Displaying publications 1 - 20 of 27 in total

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  1. 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, Single-Stranded
  2. Thevendran R, Tang TH, Citartan M
    Biotechnol J, 2023 Apr;18(4):e2200092.
    PMID: 36735817 DOI: 10.1002/biot.202200092
    Aptamers are a class of single-stranded (ss) nucleic acid molecules generated through Systematic Evolution of Ligands by Exponential Enrichment (SELEX) that involves iterations of time-consuming and tedious selection, amplification, and enrichment steps. To compensate for the drawbacks of conventional SELEX, we have devised an in-silico methodology that facilitates a cost-effective and facile manner of aptamer selection. Here, we report the isolation of DNA aptamers against androgen receptors (ARs) using androgen response elements (ARE) that possess natural affinity toward AR. A virtual library of ARE sequences was prepared and subjected to a stringent selection criterion to generate a sequence pool having stable hairpin conformations and high GC content. The 3D-structures of the selected ss AREs were modeled and screened through rigid docking and molecular dynamic (MD) simulation to examine their potency as potential AR binders. The predicted sequences were further validated using direct enzyme-linked aptasorbent assay (ELASA), which includes the measurement of their binding affinity, specificity, and target discrimination properties under complex biological enviroments. A short, 15 nucleotides (nts), ssDNA aptamer, termed ARapt1 with the estimated Kd value of 5.5 ± 3 nm, was chosen as the most prominent aptamer against AR based on the coherence of both the in-silico and in-vitro evaluation results. The high target-binding affinity and selectivity of ARapt1 signify its potential use as a versatile tool in diagnostic applications relevant to prostate cancer and related diseases.
    Matched MeSH terms: DNA, Single-Stranded
  3. Ten ST, Hashim U, Gopinath SC, Liu WW, Foo KL, Sam ST, et al.
    Biosens Bioelectron, 2017 Jul 15;93:146-154.
    PMID: 27660016 DOI: 10.1016/j.bios.2016.09.035
    Surface acoustic wave mediated transductions have been widely used in the sensors and actuators applications. In this study, a shear horizontal surface acoustic wave (SHSAW) was used for the detection of food pathogenic Escherichia coli O157:H7 (E.coli O157:H7), a dangerous strain among 225 E. coli unique serotypes. A few cells of this bacterium are able to cause young children to be most vulnerable to serious complications. Presence of higher than 1cfu E.coli O157:H7 in 25g of food has been considered as a dangerous level. The SHSAW biosensor was fabricated on 64° YX LiNbO3 substrate. Its sensitivity was enhanced by depositing 130.5nm thin layer of SiO2 nanostructures with particle size lesser than 70nm. The nanostructures act both as a waveguide as well as a physical surface modification of the sensor prior to biomolecular immobilization. A specific DNA sequence from E. coli O157:H7 having 22 mers as an amine-terminated probe ssDNA was immobilized on the thin film sensing area through chemical functionalization [(CHO-(CH2)3-CHO) and APTES; NH2-(CH2)3-Si(OC2H5)3]. The high-performance of sensor was shown with the specific oligonucleotide target and attained the sensitivity of 0.6439nM/0.1kHz and detection limit was down to 1.8femto-molar (1.8×10(-15)M). Further evidence was provided by specificity analysis using single mismatched and complementary oligonucleotide sequences.
    Matched MeSH terms: DNA, Single-Stranded/isolation & purification*; DNA, Single-Stranded/chemistry
  4. Sharman M, Thomas JE, Skabo S, Holton TA
    Arch Virol, 2008;153(1):135-47.
    PMID: 17978886 DOI: 10.1007/s00705-007-1077-z
    Two isolates of a novel babuvirus causing "bunchy top" symptoms were characterised, one from abacá (Musa textilis) from the Philippines and one from banana (Musa sp.) from Sarawak (Malaysia). The name abacá bunchy top virus (ABTV) is proposed. Both isolates have a genome of six circular DNA components, each ca. 1.0-1.1 kb, analogous to those of isolates of Banana bunchy top virus (BBTV). However, unlike BBTV, both ABTV isolates lack an internal ORF in DNA-R, and the ORF in DNA-U3 found in some BBTV isolates is also absent. In all phylogenetic analyses of nanovirid isolates, ABTV and BBTV fall in the same clade, but on separate branches. However, ABTV and BBTV isolates shared only 79-81% amino acid sequence identity for the putative coat protein and 54-76% overall nucleotide sequence identity across all components. Stem-loop and major common regions were present in ABTV, but there was less than 60% identity with the major common region of BBTV. ABTV and BBTV were also shown to be serologically distinct, with only two out of ten BBTV-specific monoclonal antibodies reacting with ABTV. The two ABTV isolates may represent distinct strains of the species as they are less closely related to each other than are isolates of the two geographic subgroups (Asian and South Pacific) of BBTV.
    Matched MeSH terms: DNA, Single-Stranded/genetics; DNA, Single-Stranded/chemistry*
  5. Saeedfar K, Heng LY, Chiang CP
    Bioelectrochemistry, 2017 Dec;118:106-113.
    PMID: 28780443 DOI: 10.1016/j.bioelechem.2017.07.012
    Multi-wall carbon nanotubes (MWCNTs) were modified to design a new DNA biosensor. Functionalized MWCNTs were equipped with gold nanoparticles (GNPs) (~15nm) (GNP-MWCNTCOOH) to construct DNA biosensors based on carbon-paste screen-printed (SPE) electrodes. GNP attachment onto functionalized MWCNTs was carried out by microwave irradiation and was confirmed by spectroscopic studies and surface analysis. DNA biosensors based on differential pulse voltammetry (DPV) were constructed by immobilizing thiolated single-stranded DNA probes onto GNP-MWCNTCOOH. Ruthenium (III) chloride hexaammoniate [Ru(NH3)6,2Cl(-)] (RuHex) was used as hybridization redox indicator. RuHex and MWCNT interaction was low in compared to other organic redox hybridization indicators. The linear response range for DNA determination was 1×10(-21) to 1×10(-9)M with a lower detection limit of 1.55×10(-21)M. Thus, the attachment of GNPs onto functionalized MWCNTs yielded sensitive DNA biosensor with low detection limit and stability more than 30days. Constructed electrode was used to determine gender of arowana fish.
    Matched MeSH terms: DNA, Single-Stranded/analysis; DNA, Single-Stranded/chemistry
  6. Ravikumar A, Panneerselvam P, Morad N
    ACS Appl Mater Interfaces, 2018 Jun 20;10(24):20550-20558.
    PMID: 29792319 DOI: 10.1021/acsami.8b05041
    In this paper, we propose a metal-polydopamine (MPDA) framework with a specific molecular probe which appears to be the most promising approach to a strong fluorescence quencher. The MPDA framework quenching ability toward various organic fluorophore such as aminoethylcoumarin acetate, 6-carboxyfluorescein (FAM), carboxyteramethylrhodamine, and Cy5 are used to establish a fluorescent biosensor that can selectively recognize Hg2+ and Ag+ ions. The fluorescent quenching efficiency was sufficient to achieve more than 96%. The MPDA framework also exhibits different affinities with ssDNA and dsDNA. In addition, the FAM-labeled ssDNA was adsorbed onto the MPDA framework, based on their interaction with the complex formed between MPDA frameworks/ssDNA taken as a sensing platform. By taking advantage of this sensor, highly sensitive and selective determination of Hg2+ and Ag+ ions is achieved through exonuclease III signal amplification activity. The detection limits of Hg2+ and Ag+ achieved to be 1.3 and 34 pM, respectively, were compared to co-existing metal ions and graphene oxide-based sensors. Furthermore, the potential applications of this study establish the highly sensitive fluorescence detection targets in environmental and biological fields.
    Matched MeSH terms: DNA, Single-Stranded
  7. Rasouli E, Shahnavaz Z, Basirun WJ, Rezayi M, Avan A, Ghayour-Mobarhan M, et al.
    Anal Biochem, 2018 09 01;556:136-144.
    PMID: 29981317 DOI: 10.1016/j.ab.2018.07.002
    Human papillomavirus (HPV) is one of the most common sexually transmitted disease, transmitted through intimate skin contact or mucosal membrane. The HPV virus consists of a double-stranded circular DNA and the role of HPV virus in cervical cancer has been studied extensively. Thus it is critical to develop rapid identification method for early detection of the virus. A portable biosensing device could give rapid and reliable results for the identification and quantitative determination of the virus. The fabrication of electrochemical biosensors is one of the current techniques utilized to achieve this aim. In such electrochemical biosensors, a single-strand DNA is immobilized onto an electrically conducting surface and the changes in electrical parameters due to the hybridization on the electrode surface are measured. This review covers the recent developments in electrochemical DNA biosensors for the detection of HPV virus. Due to the several advantages of electrochemical DNA biosensors, their applications have witnessed an increased interest and research focus nowadays.
    Matched MeSH terms: DNA, Single-Stranded/analysis*
  8. Ramanathan S, Gopinath SCB, Arshad MKM, Poopalan P, Anbu P
    Mikrochim Acta, 2019 07 18;186(8):546.
    PMID: 31321546 DOI: 10.1007/s00604-019-3696-y
    A genomic DNA-based colorimetric assay is described for the detection of the early growth factor receptor (EGFR) mutation, which is the protruding reason for non-small cell lung cancer. A DNA sequence was designed and immobilized on unmodified gold nanoparticles (GNPs). The formation of the respective duplex indicates the presence of an EGFR mutation. It is accompanied by the aggregation of the GNPs in the presence of monovalent ions, and it indicates the presence of an EGFR mutation. This is accompanied by a color change from red (520 nm) to purple (620 nm). Aggregation was evidenced by transmission electron microscopy, scanning electron microscopy and atomic force microscopy. The limit of detection is 313 nM of the mutant target strand. A similar peak shift was observed for 2.5 μM concentrations of wild type target. No significant peak shift was observed with probe and non-complementary DNA. Graphical abstract Schematic representation of high-specific genomic DNA sequence on gold nanoparticle (GNP) aggregation with sodium chloride (NaCl). It illustrates the detection method for EGFR mutation on lung cancer detection. Red and purple colors of tubes represent dispersed and aggregated GNP, respectively.
    Matched MeSH terms: DNA, Single-Stranded/chemistry*
  9. Raha AR, Hooi WY, Mariana NS, Radu S, Varma NR, Yusoff K
    Plasmid, 2006 Jul;56(1):53-61.
    PMID: 16675013
    A small plasmid designated pAR141 was isolated from Lactococcus lactis subsp. lactis M14 and its complete 1,594 base pair nucleotide sequence was determined. Analysis of the sequence indicated that this plasmid does not carry any industrially important determinants besides the elements involved in plasmid replication and control. The transcriptional repressor CopG and replication initiation protein RepB appeared as a single operon. A small countertranscribed RNA (ctRNA) coding region was found between the copG and repB genes. The double strand origin (dso) and single strand origin (sso) of rolling circle replicating (RCR) plasmids were also identified in pAR141, suggesting that this plasmid replicates by rolling circle (RC) mode. This observation was supported by S1 nuclease and Southern hybridization analyses.
    Matched MeSH terms: DNA, Single-Stranded/chemistry
  10. Phan TG, Mori D, Deng X, Rajindrajith S, Ranawaka U, Fan Ng TF, et al.
    Virology, 2015 Aug;482:98-104.
    PMID: 25839169 DOI: 10.1016/j.virol.2015.03.011
    Viruses with small circular ssDNA genomes encoding a replication initiator protein can infect a wide range of eukaryotic organisms ranging from mammals to fungi. The genomes of two such viruses, a cyclovirus (CyCV-SL) and gemycircularvirus (GemyCV-SL) were detected by deep sequencing of the cerebrospinal fluids of Sri Lankan patients with unexplained encephalitis. One and three out of 201 CSF samples (1.5%) from unexplained encephalitis patients tested by PCR were CyCV-SL and GemyCV-SL DNA positive respectively. Nucleotide similarity searches of pre-existing metagenomics datasets revealed closely related genomes in feces from unexplained cases of diarrhea from Nicaragua and Brazil and in untreated sewage from Nepal. Whether the tropism of the cyclovirus and gemycircularvirus reported here include humans or other cellular sources in or on the human body remains to be determined.
    Matched MeSH terms: DNA, Single-Stranded/genetics*; DNA, Single-Stranded/isolation & purification
  11. Parmin NA, Hashim U, Gopinath SCB, Nadzirah S, Rejali Z, Afzan A, et al.
    Mikrochim Acta, 2019 05 08;186(6):336.
    PMID: 31069542 DOI: 10.1007/s00604-019-3445-2
    A gene sensor for rapid detection of the Human Papillomavirus 16 (HPV 16) which is associated with the appearance of cervical cancer was developed. The assay is based on voltammetric determination of HPV 16 DNA by using interdigitated electrodes modified with titanium dioxide nanoparticles. Titanium dioxide nanoparticles (NPs) were used to modify a semiconductor-based interdigitated electrode (IDE). The surface of the NPs was then functionalized with a commercial 24-mer oligomer DNA probe for HPV 16 that was modified at the 5' end with a carboxyl group. If the probe interacts with the HPV 16 ssDNA, the current, best measured at a working voltage of 1.0 V, increases. The gene sensor has has a ∼ 0.1 fM limit of detection which is comparable to other sensors. The dielectric voltammetry analysis was carried out from 0 V to 1 V. The electrochemical sensitivity of the IDE is 2.5 × 10-5 μA·μM-1·cm-2. Graphical abstract Schematic of an interdigitated electrode (IDE) modified with titanium dioxide nanoparticles for voltammetric determination of HPV 16 DNA by using an appropriate DNA probe.
    Matched MeSH terms: DNA, Single-Stranded
  12. 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, Single-Stranded/chemistry*
  13. Navien TN, Thevendran R, Hamdani HY, Tang TH, Citartan M
    Biochimie, 2020 Oct 18;180:54-67.
    PMID: 33086095 DOI: 10.1016/j.biochi.2020.10.005
    Aptamers are single-stranded DNA or RNA oligonucleotides generated by SELEX that exhibit binding affinity and specificity against a wide variety of target molecules. Compared to RNA aptamers, DNA aptamers are much more stable and therefore are widely adopted in a number of applications especially in diagnostics. The tediousness and rigor associated with certain steps of the SELEX intensify the efforts to adopt in silico molecular docking approaches together with in vitro SELEX procedures in developing DNA aptamers. Inspired by these endeavors, we carry out an overview of the in silico molecular docking approaches in DNA aptamer generation, by detailing the stepwise procedures as well as shedding some light on the various softwares used. The in silico maturation strategy and the limitations of the in silico approaches are also underscored.
    Matched MeSH terms: DNA, Single-Stranded
  14. Nadzirah Sh, Azizah N, Hashim U, Gopinath SC, Kashif M
    PLoS One, 2015;10(10):e0139766.
    PMID: 26445455 DOI: 10.1371/journal.pone.0139766
    Nanoparticle-mediated bio-sensing promoted the development of novel sensors in the front of medical diagnosis. In the present study, we have generated and examined the potential of titanium dioxide (TiO2) crystalline nanoparticles with aluminium interdigitated electrode biosensor to specifically detect single-stranded E.coli O157:H7 DNA. The performance of this novel DNA biosensor was measured the electrical current response using a picoammeter. The sensor surface was chemically functionalized with (3-aminopropyl) triethoxysilane (APTES) to provide contact between the organic and inorganic surfaces of a single-stranded DNA probe and TiO2 nanoparticles while maintaining the sensing system's physical characteristics. The complement of the target DNA of E. coli O157:H7 to the carboxylate-probe DNA could be translated into electrical signals and confirmed by the increased conductivity in the current-to-voltage curves. The specificity experiments indicate that the biosensor can discriminate between the complementary sequences from the base-mismatched and the non-complementary sequences. After duplex formation, the complementary target sequence can be quantified over a wide range with a detection limit of 1.0 x 10(-13)M. With target DNA from the lysed E. coli O157:H7, we could attain similar sensitivity. Stability of DNA immobilized surface was calculated with the relative standard deviation (4.6%), displayed the retaining with 99% of its original response current until 6 months. This high-performance interdigitated DNA biosensor with high sensitivity, stability and non-fouling on a novel sensing platform is suitable for a wide range of biomolecular interactive analyses.
    Matched MeSH terms: DNA, Single-Stranded/genetics; DNA, Single-Stranded/chemistry
  15. Md Sani ND, Ariffin EY, Sheryn W, Shamsuddin MA, Heng LY, Latip J, et al.
    Sensors (Basel), 2019 Nov 22;19(23).
    PMID: 31766637 DOI: 10.3390/s19235111
    A toxicity electrochemical DNA biosensor has been constructed for the detection of carcinogens using 24 base guanine DNA rich single stranded DNA, and methylene blue (MB) as the electroactive indicator. This amine terminated ssDNA was immobilized onto silica nanospheres and deposited on gold nanoparticle modified carbon-paste screen printed electrodes (SPEs). The modified SPE was initially exposed to a carcinogen, followed by immersion in methylene blue for an optimized duration. The biosensor response was measured using differential pulse voltammetry. The performance of the biosensor was identified on several anti-cancer compounds. The toxicity DNA biosensor demonstrated a linear response range to the cadmium chloride from 0.0005 ppm to 0.01 ppm (R2 = 0.928) with a limit of detection at 0.0004 ppm. The biosensor also exhibited its versatility to screen the carcinogenicity of potential anti-cancer compounds.
    Matched MeSH terms: DNA, Single-Stranded/chemistry
  16. Marimuthu C, Tang TH, Tominaga J, Tan SC, Gopinath SC
    Analyst, 2012 Mar 21;137(6):1307-15.
    PMID: 22314701 DOI: 10.1039/c2an15905h
    The discovery that synthetic short chain nucleic acids are capable of selective binding to biological targets has made them to be widely used as molecular recognition elements. These nucleic acids, called aptamers, are comprised of two types, DNA and RNA aptamers, where the DNA aptamer is preferred over the latter due to its stability, making it widely used in a number of applications. However, the success of the DNA selection process through Systematic Evolution of Ligands by Exponential Enrichment (SELEX) experiments is very much dependent on its most critical step, which is the conversion of the dsDNA to ssDNA. There is a plethora of methods available in generating ssDNA from the corresponding dsDNA. These include asymmetric PCR, biotin-streptavidin separation, lambda exonuclease digestion and size separation on denaturing-urea PAGE. Herein, different methods of ssDNA generation following the PCR amplification step in SELEX are reviewed.
    Matched MeSH terms: DNA, Single-Stranded/chemical synthesis*; DNA, Single-Stranded/chemistry
  17. Low SS, Loh HS, Boey JS, Khiew PS, Chiu WS, Tan MTT
    Biosens Bioelectron, 2017 Aug 15;94:365-373.
    PMID: 28319904 DOI: 10.1016/j.bios.2017.02.038
    An efficient electrochemical impedance genosensing platform has been constructed based on graphene/zinc oxide nanocomposite produced via a facile and green approach. Highly pristine graphene was synthesised from graphite through liquid phase sonication and then mixed with zinc acetate hexahydrate for the synthesis of graphene/zinc oxide nanocomposite by solvothermal growth. The as-synthesised graphene/zinc oxide nanocomposite was characterised with scanning electron microscopy (SEM), transmission electron microscopy (TEM), Raman spectroscopy and X-ray diffractometry (XRD) to evaluate its morphology, crystallinity, composition and purity. An amino-modified single stranded DNA oligonucleotide probe synthesised based on complementary Coconut Cadang-Cadang Viroid (CCCVd) RNA sequence, was covalently bonded onto the surface of graphene/zinc oxide nanocomposite by the bio-linker 1-pyrenebutyric acid N-hydroxysuccinimide ester. The hybridisation events were monitored by electrochemical impedance spectroscopy (EIS). Under optimised sensing conditions, the single stranded CCCVd RNA oligonucleotide target could be quantified in a wide range of 1.0×10-11M to 1.0×10-6 with good linearity (R =0.9927), high sensitivity with low detection limit of 4.3×10-12M. Differential pulse voltammetry (DPV) was also performed for the estimation of nucleic acid density on the graphene/zinc oxide nanocomposite-modified sensing platform. The current work demonstrates an important advancement towards the development of a sensitive detection assay for various diseases involving RNA agents such as CCCVd in the future.
    Matched MeSH terms: DNA, Single-Stranded/genetics; DNA, Single-Stranded/chemistry*
  18. Lim SW, Ting KN, Bradshaw TD, Zeenathul NA, Wiart C, Khoo TJ, et al.
    J Ethnopharmacol, 2011 Nov 18;138(2):616-23.
    PMID: 22008878 DOI: 10.1016/j.jep.2011.10.005
    The seeds of Acalypha wilkesiana have been used empirically by traditional healers in Southwest Nigeria together with other plants as a powder mixture to treat patients with breast tumours and inflammation.
    Matched MeSH terms: DNA, Single-Stranded/drug effects*
  19. Lee SY, Hairul Bahara NH, Choong YS, Lim TS, Tye GJ
    J Colloid Interface Sci, 2014 Nov 01;433:183-188.
    PMID: 25129336 DOI: 10.1016/j.jcis.2014.07.033
    DNA-templated silver nanoclusters (AgNC) are a class of subnanometer sized fluorophores with good photostability and brightness. It has been applied as a diagnostic tool mainly for deoxyribonucleic acid (DNA) detection. Integration of DNA oligomers to generate AgNCs is interesting as varying DNA sequences can result in different fluorescence spectra. This allows a simple fluorescence shifting effect to occur upon DNA hybridization with the hybridization efficiency being a pronominal factor for successful shifting. The ability to shift the fluorescence spectra as a result of hybridization overcomes the issue of background intensities in most fluorescent based assays. Here we describe an optimized method for the detection of single-stranded and double-stranded synthetic forkhead box P3 (FOXP3) target by hybridization with the DNA fluorescence shift sensor. The system forms a three-way junction by successful hybridization of AgNC, G-rich strand (G-rich) to the target DNA, which generated a shift in fluorescence spectra with a marked increase in fluorescence intensity. The DNA fluorescence shift sensor presents a rapid and specific alternative to conventional DNA detection.
    Matched MeSH terms: DNA, Single-Stranded/analysis*; DNA, Single-Stranded/chemistry
  20. Jalilsood T, Baradaran A, Ling FH, Mustafa S, Yusof K, Rahim RA
    Plasmid, 2014 May;73:1-9.
    PMID: 24785193 DOI: 10.1016/j.plasmid.2014.04.004
    Lactobacillus plantarum PA18, a strain originally isolated from the leaves of Pandanus amaryllifolius, contains a pR18 plasmid. The pR18 plasmid is a 3211bp circular molecule with a G+C content of 35.8%. Nucleotide sequence analysis revealed two putative open reading frames, ORF1 and ORF2, in which ORF2 was predicted (317 amino acids) to be a replication protein and shared 99% similarity with the Rep proteins of pLR1, pLD1, pC30il, and pLP2000, which belong to the RCR pC194/pUB110 family. Sequence analysis also indicated that ORF1 was predicted to encode linA, an enzyme that enzymatically inactivates lincomycin. The result of Southern hybridization and mung bean nuclease treatment confirmed that pR18 replicated via the RCR mechanism. Phylogenetic tree analysis of pR18 plasmid proteins suggested that horizontal transfer of antibiotic resistance determinants without genes encoding mobilization has not only occurred between Bacillus and Lactobacillus but also between unrelated bacteria. Understanding this type of transfer could possibly play a key role in facilitating the study of the origin and evolution of lactobacillus plasmids. Quantitative PCR showed that the relative copy number of pR18 was approximately 39 copies per chromosome equivalent.
    Matched MeSH terms: DNA, Single-Stranded/analysis; DNA, Single-Stranded/genetics*
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