen parameters. Solitons propagate at a consistent rate and retain their original shape. They are widely used in nonlinear models and can be found everywhere in nature. To help in understanding the physical significance of the double-chain deoxyribonucleic acid model, several solutions are shown with graphics in the form of contour, 2D and 3D graphs using computer software Mathematica 13.2. All of the requisite constraint factors that are required for the completed solutions to exist appear to be met. Therefore, our method of strengthening symbolic computations offers a powerful and effective mathematical tool for resolving various moderate nonlinear wave problems. The findings demonstrate the system's potentially very rich precise wave forms with biological significance. The fundamentals of double-chain deoxyribonucleic acid model diffusion and processing are demonstrated by this work, which marks a substantial development in our knowledge of double-chain deoxyribonucleic acid model movements.
    Matched MeSH terms: DNA/chemistry
  13. Fulltext Electrical characterization of gold-DNA-gold structures in presence of an external magnetic field by means of I-V curve analysis
    Khatir NM, Banihashemian SM, Periasamy V, Ritikos R, Majid WHA, Rahman SA
    Sensors (Basel), 2012;12(3):3578-3586.
    PMID: 22737025 DOI: 10.3390/s120303578
    This work presents an experimental study of gold-DNA-gold structures in the presence and absence of external magnetic fields with strengths less than 1,200.00 mT. The DNA strands, extracted by standard method were used to fabricate a Metal-DNA-Metal (MDM) structure. Its electric behavior when subjected to a magnetic field was studied through its current-voltage (I-V) curve. Acquisition of the I-V curve demonstrated that DNA as a semiconductor exhibits diode behavior in the MDM structure. The current versus magnetic field strength followed a decreasing trend because of a diminished mobility in the presence of a low magnetic field. This made clear that an externally imposed magnetic field would boost resistance of the MDM structure up to 1,000.00 mT and for higher magnetic field strengths we can observe an increase in potential barrier in MDM junction. The magnetic sensitivity indicates the promise of using MDM structures as potential magnetic sensors.
    Matched MeSH terms: DNA/chemistry*
  14. Molecular delivery of plasmids for genetic vaccination
    Mazid R, Tan MX, Danquah MK
    Curr Pharm Biotechnol, 2013;14(6):615-22.
    PMID: 24016267
    Plasmid vaccination is a smart gene delivery application mostly achieved through the utilisation of viral or copolymeric systems as surrogated carriers in micro or nano formulations. A common polymeric protocol for plasmid vaccine formulation, which as somewhat been successful, is via the complexation of the DNA molecules with a cationic polymer, and encapsulating in a vehicular carrier polymer. Even though plasmid vaccination research has not witnessed the much anticipated success, due a number of cellular and physicochemical reasons, application of copolymeric carriers with tight functionalities is a promising strategy to optimally deliver the DNA molecules; in view of the available chemistries and physical properties that could be tuned to enable enhanced targeted delivery, uptake and specific transfection. This also enables the targeting of specific epitopes and antigen presenting cells for the treatment of many pathogenic infections and cancer. This paper provides a brief critical review of the current state of plasmid vaccines formulation and molecular delivery with analysis of performance data obtained from clinical trials.
    Matched MeSH terms: DNA/chemistry
  15. Fulltext Electronic Characterization of Au/DNA/ITO Metal-Semiconductor-Metal Diode and Its Application as a Radiation Sensor
    Al-Ta'ii HM, Periasamy V, Amin YM
    PLoS One, 2016;11(1):e0145423.
    PMID: 26799703 DOI: 10.1371/journal.pone.0145423
    Deoxyribonucleic acid or DNA molecules expressed as double-stranded (DSS) negatively charged polymer plays a significant role in electronic states of metal/silicon semiconductor structures. Electrical parameters of an Au/DNA/ITO device prepared using self-assembly method was studied by using current-voltage (I-V) characteristic measurements under alpha bombardment at room temperature. The results were analyzed using conventional thermionic emission model, Cheung and Cheung's method and Norde's technique to estimate the barrier height, ideality factor, series resistance and Richardson constant of the Au/DNA/ITO structure. Besides demonstrating a strongly rectifying (diode) characteristic, it was also observed that orderly fluctuations occur in various electrical parameters of the Schottky structure. Increasing alpha radiation effectively influences the series resistance, while the barrier height, ideality factor and interface state density parameters respond linearly. Barrier height determined from I-V measurements were calculated at 0.7284 eV for non-radiated, increasing to about 0.7883 eV in 0.036 Gy showing an increase for all doses. We also demonstrate the hypersensitivity phenomena effect by studying the relationship between the series resistance for the three methods, the ideality factor and low-dose radiation. Based on the results, sensitive alpha particle detectors can be realized using Au/DNA/ITO Schottky junction sensor.
    Matched MeSH terms: DNA/chemistry*
  16. Fulltext Measuring the Electronic Properties of DNA-Specific Schottky Diodes Towards Detecting and Identifying Basidiomycetes DNA
    Periasamy V, Rizan N, Al-Ta'ii HM, Tan YS, Tajuddin HA, Iwamoto M
    Sci Rep, 2016 07 20;6:29879.
    PMID: 27435636 DOI: 10.1038/srep29879
    The discovery of semiconducting behavior of deoxyribonucleic acid (DNA) has resulted in a large number of literatures in the study of DNA electronics. Sequence-specific electronic response provides a platform towards understanding charge transfer mechanism and therefore the electronic properties of DNA. It is possible to utilize these characteristic properties to identify/detect DNA. In this current work, we demonstrate a novel method of DNA-based identification of basidiomycetes using current-voltage (I-V) profiles obtained from DNA-specific Schottky barrier diodes. Electronic properties such as ideality factor, barrier height, shunt resistance, series resistance, turn-on voltage, knee-voltage, breakdown voltage and breakdown current were calculated and used to quantify the identification process as compared to morphological and molecular characterization techniques. The use of these techniques is necessary in order to study biodiversity, but sometimes it can be misleading and unreliable and is not sufficiently useful for the identification of fungi genera. Many of these methods have failed when it comes to identification of closely related species of certain genus like Pleurotus. Our electronics profiles, both in the negative and positive bias regions were however found to be highly characteristic according to the base-pair sequences. We believe that this simple, low-cost and practical method could be useful towards identifying and detecting DNA in biotechnology and pathology.
    Matched MeSH terms: DNA/chemistry*
  17. DNA-templated silver nanoclusters: structural correlation and fluorescence modulation
    New SY, Lee ST, Su XD
    Nanoscale, 2016 Oct 20;8(41):17729-17746.
    PMID: 27722695
    12 years after the introduction of DNA-templated silver nanoclusters (DNA-AgNCs), exciting progress has been made and yet we are still in the midst of trying to fully understand this nanomaterial. The prominent excellence of DNA-AgNCs is undoubtedly its modulatable emission property, of which how variation in DNA templates causes emission tuning remains elusive. Based on the up-to-date DNA-AgNCs, we aim to establish the correlation between the structure/sequence of DNA templates and emission behaviour of AgNCs. Herein, we systematically present a wide-range of DNA-AgNCs based on the structural complexity of the DNA templates, including single-stranded DNA (ssDNA), double-stranded DNA (dsDNA), triple-stranded DNA (tsDNA) and DNA nanostructures. For each DNA category, we discuss the emission property, quantum yield and synthesis condition of the respective AgNCs, before cross-comparing the impact of different DNA scaffolds on the properties of AgNCs. A future outlook for this area is given as a conclusion. By putting the information together, this review may shed new light on understanding DNA-AgNCs while we are expecting continuous breakthroughs in this field.
    Matched MeSH terms: DNA/chemistry*
  18. The Challenges of DNA Extraction in Different Assorted Food Matrices: A Review
    Sajali N, Wong SC, Hanapi UK, Abu Bakar Jamaluddin S, Tasrip NA, Mohd Desa MN
    J Food Sci, 2018 Oct;83(10):2409-2414.
    PMID: 30184265 DOI: 10.1111/1750-3841.14338
    High-quality DNA extracts are imperative for downstream applications in molecular identification. Most processed food products undergo heat treatments causing DNA degradation, which hampers application of DNA-based techniques for food authentication. Moreover, the presence of inhibitors in processed food products is also problematic, as inhibitors can impede the process of obtaining high qualities and quantities of DNA. Various approaches in DNA extraction and factors in structure and texture of various food matrices affecting DNA extraction are explained in this review.
    Matched MeSH terms: DNA/chemistry
  19. Fulltext Synthesis, Characterization, and Application of Poly(4,4'-Cyclohexylidene Bisphenol Oxalate) for Solid-Phase Extraction of DNA
    Al Balawi AN, Yusof NA, Kamaruzaman S, Mohammad F, Wasoh H, Al Abbosh KF, et al.
    Biomed Res Int, 2019;2019:7064073.
    PMID: 30868072 DOI: 10.1155/2019/7064073
    The present study has synthesized poly(4,4'-cyclohexylidene bisphenol oxalate) by the condensation of oxalyl chloride with 4,4'-cyclohexylidene bisphenol, where its efficacy was tested for the solid-phase extraction of DNA. The synthesized polymer in the form of a white powder was characterized by FTIR, TGA-DTG, SEM, and BET analysis. The study utilized solid-phase application of the resulting polymer to extract DNA. The analysis of results provided the information that the extraction efficiency is a strong dependent of polymer amount and binding buffer type. Among the three types of buffers tested, the GuHCl buffer produced the most satisfactory results in terms of yield and efficiency of extraction. Moreover, the absorbance ratio of A260/A280 in all of the samples varied from 1.682 to 1.491, thereby confirming the capability of poly(4,4'-cyclohexylidene bisphenol oxalate) to elute pure DNA. The results demonstrated an increased DNA binding capacity with respect to increased percentage of the polymer. The study has concluded that poly(bisphenol Z oxalate) can be applied as one of the potential candidates for the high efficiency extraction of DNA by means of a simple, cost-effective, and environmentally friendly approach compared to the other traditional solid-phase methods.
    Matched MeSH terms: DNA/chemistry
  20. A label-free electrochemical DNA biosensor used a printed circuit board gold electrode (PCBGE) to detect SARS-CoV-2 without amplification
    Zambry NS, Awang MS, Beh KK, Hamzah HH, Bustami Y, Obande GA, et al.
    Lab Chip, 2023 Mar 14;23(6):1622-1636.
    PMID: 36786757 DOI: 10.1039/d2lc01159j
    The emergence of coronavirus disease 2019 (COVID-19) motivates continuous efforts to develop robust and accurate diagnostic tests to detect severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Detection of viral nucleic acids provides the highest sensitivity and selectivity for diagnosing early and asymptomatic infection because the human immune system may not be active at this stage. Therefore, this work aims to develop a label-free electrochemical DNA biosensor for SARS-CoV-2 detection using a printed circuit board-based gold substrate (PCBGE). The developed sensor used the nucleocapsid phosphoprotein (N) gene as a biomarker. The DNA sensor-based PCBGE was fabricated by self-assembling a thiolated single-stranded DNA (ssDNA) probe onto an Au surface, which performed as the working electrode (WE). The Au surface was then treated with 6-mercapto-1-hexanol (MCH) before detecting the target N gene to produce a well-oriented arrangement of the immobilized ssDNA chains. The successful fabrication of the biosensor was characterized using cyclic voltammetry (CV), electrochemical impedance spectroscopy (EIS), and atomic force microscopy (AFM). The DNA biosensor performances were evaluated using a synthetic SARS-CoV-2 genome and 20 clinical RNA samples from healthy and infected individuals through EIS. The developed DNA biosensor can detect as low as 1 copy per μL of the N gene within 5 minutes with a LOD of 0.50 μM. Interestingly, the proposed DNA sensor could distinguish the expression of SARS-CoV-2 RNA in a patient diagnosed with COVID-19 without any amplification technique. We believe that the proposed DNA sensor platform is a promising point-of-care (POC) device for COVID-19 viral infection since it offers a rapid detection time with a simple design and workflow detection system, as well as an affordable diagnostic assay.
    Matched MeSH terms: DNA/chemistry
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