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Cold Spring Harbor Protocols Mar 2022The polymerase chain reaction (PCR) can be used to produce both nonradiolabeled DNA probes and radiolabeled DNA probes with high specific activity. In this protocol, PCR...
The polymerase chain reaction (PCR) can be used to produce both nonradiolabeled DNA probes and radiolabeled DNA probes with high specific activity. In this protocol, PCR is used to generate double-stranded probes. Related methods, including the generation of asymmetric probes by PCR, are also discussed.
Topics: DNA; DNA Probes; Polymerase Chain Reaction
PubMed: 34907078
DOI: 10.1101/pdb.prot100610 -
Molekuliarnaia Biologiia 2023This review describes the application of oligonucleotides, which are mainly obtained using DNA synthesizers of a new generation (microarray DNA synthesizers), for the... (Review)
Review
This review describes the application of oligonucleotides, which are mainly obtained using DNA synthesizers of a new generation (microarray DNA synthesizers), for the enrichment of target genomic fragments. The methods of molecular hybridization, polymerase chain reaction, and CRISPR-Cas9 system for this purpose are considered. Examples of the practical use of the developed methods for research and diagnostic purposes are given.
Topics: CRISPR-Cas Systems; DNA; Polymerase Chain Reaction; Genome; High-Throughput Nucleotide Sequencing
PubMed: 37326047
DOI: No ID Found -
Molecular Biotechnology Apr 2022The outbreak of COVID-19 pandemic and its consequences have inflicted a substantial damage on the world. In this study, it was attempted to review the recent... (Review)
Review
The outbreak of COVID-19 pandemic and its consequences have inflicted a substantial damage on the world. In this study, it was attempted to review the recent coronaviruses appeared among the human being and their epidemic/pandemic spread throughout the world. Currently, there is an inevitable need for the establishment of a quick and easily available biosensor for tracing COVID-19 in all countries. It has been known that the incubation time of COVID-19 lasts about 14 days and 25% of the infected individuals are asymptomatic. To improve the ability to determine SARS-CoV-2 precisely and reduce the risk of eliciting false-negative results produced by mutating nature of coronaviruses, many researchers have established a real-time reverse transcriptase-polymerase chain reaction (RT-PCR) assay using mismatch-tolerant molecular beacons as multiplex real-time RT-PCR to distinguish between pathogenic and non-pathogenic strains of coronaviruses. The possible mechanisms and pathways for the detection of coronaviruses by biosensors have been reviewed in this study.
Topics: Biosensing Techniques; COVID-19 Testing; CRISPR-Cas Systems; Electrochemical Techniques; Enzyme-Linked Immunosorbent Assay; Fluorescent Antibody Technique; Humans; Molecular Diagnostic Techniques; Neutralization Tests; Nucleic Acid Amplification Techniques; Polymerase Chain Reaction; SARS-CoV-2; Surface Plasmon Resonance
PubMed: 34655396
DOI: 10.1007/s12033-021-00417-5 -
Japanese Journal of Ophthalmology Mar 2021Polymerase chain reaction (PCR) can be used to confirm or deny infectious ocular inflammation such as uveitis. The purpose of this article is to review the current... (Review)
Review
BACKGROUND
Polymerase chain reaction (PCR) can be used to confirm or deny infectious ocular inflammation such as uveitis. The purpose of this article is to review the current practical use of PCR examination in ophthalmology, especially multiplex and broad-range PCR, and a novel PCR, termed Strip PCR. At first, in the Introduction, we show the development of the PCR examination in ophthalmology. We next show the clinical applications of multiplex PCR and broad-range PCR. These advances in PCR continue to contribute greatly to the ophthalmology field. We also show how the sample for PCR is collected. Recently, we established a novel examination, a multiplex real-time PCR (Strip PCR) prototype for detecting 24 pathogens responsible for ocular infectious diseases. Moreover, we developed the Direct Strip PCR method, which skips the DNA extraction step in the procedure. This PCR is anticipated to ease etiologic evaluation, increasing pathogen detection in the intraocular fluids of uveitis patients even by general ophthalmologists. We also describe the following: (1) representative cases in which PCR is useful, (2) representative cases in which PCR can exclude a diagnosis, (3) the current status of PCR in the diagnosis of infectious uveitis and advanced medical service, and (4) the prospects for clinical PCR in ophthalmology.
CONCLUSION
We have established and developed the multiplex PCR, broad-range PCR, Strip PCR, and Direct Strip PCR methods and have reported the efficacy of such tests in multicenter studies. Our goal is "rapid and simple comprehensive PCR diagnosis anywhere and by anyone" for ocular infections.
Topics: Aqueous Humor; Humans; Multiplex Polymerase Chain Reaction; Ophthalmology; Real-Time Polymerase Chain Reaction; Sensitivity and Specificity; Uveitis
PubMed: 33420538
DOI: 10.1007/s10384-020-00794-5 -
Biophysical Journal Apr 2023The polymerase chain reaction (PCR) is a central technique in biotechnology. Its ability to amplify a specific target region of a DNA sequence has led to prominent...
The polymerase chain reaction (PCR) is a central technique in biotechnology. Its ability to amplify a specific target region of a DNA sequence has led to prominent applications, including virus tests, DNA sequencing, genotyping, and genome cloning. These applications rely on the specificity of the primer hybridization and therefore require effective suppression of hybridization errors. A simple and effective method to achieve that is to add blocker strands, also called clamps, to the PCR mixture. These strands bind to the unwanted target sequence, thereby blocking the primer mishybridization. Because of its simplicity, this method is applicable to a broad nucleic-acid-based biotechnology. However, the precise mechanism by which blocker strands suppress PCR errors remains to be understood, limiting the applicability of this technique. Here, we combine experiments and theoretical modeling to reveal this mechanism. We find that the blocker strands both energetically destabilize the mishybridized complex and sculpt a kinetic barrier to suppress mishybridization. This combination of energetic and kinetic biasing extends the viable range of annealing temperatures, which reduces design constraint of the primer sequence and extends the applicability of PCR.
Topics: DNA Primers; Polymerase Chain Reaction; Nucleic Acid Hybridization; Nucleic Acids; Temperature
PubMed: 36823986
DOI: 10.1016/j.bpj.2023.02.028 -
Methods in Molecular Biology (Clifton,... 2023The derived polymorphic amplified cleaved sequence (dPACS) assay is a simple polymerase chain reaction/restriction fragment length polymorphism (PCR-RFLP)-based...
The derived polymorphic amplified cleaved sequence (dPACS) assay is a simple polymerase chain reaction/restriction fragment length polymorphism (PCR-RFLP)-based procedure for detecting known single-nucleotide polymorphisms (SNPs) and deletion-insertion polymorphisms (DIPs). It is relatively straightforward to carry out using basic and commonly available molecular biology kits. The method differs from other PCR-RFLP assays in that it employs 35-55 bp primer pairs that encompass the entire targeted DNA region except for a few diagnostic nucleotides being examined. In so doing, it allows for the introduction of nucleotide mismatches in one or both primers for differentiating wild from mutant sequences following polymerase chain reaction, restriction digestion and MetaPhor gel electrophoresis. Primer design and the selection of discriminating enzymes are achieved with the help of the dPACS 1.0 program. The method is exemplified here with the positive detection of serine 264-psbA, a key determinant for the effective binding of some photosystem II inhibitors to their target. A serine-to-glycine mutation at codon 264 of psbA causes resistance to serine-binding photosystem II herbicides in several grasses and broad-leaf weeds, including Amaranthus retroflexus, which is employed in this study.
Topics: Photosystem II Protein Complex; Polymorphism, Restriction Fragment Length; Mutation; Polymerase Chain Reaction; Codon
PubMed: 36781657
DOI: 10.1007/978-1-0716-3024-2_27 -
Methods in Molecular Biology (Clifton,... 2022The reverse transcription-quantitative real-time polymerase chain reaction (RT-qPCR) is considered to be the gold standard for gene expression research. However, for...
The reverse transcription-quantitative real-time polymerase chain reaction (RT-qPCR) is considered to be the gold standard for gene expression research. However, for this claim to be valid, RT-qPCR studies must test and optimize the quality of its RNA templates and assays. This chapter describes the experimental procedures required to generate reliable and reproducible gene expression results using RT-qPCR.
Topics: RNA; Real-Time Polymerase Chain Reaction; Reverse Transcriptase Polymerase Chain Reaction; Reverse Transcription
PubMed: 35737248
DOI: 10.1007/978-1-0716-2376-3_21 -
Scientific Reports Jul 2023The procedure illustrated in this paper represents a new method for transcriptome analysis by PCR (Polymerase Chain Reaction), which circumvents the need for elimination...
The procedure illustrated in this paper represents a new method for transcriptome analysis by PCR (Polymerase Chain Reaction), which circumvents the need for elimination of potential DNA contamination. Compared to the existing methodologies, our method is more precise, simpler and more reproducible because it preserves the RNA's integrity, does not require materials and/or reagents that are used for elimination of DNA and it also reduces the number of samples that should be set up as negative controls. This novel procedure involves the use of a specifically modified primer during reverse transcription step, which contains mismatched bases, thus producing cDNA molecules that differ from genomic DNA. By using the same modified primer in PCR amplification, only cDNA template is amplified since genomic DNA template is partially heterologous to the primer. In this way, amplification by PCR is unaffected by any potential DNA contamination since it is specific only for the cDNA template. Furthermore, it accurately reflects the initial RNA concentration of the sample, which is prone to changes due to various physical or enzymatic treatments commonly used by the current methodologies for DNA elimination. The method is particularly suitable for quantification of highly repetitive DNA transcripts, such as satellite DNA.
Topics: DNA, Complementary; Reverse Transcription; Polymerase Chain Reaction; DNA; RNA; Reverse Transcriptase Polymerase Chain Reaction
PubMed: 37454173
DOI: 10.1038/s41598-023-38383-4 -
Biosensors May 2022Polymerase chain reaction (PCR) is limited by the long reaction time for point-of-care. Currently, commercial benchtop rapid PCR requires 30−40 min, and this time is...
Polymerase chain reaction (PCR) is limited by the long reaction time for point-of-care. Currently, commercial benchtop rapid PCR requires 30−40 min, and this time is limited by the absence of rapid and stable heating and cooling platforms rather than the biochemical reaction kinetics. This study develops an ultrafast PCR (<3 min) platform using flow-through microchannel chips. An actin gene amplicon with a length of 151 base-pairs in the whole genome was used to verify the ultrafast PCR microfluidic chip. The results demonstrated that the channel of 56 μm height can provide fast heat conduction and the channel length should not be short. Under certain denaturation and annealing/extension times, a short channel design will cause the sample to drive slowly in the microchannel with insufficient pressure in the channel, causing the fluid to generate bubbles in the high-temperature zone and subsequently destabilizing the flow. The chips used in the experiment can complete 40 thermal cycles within 160 s through a design with the 56 µm channel height and with each thermal circle measuring 4 cm long. The calculation shows that the DNA extension speed is ~60 base-pairs/s, which is consistent with the theoretical speed of the Klen Taq extension used, and the detection limit can reach 67 copies. The heat transfer time of the reagent on this platform is very short. The simple chip design and fabrication are suitable for the development of commercial ultrafast PCR chips.
Topics: DNA; Microfluidics; Polymerase Chain Reaction
PubMed: 35624604
DOI: 10.3390/bios12050303 -
Archives of Razi Institute Aug 2023is the main cause of glanders as a dangerous contagious zoonosis disease that is mostly observed in single-hoofed animals, especially horses. Modern molecular...
is the main cause of glanders as a dangerous contagious zoonosis disease that is mostly observed in single-hoofed animals, especially horses. Modern molecular techniques have been recently employed to improve epidemiology for identifying and searching for strains of this bacterium at different times and locations. Due to the unknown number of circulating strains and lack of preventive methods, glanders is still observed in the form of epidemics. The present study aimed to evaluate six field isolates plus two laboratory strains of and using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. All the isolates and strains were microbially cultured in the glycerol nutrient and glycerol agar media. The individually grown colonies of the bacterium were used in the biochemical tests. The DNA of isolates was extracted by boiling, and the PCR-RFLP test was conducted on their genome. Finally, the bacterium was injected into guinea pigs to induce the Straus reaction. The biochemical assays (or bioassays) confirmed the isolates as . The PCR-RFLP assay demonstrated a product for with a length of 650 bp. Nevertheless, 250 and 400 bp were produced for . The swollen scrotum pointed to the occurrence of the Straus reaction. The PCR-RFLP is a proper differential diagnosis technique for ; moreover, it is a suitable method for differentiating between and . This technique can detect in a short time with high precision and sensitivity.
Topics: Horses; Animals; Guinea Pigs; Burkholderia mallei; Glanders; Polymorphism, Restriction Fragment Length; Glycerol; Burkholderia pseudomallei; Polymerase Chain Reaction; Horse Diseases
PubMed: 38226390
DOI: 10.32592/ARI.2023.78.4.1305