Short sequences (generally about 10 base pairs) of DNA that are complementary to sequences of messenger RNA and allow reverse transcriptases to start copying the adjacent sequences of mRNA. Primers are used extensively in genetic and molecular biology techniques.
Macromolecular molds for the synthesis of complementary macromolecules, as in DNA REPLICATION; GENETIC TRANSCRIPTION of DNA to RNA, and GENETIC TRANSLATION of RNA into POLYPEPTIDES.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
A reverse transcriptase encoded by the POL GENE of HIV. It is a heterodimer of 66 kDa and 51 kDa subunits that are derived from a common precursor protein. The heterodimer also includes an RNAse H activity (RIBONUCLEASE H, HUMAN IMMUNODEFICIENCY VIRUS) that plays an essential role the viral replication process.
An enzyme that synthesizes DNA on an RNA template. It is encoded by the pol gene of retroviruses and by certain retrovirus-like elements. EC 2.7.7.49.
A ribonuclease that specifically cleaves the RNA moiety of RNA:DNA hybrids. It has been isolated from a wide variety of prokaryotic and eukaryotic organisms as well as RETROVIRUSES.
A genus of ciliate protozoa having a dorsoventrally flattened body with widely spaced rows of short bristle-like cilia on the dorsal surface.
Guanine nucleotides which contain deoxyribose as the sugar moiety.
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.
DNA-dependent DNA polymerases found in bacteria, animal and plant cells. During the replication process, these enzymes catalyze the addition of deoxyribonucleotide residues to the end of a DNA strand in the presence of DNA as template-primer. They also possess exonuclease activity and therefore function in DNA repair.
A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
The phosphate esters of DIDEOXYNUCLEOSIDES.
The process by which a DNA molecule is duplicated.
An essential ribonucleoprotein reverse transcriptase that adds telomeric DNA to the ends of eukaryotic CHROMOSOMES.
An antiviral antibiotic produced by Cephalosporium aphidicola and other fungi. It inhibits the growth of eukaryotic cells and certain animal viruses by selectively inhibiting the cellular replication of DNA polymerase II or the viral-induced DNA polymerases. The drug may be useful for controlling excessive cell proliferation in patients with cancer, psoriasis or other dermatitis with little or no adverse effect upon non-multiplying cells.
A single chain of deoxyribonucleotides that occurs in some bacteria and viruses. It usually exists as a covalently closed circle.
Deoxyribonucleic acid that makes up the genetic material of viruses.
A DNA-dependent DNA polymerase characterized in prokaryotes and may be present in higher organisms. It has both 3'-5' and 5'-3' exonuclease activity, but cannot use native double-stranded DNA as template-primer. It is not inhibited by sulfhydryl reagents and is active in both DNA synthesis and repair. EC 2.7.7.7.
The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.
The monomeric units from which DNA or RNA polymers are constructed. They consist of a purine or pyrimidine base, a pentose sugar, and a phosphate group. (From King & Stansfield, A Dictionary of Genetics, 4th ed)
A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.
Inhibitors of reverse transcriptase (RNA-DIRECTED DNA POLYMERASE), an enzyme that synthesizes DNA on an RNA template.
The rate dynamics in chemical or physical systems.
Ribonucleic acid that makes up the genetic material of viruses.
Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.
The parts of a macromolecule that directly participate in its specific combination with another molecule.
A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.
The type species of LENTIVIRUS and the etiologic agent of AIDS. It is characterized by its cytopathic effect and affinity for the T4-lymphocyte.
A multistage process that includes cloning, physical mapping, subcloning, determination of the DNA SEQUENCE, and information analysis.
Deoxyribonucleic acid that makes up the genetic material of bacteria.
Technique that utilizes low-stringency polymerase chain reaction (PCR) amplification with single primers of arbitrary sequence to generate strain-specific arrays of anonymous DNA fragments. RAPD technique may be used to determine taxonomic identity, assess kinship relationships, analyze mixed genome samples, and create specific probes.
Binary classification measures to assess test results. Sensitivity or recall rate is the proportion of true positives. Specificity is the probability of correctly determining the absence of a condition. (From Last, Dictionary of Epidemiology, 2d ed)
The insertion of recombinant DNA molecules from prokaryotic and/or eukaryotic sources into a replicating vehicle, such as a plasmid or virus vector, and the introduction of the resultant hybrid molecules into recipient cells without altering the viability of those cells.
A transfer RNA which is specific for carrying lysine to sites on the ribosomes in preparation for protein synthesis.
The relationships of groups of organisms as reflected by their genetic makeup.
The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.
Constituent of 30S subunit prokaryotic ribosomes containing 1600 nucleotides and 21 proteins. 16S rRNA is involved in initiation of polypeptide synthesis.
The restriction of a characteristic behavior, anatomical structure or physical system, such as immune response; metabolic response, or gene or gene variant to the members of one species. It refers to that property which differentiates one species from another but it is also used for phylogenetic levels higher or lower than the species.
DNA sequences encoding RIBOSOMAL RNA and the segments of DNA separating the individual ribosomal RNA genes, referred to as RIBOSOMAL SPACER DNA.
The biosynthesis of RNA carried out on a template of DNA. The biosynthesis of DNA from an RNA template is called REVERSE TRANSCRIPTION.
A single-stranded DNA-dependent RNA polymerase that functions to initiate, or prime, DNA synthesis by synthesizing oligoribonucleotide primers. EC 2.7.7.-.
Acrylic acids or acrylates which are substituted in the C-2 position with a methyl group.
The sequential correspondence of nucleotides in one nucleic acid molecule with those of another nucleic acid molecule. Sequence homology is an indication of the genetic relatedness of different organisms and gene function.
An adhesion procedure for orthodontic attachments, such as plastic DENTAL CROWNS. This process usually includes the application of an adhesive material (DENTAL CEMENTS) and letting it harden in-place by light or chemical curing.
The functional hereditary units of BACTERIA.
Laboratory techniques that involve the in-vitro synthesis of many copies of DNA or RNA from one original template.
Dental cements composed either of polymethyl methacrylate or dimethacrylate, produced by mixing an acrylic monomer liquid with acrylic polymers and mineral fillers. The cement is insoluble in water and is thus resistant to fluids in the mouth, but is also irritating to the dental pulp. It is used chiefly as a luting agent for fabricated and temporary restorations. (Jablonski's Dictionary of Dentistry, 1992, p159)
The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.
Polymers made up of a few (2-20) nucleotides. In molecular genetics, they refer to a short sequence synthesized to match a region where a mutation is known to occur, and then used as a probe (OLIGONUCLEOTIDE PROBES). (Dorland, 28th ed)
Synthetic or natural oligonucleotides used in hybridization studies in order to identify and study specific nucleic acid fragments, e.g., DNA segments near or within a specific gene locus or gene. The probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the probe include the radioisotope labels 32P and 125I and the chemical label biotin.
A heat stable DNA-DIRECTED DNA POLYMERASE from the bacteria Thermus aquaticus. It is widely used for the amplification of genes through the process of POLYMERASE CHAIN REACTION. EC 2.7.7.-.
A technique for identifying individuals of a species that is based on the uniqueness of their DNA sequence. Uniqueness is determined by identifying which combination of allelic variations occur in the individual at a statistically relevant number of different loci. In forensic studies, RESTRICTION FRAGMENT LENGTH POLYMORPHISM of multiple, highly polymorphic VNTR LOCI or MICROSATELLITE REPEAT loci are analyzed. The number of loci used for the profile depends on the ALLELE FREQUENCY in the population.
RNA sequences that serve as templates for protein synthesis. Bacterial mRNAs are generally primary transcripts in that they do not require post-transcriptional processing. Eukaryotic mRNA is synthesized in the nucleus and must be exported to the cytoplasm for translation. Most eukaryotic mRNAs have a sequence of polyadenylic acid at the 3' end, referred to as the poly(A) tail. The function of this tail is not known for certain, but it may play a role in the export of mature mRNA from the nucleus as well as in helping stabilize some mRNA molecules by retarding their degradation in the cytoplasm.
Species- or subspecies-specific DNA (including COMPLEMENTARY DNA; conserved genes, whole chromosomes, or whole genomes) used in hybridization studies in order to identify microorganisms, to measure DNA-DNA homologies, to group subspecies, etc. The DNA probe hybridizes with a specific mRNA, if present. Conventional techniques used for testing for the hybridization product include dot blot assays, Southern blot assays, and DNA:RNA hybrid-specific antibody tests. Conventional labels for the DNA probe include the radioisotope labels 32P and 125I and the chemical label biotin. The use of DNA probes provides a specific, sensitive, rapid, and inexpensive replacement for cell culture techniques for diagnosing infections.
Electrophoresis in which agar or agarose gel is used as the diffusion medium.
Deoxyribonucleic acid that makes up the genetic material of plants.
A variety of simple repeat sequences that are distributed throughout the GENOME. They are characterized by a short repeat unit of 2-8 basepairs that is repeated up to 100 times. They are also known as short tandem repeats (STRs).
The genetic constitution of the individual, comprising the ALLELES present at each GENETIC LOCUS.
Ribonucleic acid in bacteria having regulatory and catalytic roles as well as involvement in protein synthesis.
Single-stranded complementary DNA synthesized from an RNA template by the action of RNA-dependent DNA polymerase. cDNA (i.e., complementary DNA, not circular DNA, not C-DNA) is used in a variety of molecular cloning experiments as well as serving as a specific hybridization probe.
Variation occurring within a species in the presence or length of DNA fragment generated by a specific endonuclease at a specific site in the genome. Such variations are generated by mutations that create or abolish recognition sites for these enzymes or change the length of the fragment.
Widely used technique which exploits the ability of complementary sequences in single-stranded DNAs or RNAs to pair with each other to form a double helix. Hybridization can take place between two complimentary DNA sequences, between a single-stranded DNA and a complementary RNA, or between two RNA sequences. The technique is used to detect and isolate specific sequences, measure homology, or define other characteristics of one or both strands. (Kendrew, Encyclopedia of Molecular Biology, 1994, p503)
Deoxyribonucleic acid that makes up the genetic material of fungi.
Genotypic differences observed among individuals in a population.
The internal resistance of a material to moving some parts of it parallel to a fixed plane, in contrast to stretching (TENSILE STRENGTH) or compression (COMPRESSIVE STRENGTH). Ionic crystals are brittle because, when subjected to shear, ions of the same charge are brought next to each other, which causes repulsion.
A variation of the PCR technique in which cDNA is made from RNA via reverse transcription. The resultant cDNA is then amplified using standard PCR protocols.
A method (first developed by E.M. Southern) for detection of DNA that has been electrophoretically separated and immobilized by blotting on nitrocellulose or other type of paper or nylon membrane followed by hybridization with labeled NUCLEIC ACID PROBES.
A phenotypically recognizable genetic trait which can be used to identify a genetic locus, a linkage group, or a recombination event.
Proteins found in any species of bacterium.
Use of restriction endonucleases to analyze and generate a physical map of genomes, genes, or other segments of DNA.
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
The regular and simultaneous occurrence in a single interbreeding population of two or more discontinuous genotypes. The concept includes differences in genotypes ranging in size from a single nucleotide site (POLYMORPHISM, SINGLE NUCLEOTIDE) to large nucleotide sequences visible at a chromosomal level.
The intergenic DNA segments that are between the ribosomal RNA genes (internal transcribed spacers) and between the tandemly repeated units of rDNA (external transcribed spacers and nontranscribed spacers).
Constituent of the 40S subunit of eukaryotic ribosomes. 18S rRNA is involved in the initiation of polypeptide synthesis in eukaryotes.
Cements that act through infiltration and polymerization within the dentinal matrix and are used for dental restoration. They can be adhesive resins themselves, adhesion-promoting monomers, or polymerization initiators that act in concert with other agents to form a dentin-bonding system.
Enzymes that catalyze the template-directed incorporation of ribonucleotides into an RNA chain. EC 2.7.7.-.
A large collection of DNA fragments cloned (CLONING, MOLECULAR) from a given organism, tissue, organ, or cell type. It may contain complete genomic sequences (GENOMIC LIBRARY) or complementary DNA sequences, the latter being formed from messenger RNA and lacking intron sequences.
A group of deoxyribonucleotides (up to 12) in which the phosphate residues of each deoxyribonucleotide act as bridges in forming diester linkages between the deoxyribose moieties.

Activation of systemic acquired silencing by localised introduction of DNA. (1/43244)

BACKGROUND: In plants, post-transcriptional gene silencing results in RNA degradation after transcription. Among tobacco transformants carrying a nitrate reductase (Nia) construct under the control of the cauliflower mosaic virus 35S promoter (35S-Nia2), one class of transformants spontaneously triggers Nia post-transcriptional gene silencing (class II) whereas another class does not (class I). Non-silenced plants of both classes become silenced when grafted onto silenced stocks, indicating the existence of a systemic silencing signal. Graft-transmitted silencing is maintained in class II but not in class I plants when removed from silenced stocks, indicating similar requirements for spontaneous triggering and maintenance. RESULTS: Introduction of 35S-Nia2 DNA by the gene transfer method called biolistics led to localised acquired silencing (LAS) in bombarded leaves of wild-type, class I and class II plants, and to systemic acquired silencing (SAS) in class II plants. SAS occurred even if the targeted leaf was removed 2 days after bombardment, indicating that the systemic signal is produced, transmitted and amplified rapidly. SAS was activated by sense, antisense and promoterless Nia2 DNA constructs, indicating that transcription is not required although it does stimulate SAS. CONCLUSIONS: SAS was activated by biolistic introduction of promoterless constructs, indicating that the DNA itself is a potent activator of post-transcriptional gene silencing. The systemic silencing signal invaded the whole plant by cell-to-cell and long-distance propagation, and reamplification of the signal.  (+info)

Impaired translesion synthesis in xeroderma pigmentosum variant extracts. (2/43244)

Xeroderma pigmentosum variant (XPV) cells are characterized by a cellular defect in the ability to synthesize intact daughter DNA strands on damaged templates. Molecular mechanisms that facilitate replication fork progression on damaged DNA in normal cells are not well defined. In this study, we used single-stranded plasmid molecules containing a single N-2-acetylaminofluorene (AAF) adduct to analyze translesion synthesis (TLS) catalyzed by extracts of either normal or XPV primary skin fibroblasts. In one of the substrates, the single AAF adduct was located at the 3' end of a run of three guanines that was previously shown to induce deletion of one G by a slippage mechanism. Primer extension reactions performed by normal cellular extracts from four different individuals produced the same distinct pattern of TLS, with over 80% of the products resulting from the elongation of a slipped intermediate and the remaining 20% resulting from a nonslipped intermediate. In contrast, with cellular extracts from five different XPV patients, the TLS reaction was strongly reduced, yielding only low amounts of TLS via the nonslipped intermediate. With our second substrate, in which the AAF adduct was located at the first G in the run, thus preventing slippage from occurring, we confirmed that normal extracts were able to perform TLS 10-fold more efficiently than XPV extracts. These data demonstrate unequivocally that the defect in XPV cells resides in translesion synthesis independently of the slippage process.  (+info)

Overexpression of CuZn superoxide dismutase protects RAW 264.7 macrophages against nitric oxide cytotoxicity. (3/43244)

Initiation of nitric oxide (NO.)-mediated apoptotic cell death in RAW 264.7 macrophages is associated with up-regulation of mitochondrial manganese superoxide dismutase (MnSOD; SOD2) and down-regulation of cytosolic copper zinc superoxide dismutase (CuZnSOD; SOD1) at their individual mRNA and protein levels. To evaluate the decreased CuZnSOD expression and the initiation of apoptosis we stably transfected macrophages to overexpress human CuZnSOD. Individual clones revealed a 2-fold increase in CuZnSOD activity. Expression of a functional and thus protective CuZnSOD was verified by attenuated superoxide (O2(.)-)-mediated apoptotic as well as necrotic cell death. In this study we showed that SOD-overexpressing macrophages (R-SOD1-12) were also protected against NO.-initiated programmed cell death. Protection was substantial towards NO. derived from exogenously added NO donors or when NO. was generated by inducible NO synthase activation, and was evident at the level of p53 accumulation, caspase activation and DNA fragmentation. Stimulation of parent and SOD-overexpressing cells with a combination of lipopolysaccharide and murine interferon gamma produced equivalent amounts of nitrite/nitrate, which ruled out attenuated inducible NO. synthase activity during protection. Because protection by a O2(.)--scavenging system during NO. -intoxication implies a role of NO. and O2(.)- in the progression of cell damage, we used uric acid to delineate the role of peroxynitrite during NO.-elicited apoptosis. The peroxynitrite scavenger uric acid left S-nitrosoglutathione or spermine-NO-elicited apoptosis unaltered, blocking only 3-morpholinosydnonimine-mediated cell death. As a result we exclude peroxynitrite from contributing, to any major extent, to NO. -mediated apoptosis. Therefore protection observed with CuZnSOD overexpression is unlikely to stem from interference with peroxynitrite formation and/or action. Unequivocally, the down-regulation of CuZnSOD is associated with NO. cytotoxicity, whereas CuZnSOD overexpression protects macrophages from apoptosis.  (+info)

Co-expression of glutathione S-transferase with methionine aminopeptidase: a system of producing enriched N-terminal processed proteins in Escherichia coli. (4/43244)

We describe here an Escherichia coli expression system that produces recombinant proteins enriched in the N-terminal processed form, by using glutathione S-transferase cGSTM1-1 and rGSTT1-1 as models, where c and r refer to chick and rat respectively. Approximately 90% of the cGSTM1-1 or rGSTT1-1 overexpressed in E. coli under the control of a phoA promoter retained the initiator methionine residue that was absent from the mature isoenzymes isolated from tissues. The amount of initiator methionine was decreased to 40% of the expressed cGSTM1-1 when the isoenzyme was co-expressed with an exogenous methionine aminopeptidase gene under the control of a separate phoA promoter. The recombinant proteins expressed were mainly methionine aminopeptidase. The yield of cGSTM1-1 was decreased to 10% of that expressed in the absence of the exogenous methionine aminopeptidase gene. By replacing the phoA with its natural promoter, the expression of methionine aminopeptidase decreased drastically. The yield of the co-expressed cGSTM1-1 was approx. 60% of that in the absence of the exogenous methionine aminopeptidase gene; approx. 65% of the initiator methionine residues were removed from the enzyme. Under similar conditions, N-terminal processing was observed in approx. 70% of the recombinant rGSTT1-1 expressed. By increasing the concentration of phosphate in the growth medium, the amount of initiator methionine on cGSTM1-1 was decreased to 14% of the overexpressed isoenzymes, whereas no further improvement could be observed for rGSTT1-1. The initiator methionine residue does not affect the enzymic activities of either cGSTM1-1 or rGSTT1-1. However, the epoxidase activity and the 4-nitrobenzyl chloride-conjugating activity of the purified recombinant rGSTT1-1 are markedly higher that those reported recently for the same isoenzyme isolated from rat livers.  (+info)

Differential regulation of the human nidogen gene promoter region by a novel cell-type-specific silencer element. (5/43244)

Transfection analyses of the human nidogen promoter region in nidogen-producing fibroblasts from adult skin revealed multiple positive and negative cis-acting elements controlling nidogen gene expression. Characterization of the positive regulatory domains by gel mobility-shift assays and co-transfection studies in Drosophila SL2 cells unequivocally demonstrated that Sp1-like transcription factors are essential for a high expression of the human nidogen gene. Analysis of the negative regulatory domains identified a novel silencer element between nt -1333 and -1322, which is bound by a distinct nuclear factor, by using extracts from adult but not from embryonal fibroblasts. In embryonal fibroblasts, which express significantly higher amounts of nidogen mRNA as compared with adult fibroblasts, this inhibitory nidogen promoter region did not affect nidogen and SV40 promoter activities. The silencer element seems to be active only in nidogen-producing cells. Therefore this regulatory element might function in vivo to limit nidogen gene expression in response to external stimuli. However, none of the identified regulatory elements, including the silencer, contribute significantly to cell-specific expression of the human nidogen gene. Instead we provide evidence that gene expression in epidermal keratinocytes that are not producing nidogen is repressed by methylation-specific and chromatin-dependent mechanisms.  (+info)

Role of retinoid receptors in the regulation of mucin gene expression by retinoic acid in human tracheobronchial epithelial cells. (6/43244)

To investigate which retinoid receptors are critical in the regulation by all-trans-retinoic acid (RA) of the mucin genes MUC2, MUC5AC and MUC5B in cultured normal human tracheobronchial epithelial (NHTBE) cells, we used pan-RAR-, pan-RXR- and RAR- isotype (alpha, beta and gamma)-selective agonists and RARalpha- and RARgamma-selective antagonists (RAR is RA receptor and RXR is retinoid X receptor). RAR-, RARalpha- and RARgamma-selective agonists strongly induced mucin mRNAs in a dose-dependent manner, while the RARbeta-selective retinoid only weakly induced mucin gene expression at very high concentrations (1 microM). The pan-RXR-selective agonist by itself did not induce mucin gene expression, but acted synergistically with suboptimal concentrations of the pan-RAR agonist. A retinoid with selective anti-activator-protein-1 activity only marginally induced mucin gene expression. The RARalpha antagonist strongly inhibited mucin gene induction and mucous cell differentiation caused by RA and by the RARalpha- and RARgamma-selective retinoids. In contrast, the RARgamma antagonist only weakly inhibited RARalpha-selective-retinoid-induced mucin gene expression, but completely blocked mucin gene expression induced by the RARgamma-selective retinoid. Our studies indicate that RARalpha is the major retinoid receptor subtype mediating RA-dependent mucin gene expression and mucous cell differentiation, but that the RARgamma isotype can also induce mucin genes. Furthermore these studies suggest that RARbeta is probably not (directly) involved in RA-induced mucin gene expression.  (+info)

Differential regulation of vascular endothelial growth factor and its receptor fms-like-tyrosine kinase is mediated by nitric oxide in rat renal mesangial cells. (7/43244)

Under conditions associated with local and systemic inflammation, mesangial cells and invading immune cells are likely to be responsible for the release of large amounts of nitric oxide (NO) in the glomerulus. To further define the mechanisms of NO action in the glomerulus, we attempted to identify genes which are regulated by NO in rat glomerular mesangial cells. We identified vascular endothelial growth factor (VEGF) and its receptor fms-like tyrosine kinase (FLT-1) to be under the regulatory control of exogenously applied NO in these cells. Using S-nitroso-glutathione (GSNO) as an NO-donating agent, VEGF expression was strongly induced, whereas expression of its FLT-1 receptor simultaneously decreased. Expressional regulation of VEGF and FLT-1 mRNA was transient and occurred rapidly within 1-3 h after GSNO treatment. Expression of a second VEGF-specific receptor, fetal liver kinase-1 (FLK-1/KDR), could not be detected. The inflammatory cytokine interleukin-1beta mediated a moderate increase in VEGF expression after 24 h and had no influence on FLT-1 expression. In contrast, platelet-derived growth factor-BB and basic fibroblast growth factor had no effect on VEGF expression, but strongly induced FLT-1 mRNA levels. Obviously, there is a differential regulation of VEGF and its receptor FLT-1 by NO, cytokines and growth factors in rat mesangial cells.  (+info)

Comparison of the fibrin-binding activities in the N- and C-termini of fibronectin. (8/43244)

Fibronectin (Fn) binds to fibrin in clots by covalent and non-covalent interactions. The N- and C-termini of Fn each contain one non-covalent fibrin-binding site, which are composed of type 1 (F1) structural repeats. We have previously localized the N-terminal site to the fourth and fifth F1 repeats (4F1.5F1). In the current studies, using proteolytic and recombinant proteins representing both the N- and C-terminal fibrin-binding regions, we localized and characterized the C-terminal fibrin-binding site, compared the relative fibrin-binding activities of both sites and determined the contribution of each site to the fibrin-binding activity of intact Fn. By fibrin-affinity chromatography, a protein composed of the 10F1 repeat through to the C-terminus of Fn (10F1-COOH), expressed in COS-1 cells, and 10F1-12F1, produced in Saccharomyces cerevisiae, displayed fibrin-binding activity. However, since 10F1 and 10F1.11F1 were not active, the presence of 12F1 is required for fibrin binding. A proteolytic fragment of 14.4 kDa, beginning 14 residues N-terminal to 10F1, was isolated from the fibrin-affinity matrix. Radio-iodinated 14.4 kDa fibrin-binding peptide/protein (FBP) demonstrated a dose-dependent and saturable binding to fibrin-coated wells that was both competitively inhibited and reversed by unlabelled 14.4 kDa FBP. Comparison of the fibrin-binding affinities of proteolytic FBPs from the N-terminus (25.9 kDa FBP), the C-terminus (14.4 kDa) and intact Fn by ELISA yielded estimated Kd values of 216, 18 and 2.1 nM, respectively. The higher fibrin-binding affinity of the N-terminus was substantiated by the ability of both a recombinant 4F1.5F1 and a monoclonal antibody (mAb) to this site to maximally inhibit biotinylated Fn binding to fibrin by 80%, and by blocking the 90% inhibitory activity of a polyclonal anti-Fn, by absorption with the 25.9 kDa FBP. We propose that whereas the N-terminal site appears to contribute to most of the binding activity of native Fn to fibrin, the specific binding of the C-terminal site may strengthen this interaction.  (+info)

This month in Alkami PCR Reviews, Lance Larka talks about free online primer design software. Featured in June are DOPE2, DoPrimer, NetPrimer, and Oligos-U-Like/Primers3. His article is at: http://www.alkami.com/reviews/rvwdsgn3.htm Our current list of primer tool links and brief descriptions that we have at http://www.alkami.com/primers/refdsgn.htm includes: * CODEHOP * DOPE2 * DoPrimer * The GPRIME Package * NetPrimer * Oligos-U-Like * Primer Design * Primer3 * Primers! * Primers! Lite * Primer Selection * STS Pipeline v1.2 * The Primer Generator * Web Primer (Stanford) * Web Primers * WWW GeneFisher * xprimer Other primer design resources are listed at http://www.alkami.com/primers/idxprmr.htm The Alkami Biosystems site, http://www.alkami.com, is a comprehensive resource for the polymerase chain reaction. We have online references that include primer design tips and tools, reagent concentrations, polymerase characteristics, PCR methods, and temperature calculations. In addition, you will find ...
Primer Design for PCR: Primer guidelines page offers a look at the general and useful guidelines laid for designing primers for PCR reaction including Primer Tm considerations, PCR primer cross dimer values, annealing temperature and primer GC%
In general, primers are designed to identify specific locations within a long region of DNA, either plasmid or genomic. Primer binding sites are ideally unique within the range of DNA found in the reaction tube. Single primers are used to amplify and label DNA fragments for sequencing reactions, or as probes for Southern blots. Pairs of primers are used to delimit the range of DNA amplified during a PCR reaction. Because biological enzymes selectively add bases on the 3 end of primed double stranded DNA, the binding of the 3 end of the primer is especially important, while the 5 end of the primer can either bind or not, with relatively little effect on most uses of the primer. The binding of the 4-e 3 to the 5 end, the opposite from the DNA synthesis direction found in biological systems. Synthesis starts with a glass bead filled column containing a specific 3 base bound to the glass. Chemically activated nucleotides, termed phosphoramidites, are linked in 3 to 5 order to fabricate the ...
In general, primers are designed to identify specific locations within a long region of DNA, either plasmid or genomic. Primer binding sites are ideally unique within the range of DNA found in the reaction tube. Single primers are used to amplify and label DNA fragments for sequencing reactions, or as probes for Southern blots. Pairs of primers are used to delimit the range of DNA amplified during a PCR reaction. Because biological enzymes selectively add bases on the 3 end of primed double stranded DNA, the binding of the 3 end of the primer is especially important, while the 5 end of the primer can either bind or not, with relatively little effect on most uses of the primer. The binding of the 4-e 3 to the 5 end, the opposite from the DNA synthesis direction found in biological systems. Synthesis starts with a glass bead filled column containing a specific 3 base bound to the glass. Chemically activated nucleotides, termed phosphoramidites, are linked in 3 to 5 order to fabricate the ...
Download Primer3 - PCR primer design tool for free. Design PCR primers from DNA sequence. Widely used (190k Google hits for primer3).
Dear All, I searched for an 18S rRNA gene of an organism on the NCBI website. I found the sequence and designed primers using the primer tool on the same website. Now, I want to check the primer specificity (i.e. can I use this primer as an identification tool to detect a specific species using PCR) and the question is: do I need to BLAST the primer sequence (both forward and reverse) or to BLAST the sequence of the amplified fragment (PCR product). Many thanks in advance. Best regards Mohammad Email: moh_aldeeb from yahoo.com Personal Website: http://sites.google.com/site/draldeebsite/ --- On Wed, 7/6/11, mnr mnr ,mnr475 from gmail.com, wrote: , From: mnr mnr ,mnr475 from gmail.com, , Subject: Blunt end cloning , To: methods from magpie.bio.indiana.edu , Date: Wednesday, July 6, 2011, 1:23 PM , Hi all. , , I have tried cloning a potential toxic gene about 1.2 kbp , into E.coli with , T7 promoter. After two months, I am still not successful. I , am now plannig , to do cloning into pUC18 vector ...
This was important enough that I wanted to get it out immediately. My research into the NCBI database for nucleotide sequences has lead to a stunning discovery. One of the WHO primer sequences in the PCR test for SARS-CoV-2 is found in all human DNA!. The sequence CTCCCTTTGTTGTGTTGT is an 18-character primer sequence found in the WHO coronavirus PCR testing protocol document. The primer sequences are what get amplified by the PCR process in order to be detected and designated a positive test result. It just so happens this exact same 18-character sequence, verbatim, is also found on Homo sapiens chromosome 8! As far as I can tell, this means that the WHO test kits should find a positive result in all humans. Can anyone explain this otherwise?. I really cannot overstate the significance of this finding. At minimum, it should have a notable impact on test results.. ...
(KudoZ) English to Czech translation of Oligos/Primers/Probes: Oligonukleotidy / primery / sondy [Biochemie - Chemistry; Chem Sci/Eng (Science)].
Sequencing Primers and Plasmids - posted in Molecular Biology: Im a little confused about the notation of the sequencing primers listed on the plasmid map for Invitrogens pCR 2.1 and 4.0 used in TOPO TA cloning. Why is the forward primer 3 insertion site while the reverse primer 5 insertion. I thought it is opposite of that. Looking for some explanation. Wondering if Im looking at the map wrong, or if Im not understanding something. Link for map is below.http:...
A rapid and versatile method has been developed for the synthesis of oligonucleotides which contain an aliphatic amino group at their 5 terminus. This amino group reacts specifically with a variety of electrophiles, thereby allowing other chemical species to be attached to the ohgonucleotide. This chemistry has been utilized to synthesize several fluorescent derivatives of an oligonucleotide primer used in DNA sequence analysis by the dideoxy (enzymatic) method. The modified primers are highly fluorescent and retain their ability to specifically prime DNA synthesis. The use of these fluorescent primers in DNA sequence analysis will enable DNA sequence analysis to be automated. ...
The sequence CTCCCTTTGTTGTGTTGT is an 18-character primer sequence found in the WHO coronavirus PCR testing protocol document. The primer sequences are what get amplified by the PCR process in order to be detected and designated a positive test result. It just so happens this exact same 18-character sequence, verbatim, is also found on Homo sapiens chromosome 8! As far as I can tell, this means that the WHO test kits should find a positive result in all humans. Can anyone explain this otherwise ...
The Silk Canvas - Tatcha. Primers once applied might feel a little sticky on the skin. Primer will hold the foundation and other products onto the skin while targeting the skin issue like blocking oil from breaking through and ruining the foundation. Primers do need to have time to soak into the skin especially if they are oil based. Did you know there is more than just face primer? There is eyeshadow primer, lip primer, and lash primer: all with the same goals in mind. Eyeshadow primer should always be used. It will fix almost any problem you might have with eyeshadow. Is your eyeshadow moving? Is the pigment just not showing up? Is your eyeshadow disappearing? Then invest in a good eyeshadow primer. One of my favorites is the Urban Decay Eyeshadow Primer Potion in Original. I did a trial to see how long my eyeshadow would last. It lasted over three days! I have had clients who have worn their makeup two plus days! A quick trick is to lightly set the eyeshadow primer with your setting powder. ...
GENEWIZ offers a variety of free universal primers for sequencing. These free universal primers are being updated to reflect the needs of our customers. Users in our new CLIMS Online Ordering and Data Management System have access to the Updated GENEWIZ Universal Primer list (see below). If you are unsure which CLIMS system you are using, please contact our Technical Support team at 877-GENEWIZ, ext. 2. ...
OLIGO performs a range of functions for researchers in PCR and related technologies, enables to design consensus, multiplex and degenerate primers. Reverse translation, restriction enzyme and open reading frames analysis, oligonucleotide database, primer secondary structure, LCR, siRNA, molecular beacons and nested primers design, real time PCR, batch file processing.
The reasons for primer dimer formation in an NTC are often due to multiple factors. These include: sub-optimal primer annealing temperature (often due to differences in buffering conditions between different qPCR kits), sub-optimal primer synthesis (HPLC-purified primers result in less primer dimer formation and are useful for low copy number detection), and poor primer design (using software such as Primer3 is recommended when designing primers). An alternative is to reduce the total number of cycles in a qPCR reaction if amplification of the primer dimer lies outside of the range of the experimental data eg. if the sample being tested has an average Cq of 28 cycles and contains specific product only (no primer dimer), and the NTC amplifies a primer dimer after 37 cycles, the reaction can be run for 35 cycles, rather than 40. This approach can be taken only when the sample being tested gives rise to a specific product and not a combination of specific product and primer dimer, and also when the ...
RT-PCR primer design - posted in PCR, RT-PCR and Real-Time PCR: Hi, I want to ask about how to design primer for RT-PCR. Specifically, i want to design primer based on the human mRNA encoding the c-myc, p53, caspase-3 and bcl-2 gene. I have no clue where to start and what to do... thank you..
( http://www.abnova.com ) - Primer-BLAST was developed to help users make primers that are specific to the input PCR template. It uses Primer3 to design PCR primers and then submits them to BLAST...
Gel Layout:. Lane 1 - Hyperladder 1. Lanes 2-6 = 5′ RACE Library. Lane 2 - nGSP1 (5′ RACE primer). Lane 3 - nGSP2 (3′ RACE primer). Lane 4 - Neg. Control (no RACE primers). Lane 5 - Neg. Control (nGSP1, no Universal primer). Lane 6 - Neg. Control (nGSP2, no Universal primer). Lane 7 - Empty. Lanes 8-12 = 3′ RACE Library. Lane 8 - nGSP1 (5′ RACE primer). Lane 9 - nGSP2 (3′ RACE primer). Lane 10 - Neg. Control (no RACE primers). Lane 11 - Neg. Control (nGSP1, no Universal primer). Lane 12 - Neg. Control (nGSP2, no Universal primer). First of all, we see the appropriate response of each primer only producing amplicons in their respective libraries (i.e. 5′ primer only works in 5′ RACE library). This simply confirms that the primers were designed correctly. Secondly, our negative controls are clean. Thirdly, we get distinct bands from both primers. The bands marked with blue arrows in the image above were excised and purified using Ultrafree DA spin columns (Millipore). These ...
Methylated/Non-methylated Control DNA & Primer Set DNA ZD5101-2 Methylated/Non-methylated Control DNA & Primer Set DNA ZD5101-2
Again, follow the manufacturers instructions to … Wickes Waterproof PVA is a resin based adhesive that can be used internally or externally and provides a high strength, impact resistant bond. It has incan antibacterial properties. Due to its great flow and leveling properties, Valspar PVA primer can be brushes, rolls and sprays with ease. In liquid form they come in two parts, liquid and powder, to be mixed together. Solvent free formulation making the product safe to … Can be used as a building adhesive, primer, admixture, bonding agent and dustproofer. Work in sections and be sure to clean every bit of the concrete and wash off the acid mixture. World Class Manufacturing. Why is Acrylic Primer Different or Better? National PVA Primer Sealer for Masonry is a general-purpose primer clear for cementitious surface. Rated 5 out of 5 by nutcracker33 from mapei primer very good primer for plaster walls prior to tiling. Before adding your color, you need to use primer to ensure that the paint ...
Now that my lab is fully equipped, Im taking on rotation students. Unfortunately, with the pandemic, its harder to have one-on-one meetings where I can sit down and walk the new students through every method. Furthermore, why repeat teaching the same thing to multiple students when I can just make an initial written record that everyone can reference and just ask me questions about? Thus, heres my instructional tutorial on how I design primers in the lab.. First, its good to start out by making a new benchling file for whatever youre trying to engineer. If youre just making a missense mutation, then you can start out by copying the map for the plasmid youre going to use as a template. Today, well be mutating a plasmid called G619C_AttB_hTrim-hCPSF6(301-358)-IRES-mCherry-P2A-PuroR to encode the F321N mutation the CPSF6 region. This should abrogate the binding of this peptide to the HIV capsid protein. Eventually every plasmid in the lab gets a unique identifier based on the order it ...
Picks PCR primers and hybridization oligos Version: EMBOSS:6.4.0.0 Standard (Mandatory) qualifiers: [-sequence] seqall The sequence from which to choose primers. The sequence must be presented 5 to 3 [-outfile] outfile [*.eprimer3] Whitehead primer3_core program output file Additional (Optional) qualifiers (* if not always prompted): -[no]primer toggle [Y] Tell EPrimer3 to pick primer(s) * -task menu [1] Tell EPrimer3 what task to perform. Legal values are 1: Pick PCR primers, 2: Pick forward primer only, 3: Pick reverse primer only, 4: No primers needed. (Values: 1 (Pick PCR primers); 2 (Pick forward primer only); 3 (Pick reverse primer only); 4 (No primers needed)) -hybridprobe toggle [N] An internal oligo is intended to be used as a hybridization probe (hyb probe) to detect the PCR product after amplification. * -mishyblibraryfile infile Similar to MISPRIMING-LIBRARY, except that the event we seek to avoid is hybridization of the internal oligo to sequences in this library rather ...
Pick PCR primers and hybridization oligos Version: EMBOSS:6.6.0.0 Standard (Mandatory) qualifiers: [-sequence] seqall The sequence from which to choose primers. The sequence must be presented 5 to 3 [-outfile] outfile [*.eprimer32] Whitehead primer3_core program output file Additional (Optional) qualifiers (* if not always prompted): -[no]primer toggle [Y] Tell Eprimer32 to pick primer(s) * -task menu [1] Tell Eprimer32 what task to perform. Legal values are 1: Pick PCR primers, 2: Pick forward primer only, 3: Pick reverse primer only, 4: No primers needed. (Values: 1 (Pick PCR primers); 2 (Pick forward primer only); 3 (Pick reverse primer only); 4 (No primers needed)) -hybridprobe toggle [N] An internal oligo is intended to be used as a hybridization probe (hyb probe) to detect the PCR product after amplification. * -mishyblibraryfile infile Similar to MISPRIMING-LIBRARY, except that the event we seek to avoid is hybridization of the internal oligo to sequences in this library ...
Dear all, I obtained the job and need to identify presence of some bacteria in clinical samples by PCR with species/strain specific primers. The primers are already available in the lab, but the person who designed/find/order the primers were not available in the lab anymore and nobody knows the details. Therefore, I know primer sequences, the names of the strains, but I do not know the target (genome, 16S, ...), the size of the amplicon - actually I have no data to check the PCR result... I tried to blast them, but only one pair is found on the NCBI. How to find the target sequences, can anyone help me. Are there are softwares or databases for blasting the bacterial genome/transcriptome? ...
use Bio::PrimerDesigner; my $pd = Bio::PrimerDesigner-,new; # # Define the DNA sequence, etc. # my $dna = CGTGC...TTCGC; my $seqID = sequence 1; # # Define design parameters (native primer3 syntax) # my %params = ( PRIMER_NUM_RETURN =, 2, PRIMER_SEQUENCE_ID =, $seqID, SEQUENCE =, $dna, PRIMER_PRODUCT_SIZE =, 500-600 ); # # Or use input aliases # %param = ( num =, 2, id =, $seqID, seq =, $dna, sizerange =, 500-600 ); # # Design primers # my $results = $pd-,design( %params ) or die $pd-,error; # # Make sure the design was successful # if ( !$results-,left ) { die No primers found\n, $results-,raw_data; } # # Get results (single primer set) # my $left_primer = $results-,left; my $right_primer = $results-,right; my $left_tm = $results-,lefttm; # # Get results (multiple primer sets) # my @left_primers = $results-,left(1..3); my @right_primers = $results-,right(1..3); my @left_tms = $results-,lefttm(1..3 ...
Explore our makeup primer, face primer and foundation primer for the face, including perfecting primer, morning retexturing primer, and advanced eye-fix primer.
Explore our makeup primer, face primer and foundation primer for the face, including perfecting primer, morning retexturing primer, and advanced eye-fix primer.
Color Studio Professional most advanced primer ever. Created for skin repair and conditioning giving flawless results with any foundation.The DNA primer is a silky cream primer that contains a mix of anti-blemish and focused whitening agents that...
This is the amplicon context sequence in accordance with the minimum information for the publication of real-time quantitative PCR experiements (MIQE) guidelines. For more details, please refer to the following publication, Primer Sequence Disclosure: A Clarification of the MIQE Guidelines. ...
This is the amplicon context sequence in accordance with the minimum information for the publication of real-time quantitative PCR experiements (MIQE) guidelines. For more details, please refer to the following publication, Primer Sequence Disclosure: A Clarification of the MIQE Guidelines. ...
Usually the sequencing primer is used at 0.3µM in annealing buffer but some assays might require additional optimization of the sequencing primer concentration.. For PyroMark Q24 and PyroMark Q96 MD the final concentration of the sequencing primer is 0.3µM and for PyroMark Q96 ID 0.4µM ...
Choosing appropriate primers is probably the single most important factor affecting the polymerase chain reaction (PCR). Specific amplification of the intended target requires that primers do not have matches to other targets in certain orientations and within certain distances that allow undesired amplification. The process of designing specific primers typically involves two stages. First, the primers flanking regions of interest are generated either manually or using software tools; then they are searched against an appropriate nucleotide sequence database using tools such as BLAST to examine the potential targets. However, the latter is not an easy process as one needs to examine many details between primers and targets, such as the number and the positions of matched bases, the primer orientations and distance between forward and reverse primers. The complexity of such analysis usually makes this a time-consuming and very difficult task for users, especially when the primers have a large number of
There are three choices of RT primer: oligo(dT), random primers, or a gene-specific primer. The priming strategy has a strong impact on the workflow applied, since each priming method has prerequisites and consequences.. Oligo(dT) priming is used to receive full-length copies of the mRNA. For cDNA library construction or cDNA labeling applications, oligo(dT) primers are almost always used to prime cDNA synthesis. Anchored oligo(dT)18 primers are designed to bind at the beginning of the poly(A) tail (rather than randomly within the often long tail) to generate full-length cDNAs. This avoids mispriming and unnecessary reverse transcription of the long poly(A) tail. Since the 5´ ends of long mRNAs are often underrepresented in cDNA mixtures, this primer is preferred for most applications.. However, if the message is long or does not have a poly(A) tail (as with prokaryotic mRNA), then random hexamer primers are used. Random hexamer primers bind throughout the entire length of RNA, ensuring reverse ...
For each QuantiTect Primer Assay, we retrieve the sequence of the target gene from curated databases and exclude SNP regions from assay design.. We then use our proprietary algorithm to design assays that amplify RNA sequences only (i.e., at least one primer overlaps a splice site), provided that information on the position of splice sites is available. The assays are designed to provide optimal performance with QuantiFast and QuantiTect SYBR Green Kits. After assay design, we validate randomly selected QuantiTect Primer Assays using real-time RT-PCR to check their compatibility with various real-time cyclers. Both two-step and one-step RT-PCR are carried out. Successful amplification of the target is indicated by the following factors: high sensitivity, high efficiency, high specificity (i.e., a single peak in melting curve analysis), and no primer-dimers in the no-template control (NTC). To find a QuantiTect Primer Assay for your target gene of interest, please visit our GeneGlobe data ...
Cross-species primers have been used with moderate success to address a variety of questions concerning genome structure, evolution, and gene function. However, the factors affecting their success have never been adequately addressed, particularly with respect to producing a consistent method to achieve high throughput. Using 1,147 mammalian cross-species primer pairs (1089 not previously reported), we tested several factors to determine their influence on the probability that a given target will amplify in a given species under a single amplification condition. These factors included: number of mismatches between the two species (the index species) used to identify conserved regions to which the primers were designed, GC-content of the gene and amplified region, CpG dinucleotides in the primer region, degree of encoded protein conservation, length of the primers, and the degree of evolutionary distance between the target species and the two index species. The amplification success rate for the cross
Despite the many methodological options available for mutation detection, the choice is limited, by the necessity to ensure the highest sensitivity of detection for all types of changes while keeping costs and time of analysis within a reasonable limit. The present study extends to large and complex genes, like BRCA1, the applications of the FAMA method using large PCR amplicons (up to 1.4 kb). A key feature of this diagnostic strategy is the robust and economical two-step procedure for strand-specific labeling of PCR products using chimeric oligonucleotides and universal fluorescent primers (Fig. 1)⇓ . This labeling method is cost-effective, because it requires only one set of universal fluorescent primers, and allows reproducible amplification of all exons and splice sites of BRCA1 using homogeneous PCR conditions.. In the blind-test screening for changes in exon 11 (Table 2)⇓ different kinds of mutations and polymorphisms (various microdeletions/insertions involving 1 to 11 nucleotides as ...
Thermo Scientific™ M13/pUC sequencing primer (-20), 17-mer 10uM, 6nmol Unlabeled Oligonucleotides and Primers Oligonucleotides
Lasergenes PrimerSelect offers the best in advanced primer design software, enabling you to design and analyze primers for PCR, sequencing, probe hybridization and transcription.
Note: Optimal annealing temperatures are often higher than the Tm of the primers (approximately +5 to +10°C) and have to be determined empirically. For both primers, the Tm should be similar.. Bases that do not hybridize to the template may be added at the 5´ end of a primer (e.g., for introducing restriction sites into the amplification product). Primer concentrations between 0.1 and 0.6 µM are generally optimal. Higher primer concentrations may promote mispriming and accumulation of nonspecific product. Lower primer concentrations may be exhausted before the reaction is completed, resulting in lower yields of desired product.. Note: For some systems, a higher primer concentration (up to 1 µM) may improve results. When testing new primers, always include a positive control reaction with a template that has been tested for function in PCR. This control shows whether the primers are working. The Human Genomic DNA from Roche is a good control template for evaluation of human primer ...
You need to first build an initial protocol and then optimize it.. The most important to determine the conditions is the polymerase used. Some polymerases work at higher or lower temperatures and will work faster or slower. Find the default protocol from the polymerase seller and this will give you a good idea where to start.. The second most important is the primers used. Depending on the GC % in the primers and their length, the times or temperature of each step will change, or if you prefer will need to be Optimized. The length of the DNA fragments will also determine the length of the cycles. Most polymerase sellers will includes steps to optimize the reaction depending on the quantity of DNA used, primer length and other parameters. For more information: Designing primers: Taq DNA polymerase protocol example:. Optimizing PCR ...
The first set of primers is designed to anneal to sequences upstream from the second set of primers, whereas the second set of primers is situated internally or nested with respect to the first set of primers. First set of primers also called outer primers amplify a large fragment of the gene which is used as a template in the second round of PCR that targets a smaller region of the amplicon using the second set of primers also known as inner primers or nested primers. The traditional approach to nested PCR was to perform a number of PCR cycles using first set of primers, and then open the reaction vessel and add the second, nested, set of primers to run second PCR cycle. The major problem with this approach is amplicon contamination in the laboratory and a consequential loss of specificity of the assay. To address this issue single-tube nested PCR (STNPCR) reactions have been developed, wherein both sets of primers are added to the initial reaction vessel and an extended PCR is performed. ...
Now more than ever, PCR has become a household name akin to Harry Potter or Gandalf the Grey, and in most cases no less mysterious nor magical. Whilst the distillation of molecular magic that is PCR has been invaluable (despite controversy) for screening your swabs, spit and other bodily fluids for COVID-19, it is also…
Further examination of the map shows that all of the reverse primers start at about the same place within the promoter region (~299,000), and the length differences are primarily due to choice of the forward primer, in the 3 downstream region of the gene. Since we are mostly interested in maximizing the promoter region, well choose Primer Pair 3 for further work. To save the sequence of the PCR product, along with its gene annotation, mouse over the map for Primer Pair 3 to bring up the menu shown above, and click on GenBank view. The GenBank view will appear in a new tab or window ...
Further examination of the map shows that all of the reverse primers start at about the same place within the promoter region (~299,000), and the length differences are primarily due to choice of the forward primer, in the 3 downstream region of the gene. Since we are mostly interested in maximizing the promoter region, well choose Primer Pair 3 for further work. To save the sequence of the PCR product, along with its gene annotation, mouse over the map for Primer Pair 3 to bring up the menu shown above, and click on GenBank view. The GenBank view will appear in a new tab or window ...
BiSearch software is composed of two basic algorithms. The first one is a primer design algorithm the second one is a search with the selected primers through genomic sequences to find potential non-specific PCR products.
BioMed Research International is a peer-reviewed, Open Access journal that publishes original research articles, review articles, and clinical studies covering a wide range of subjects in life sciences and medicine. The journal is divided into 55 subject-specific sections.
Chlamydiae are implicated in a variety of clinically and economically important diseases in livestock and companion animals. These bacteria are associated with abortion, conjunctivitis, encephalomyelitis, enteritis, pneumonia, and polyarthritis in ruminants. Infection with these bacteria is the most common cause of abortion in sheep and goats and also causes zoonotic infection in humans which, in pregnant women, can result in spontaneous abortion.
The goals of this investigation were to identify and evaluate the use of polymorphic microsatellite marker (PMM) analysis for molecular typing of seventeen plant pathogenic fungi. Primers for di-, tri-, and tetranucleotide loci were designed directly from the recently published genomic sequence of Mycospherlla graminicola and Fusarium graminearum. A total of 20 new microsatellite primers as easy-to-score markers were developed. Microsatellite primer PCR (MP-PCR) yielded highly reproducible and complex genomic fingerprints, with several bands ranging in size from 200 to 3000 bp. Of the 20 primers tested, only (TAGG)4, (TCC)5 and (CA)7T produced a high number of polymorphic bands from either F. graminearum or F. culmorum. (ATG)5 led to successful amplifications in M. graminicola isolates collected from Germany. Percentage of polymorphic bands among Fusarium species ranged from 9 to 100%. Cluster analysis of banding patterns of the isolates corresponded well to the established species delineations based
RAPD Primer Design from Metagenomes RPDM scans metagenome sequences identifying and determining relative frequency of candidate primers for Random Amplification of Polymorphic DNA RAPD assays
Applicability of the polymerase chain reaction (PCR) with species-specific primers to obtaining molecular markers for identification of the sibling species of Chironomus plumosus group - C. plumosus and C. balatonicus - has been estimated. The nucleotide sequences of internal transcribed spacer (ITS) from the locus encoding ribosomal RNA (rRNA) were used as the source for designing the species-specific primers. The primers allowing for identification of C. plumosus and C. balatonicus were constructed. One primer pair (plu107F/plu363R) gives the PCR product MAR2, specific of C. plumosus, and the other (bal86F/plu363R), the PCR product MAR6, specific of C. balatonicus. The testing involving 18 species of the genus Chironomus confirmed the specificity of the primers. The results suggest that the PCR with species-specific primers is promising for construction of molecular markers for identification not only of these two, but also of other Chironomus species.. doi: 10.5324/fn.v31i0.1381.. Published ...
Battling infection is a major healthcare objective. Untreated infections can rapidly evolve toward the condition of sepsis in which the body begins to fail and resuscitation becomes critical and tenuous. Identification of infection followed by rapid antimicrobial treatment are primary goals of medical care, but precise identification of offending organisms by current methods is slow and broad spectrum empirical therapy is employed to cover most potential pathogens. Current methods for identification of bacterial pathogens in a clinical setting typically require days of time, or a four- to eight-hour growth phase followed by DNA extraction, purification and PCR-based amplification. We demonstrate rapid (70-120 minutes) genetic diagnostics methods utilizing loop-mediated isothermal amplification (LAMP) to test for 15 common infection pathogen targets, called the Infection Diagnosis Panel (In-Dx). The method utilizes filtration to rapidly concentrate bacteria in sample matrices with lower bacterial loads
The Random Primer DNA Labeling Kit, Version 2 is designed for radioactive labeling for hybridization probes. Probe labeling can label DNA with [32P]-alpha-, [35S]-alpha- or [3H]-alpha-dCTP. This random primer DNA labeling kit is based on a modified method by Feinberg and Vogelstein and utilizes random oligonucleotide primers and cloned exonuclease-free E.coli DNA polymerase I, Klenow fragment. Using primers that are 9-mer and longer and exonuclease-free enzyme results in higher labeling efficiency and longer probes. This probe labeling method overcomes many of the disadvantages of conventional nick translation procedures while producing hybridization probes from very small amounts of DNA (10 to 20 ng). The Radioactive Labeling for Hybridization Probes kit can also be used to label DNA fragments that are embedded in low-melting temperature agarose gel slices.. ...
Two different molecular approaches, a multiplex PCR and PCR-RFLP of ITS-rDNA, were developed for the identification of Hoplolaimus species. DNA sequences of H. columbus, H. galeatus, H. concaudajuvencus, H. magnistylus, H. seinhorsti and three undescribed Hoplolaimus species were used to design species-specific primers. Three reverse species-specific PCR primers for H. columbus, H. galeatus and H. magnistylus were developed using the ITS1 region exhibiting interspecific variation. Three species-specific PCR primers in combination with the forward primer, Hoc-1f, produced distinct amplicons of 580 bp for H. columbus, 120 bp for H. galeatus and 340 bp for H. magnistylus. We successfully identified each of three species by multiplex PCR when all three were mixed in a single PCR reaction. Restriction enzyme digests of the PCR amplicon using HaeIII and RsaI permitted discrimination of H. columbus, H. galeatus, H. magnistylus, H. concaudajuvencus, H. sp. 1, H. sp. 2 and H. sp. 3 from each other. These results
Researchers showed how an isothermal amplification technique could detect S. enterica serovars from culture by targeting specific gene markers.
GenemerTM Products. The GenemerTM product line is PCR based. The product includes a specific primer pair for gene or mutation specific amplification. Genemer products are available for the gene fragment and disorders listed. Specialized optimized conditions may be required for certain triple repeat disorder amplifications. The GenemerTM kit is a complete easy-to-use kit for reliable genotyping of a gene fragment. The product includes a specific primer pair for gene or mutation specific amplification, optimized buffers and dNTPs and in most cases, control DNA. These kits contain specialized and optimized conditions that are required for amplification of large repeats in certain triple repeat disorder amplifications. Gene Link recommends these GenemerTM kits for researchers who have not established their own optimized amplification conditions. GenemerTM kits are also available for conventional radioactive-based detection methods. A Radioactive component is not present in these kits. Gene Link ...
17138DNAArtificial SequenceSequence source PCR primer, 38 bases 1catgcatggg atccaacttg ctagacgcaa atatcgca 38239DNAArtificial SequenceSequence source PCR primer, 39 bases 2catgcatgcc cgggtcatga ttcttctttg atcatcacg 39328DNAArtificial SequenceSequence source PCR primer, 28 bases 3caccttctct tacgaatgtt tcgttggc 28439DNAArtificial SequenceSequence source PCR primer, 39 bases 4catgcatgcc cgggtcatga ttcttctttg atcatcacg 39539DNAArtificial SequenceSequence source PCR primer, 39 bases 5catgcatggg atccaactta ctggataaag aaagccgtt 39624DNAArtificial SequenceSequence source PCR primer, 24 bases 6tcaggcttct tcaatacaga ttgc 24737DNAArtificial SequenceSequence source PCR primer, 37 bases 7catgcatggg atccttcagc ttcgaactca gtaccga 37824DNAArtificial SequenceSequence source PCR primer, 24 bases 8tcaggcttct tcaatacaga ttgc 24928DNAArtificial SequenceSequence source PCR primer, 28 bases 9caccaacttg ctagacgcaa atatcgca 281024DNAArtificial SequenceSequence source PCR primer, 24 bases 10tcaggcttct tcaatacaga ttgc ...
The RT² qPCR Primer Assay is the most reliable SYBR® Green-based quantitative real-time PCR assay for gene expression analysis. Our experimentally verified design algorithm yields gene-specific qPCR assays characterized by uniform and high PCR efficiencies and standardized amplification conditions. Every RT² Primer Assay is subjected to rigorous experimental verification. Single product amplification of the correct size and high PCR efficiency are guaranteed when using the appropriate RT² qPCR Master Mixes. The uniform PCR amplification efficiencies and PCR conditions of the RT² qPCR Primer Assays provide an accurate and scalable solution for multiple gene expression analyses. Browse Primer Assays By Gene ...
The RT² qPCR Primer Assay is the most reliable SYBR® Green-based quantitative real-time PCR assay for gene expression analysis. Our experimentally verified design algorithm yields gene-specific qPCR assays characterized by uniform and high PCR efficiencies and standardized amplification conditions. Every RT² Primer Assay is subjected to rigorous experimental verification. Single product amplification of the correct size and high PCR efficiency are guaranteed when using the appropriate RT² qPCR Master Mixes. The uniform PCR amplification efficiencies and PCR conditions of the RT² qPCR Primer Assays provide an accurate and scalable solution for multiple gene expression analyses. Browse Primer Assays By Gene ...
Biological RNA generally comprises secondary structure motifs which cause a problem for target RNA detection by isothermal amplification methods. The complexity of the secondary structures makes RNA targets inaccessible for probe hybridization, resulting in decreased sensitivity and selectivity. This is particularly important because the hybridization step of the isothermal amplification method re ...
Since presently-available DNA sequencing technologies are ill-suited for reading long sequences, large pieces of DNA (such as ... Wooley, JC; Godzik, A; Friedberg, I (Feb 26, 2010). "A primer on metagenomics". PLoS Comput Biol. 6 (2): e1000667. doi:10.1371/ ... Sequence assembly refers to the reconstruction of a DNA sequence by aligning and merging small DNA fragments. It is an integral ... In bioinformatics, sequence analysis is the process of subjecting a DNA, RNA or peptide sequence to any of a wide range of ...
Universal matK primers can be used for DNA barcoding of angiosperms. LtrA, an open reading frame found in the Lactococcus ... Jing YU, Jian-Hua XU, Shi-Liang ZH (May 2011). "New universal matK primers for DNA barcoding angiosperms". Journal of ...
The thermal cycler (also known as a thermocycler, PCR machine or DNA amplifier) is a laboratory apparatus most commonly used to ... This is particularly useful when testing suitable annealing temperatures for PCR primers. ... Later, the PCR process was adapted to the use of thermostable DNA polymerase from Thermus aquaticus, which greatly simplified ... Weier, HU; Gray, JW (Jul-Aug 1988). "A programmable system to perform the polymerase chain reaction". DNA (Mary Ann Liebert, ...
Primosomes gives RNA primers for DNA synthesis to strands. ΦX174 is closely related to other microviridae, especially the NC ... The phi X 174 (or ΦX174) bacteriophage is a single-stranded DNA (ssDNA) virus that infects Escherichia coli, and the first DNA- ... The DNA is ejected through a hydrophilic channel at the 5-fold vertex. It is understood that H protein resides in this area but ... Nobel prize winner Arthur Kornberg used ΦX174 as a model to first prove that DNA synthesized in a test tube by purified enzymes ...
Excision of gene coding sequences from genomic DNA. "BRENDA: 3.1.30.1". Eun, HM (1996). "Nucleases". Enzymology primer for ... An excess of the enzyme is required to degrade double-stranded DNA or RNA and DNA-RNA hybrids, and in this case, AT-rich ... Nuclease MB is a specific DNA and RNA exo-endonuclease which will degrade single-stranded extensions from the ends of DNA and ... The enzyme degrades single-stranded DNA or RNA to nucleoside 5'-monophosphates, but does not digest double-stranded DNA, double ...
Da bei der LAMP vier bis sechs Primer an sechs bis acht DNA-Sequenzen binden,[7] ist das Primerdesign im Vergleich zu anderen ... Die LAMP verwendet eine strangversetzende DNA-Polymerase (z. B. Bst-DNA-Polymerase oder Bst 2.0)[3] und läuft bei einer ... Analog zur qPCR kann die entstehende DNA quantifiziert werden.[10][11] Analog zur Multiplex-PCR können mehrere DNA-Sequenzen ... von DNA.[1] Sie ist eine Variante der isothermalen DNA-Amplifikation.[2] ...
DNA polymorphisms amplified by arbitrary primers are useful genetic markers. Nucleic Acids Research. 18, 6531-6535 (1990). ... as well as on DNA-DNA hybridization assays and phenotypic characterizations. The type strain EN-119T was isolated from ... On the basis of DNA relatedness, both organisms could be included in a single taxon. However, the CDC enteric group 69 was ... 8, 281-289 (2002). Ruiz J. Mechanisms of resistance to quinolones: target alterations, decreased accumulation and DNA gyrase ...
Two sets of primers are used in two successive reactions. In the first PCR, one pair of primers is used to generate DNA ... January 1988). "Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase". Science. 239 (4839): 487-91 ... Two amplifications are then carried out on the bisulfite-treated DNA: One primer set anneals to DNA with cytosines ( ... uses a recombinase to specifically pair primers with double-stranded DNA on the basis of homology, thus directing DNA synthesis ...
Universal primer cocktails for fish DNA barcoding. Molecular Ecology Notes. 7, 544-54. Prince C. 2009. Practical Manual of ...
"Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase". Science. 239 (4839): 487-91. Bibcode: ...
A genetic marker is a gene or DNA sequence with a known location on a chromosome that can be used to identify individuals or ... the development and use of evolutionarily conserved sets of PCR primers. the use of microsatellite loci that vary among ... The marker could be a short DNA sequence, such as a sequence surrounding a single base-pair change, known as a single ... the development of advanced DNA sequencing techniques. Many things utilized for studying larger organisms has not been possible ...
An additional pair of "loop primers" can further accelerate the reaction. The amount of DNA produced in LAMP is considerably ... The larger number of primers per target in LAMP increases the likelihood of primer-primer interactions for multiplexed target ... Because LAMP uses 4 (or 6) primers targeting 6 (or 8) regions within a fairly small segment of the genome, and because primer ... open-source or commercial software packages are generally used to assist with LAMP primer design, although the primer design ...
"DNA Polymorphisms Amplified by Arbitrary Primers Are Useful as Genetic Markers". Nucleic Acids Research. 18 (22): 6531-6535. ... Books Kidwell, K. K.; Osborn, T. C. (1992). "Simple Plant DNA Isolation Procedures". In Beckman, J. S.; Osborn, T. C. (eds.). ... Doyle, J. J.; Doyle, J. L. (1987). "A Rapid DNA Isolation Procedure for Small Quantities of Fresh Leaf Tissue". Phytochemical ... Sharma, R.; Mahla, R. H.; Mohapatra, T.; Bhargava, C. S.; Shama, M. M. (2003). "Isolating Plant Genomic DNA Without Liguid ...
"Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase". Science. 239 (4839): 487-491. Bibcode: ... DNA, based on A-T, C-G base pairs, are formed in well-aligned sequences. Through precise sequences of DNA, 20 amino acids are ... At first, taking DNA or RNA as templates, scientists developed a series of peptide nucleic acid (PNA)-based polymers, without ... In nature, DNA, RNA, proteins and other macromolecules can also be recognized as sequence-controlled polymers for their well- ...
of the domestic fowl using DNA polymorphisms amplified by arbitrary primers". Parasitology Research. 79 (2): 98-102. doi: ... DNA assays and recombinant DNA techniques. PCR has proven most useful for outbreak surveillance. Prior to these methods, ...
MethPrimerDB Contains 259 primer sets from human, mouse and rat for DNA methylation analysis. The Histone Database Contains 254 ... "methPrimerDB: the DNA methylation analysis PCR primer database". Archived from the original on 2014-07-15. Retrieved 2010-01-29 ... MethyLogiX DNA methylation database Contains DNA methylation data of human chromosomes 21 and 22, male germ cells and late- ... The Krembil Family Epigenetics Laboratory Contains DNA methylation data of human chromosomes 21, 22, male germ cells and DNA ...
These tools are used to optimize the design of primers for target DNA or cDNA sequences. Primer optimization has two goals: ... The last 10-12 bases at the 3' end of a primer are sensitive to initiation of polymerase extension and general primer stability ... On the other hand, FastPCR, a commercial application, allows simultaneous testing of a single primer or a set of primers ... nor should the primer pairs bind to conserved regions of a gene family. If the selectivity is poor, a set of primers will ...
... more on AM fungal specific primers below) 2 μl template DNA PCR: Run on an MWG AG Biotech Primus 96 Plus thermocycler 15 ... "Kruger" primers yielded relatively higher diversity parameters than other comparable primers (LSU, ITS2) "Kruger" primers ... primer utilizes the partial SSU and the ITS. Currently, there is no consensus as to which primers or primer sets, being used ... and repeatable primers or primer sets. Currently there are four common AM fungal specific markers/primers used in genetic ...
"Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase". Science. 239 (4839): 487-91. Bibcode: ... DNA polymerase ("Taq pol")[edit]. Further information: Taq polymerase. DNA polymerase was first isolated from T. aquaticus in ... The first polymerase enzyme isolated from T. aquaticus in 1974 was a DNA-dependent RNA polymerase,[8] used in the process of ... It is the source of the heat-resistant enzyme Taq DNA polymerase, one of the most important enzymes in molecular biology ...
The thermal cycler (also known as a thermocycler, PCR machine or DNA amplifier) is a laboratory apparatus most commonly used to ... This is particularly useful when testing suitable annealing temperatures for PCR primers. Weier, HU; Gray, JW (Jul-Aug 1988). " ... The earliest thermal cyclers were designed for use with the Klenow fragment of DNA polymerase I. Since this enzyme is destroyed ... Later, the PCR process was adapted to the use of thermostable DNA polymerase from Thermus aquaticus, which greatly simplified ...
Padmanabhan, R.; Wu, Ray (1972). "Use of oligonucleotides of defined sequences as primers in DNA sequence analysis". ... Plant genetics pioneer Ray Wu invented the first method for sequencing DNA, considered a major breakthrough in genetics as it ... Wu, Ray (April 19, 1972). "Nucleotide Sequence Analysis of DNA". Nature. 236 (68): 198-200. doi:10.1038/newbio236198a0. PMID ...
Finally, the strand displacing polymerase begins DNA synthesis where the primer has bound to the target DNA. By using two ... for rapid detection of viral genomic DNA or RNA, pathogenic bacterial genomic DNA, as well as short length aptamer DNA. The ... "Rapid PCR". Dna.utah.edu. Retrieved 2014-06-21. CS1 maint: discouraged parameter (link) "PCR primers work using standard RPA ... Recombinases are capable of pairing oligonucleotide primers with homologous sequence in duplex DNA. SSB bind to displaced ...
The target DNA undergoes the first run of polymerase chain reaction with the first set of primers, shown in green. The ... Conventional PCR requires primers complementary to the termini of the target DNA. The amount of product from the PCR increases ... A commonly occurring problem is primers binding to incorrect regions of the DNA, giving unexpected products. This problem ... Polymerase chain reaction itself is the process used to amplify DNA samples, via a temperature-mediated DNA polymerase. The ...
PCR is a method that a template DNA is amplified using synthetic primers, a DNA polymerase, and dNTPs. The mixture is cycled ... With rising government support in DNA molecular diagnostics, it is expected that an increasing number of clinical DNA detection ... a high temperature for denaturing double-stranded DNA into single-stranded molecules and a low temperature for the primer to ... end of primer. Many different companies have developed diagnostics tests based on ARMS PCR primers. For instance, Qiagen ...
"Primers, 16S ribosomal DNA - François Lutzoni's Lab". lutzonilab.net. Arquivado dende o orixinal o 2012-12-27.. ... O par cebador ou primer máis común foi concibido por Weisburg et al.[5] e denomínase actualmente 27F e 1492R; porén, para ... James, Greg (15 May 2018). "Universal Bacterial Identification by PCR and DNA Sequencing of 16S rRNA Gene". PCR for Clinical ... Kolbert CP, Persing DH (June 1999). "Ribosomal DNA sequencing as a tool for identification of bacterial pathogens". Current ...
... end of an existing DNA molecule. Terminal transferase is one of the few DNA polymerases that can function without an RNA primer ... a DNA methyltransferase is a transferase that catalyzes the transfer of a methyl group to a DNA acceptor. In practice, many ... Terminal transferases are transferases that can be used to label DNA or to produce plasmid vectors. It accomplishes both of ... In the EC system of classification, the accepted name for RNA Polymerase is DNA-directed RNA polymerase. Described primarily ...
British Isles DNA Project Haplogroup G Project in Family Tree DNA G Arabia Project in Family Tree DNA. ... forward primer is tatgcatttgttgagtatatgtc.....reverse primer is gttctgaatgaaagttcaaacg.....the mutation involves a change from ... populations of Europe Y-DNA haplogroups in populations of the Caucasus Y-DNA haplogroups in populations of the Near East Y-DNA ... "ISOGG 2015 Y-DNA Haplogroup Tree". isogg.org. Underhill PA, Passarino G, Lin AA, Shen P, Mirazón Lahr M, Foley RA, Oefner PJ, ...
"Primer directed enzymatic amplification of DNA with thermostable DNA polymerase". Science. 239 (238): 487-491. doi:10.1126/ ... Cite journal requires ,journal= (help) Lynch, M.; Crease, T.J. (1990). "The Analysis of Population Survey Data of DNA sequence ... and Cyprus analyzing mitochondrial DNA segments and finding differences in enzymatic restrictions, resulting in Apis mellifera ...
SGI-DNA Gibson Assembly Cloning Guide. *Gibson Assembly Primer Design Tool. *Gibson Assembly Site Directed Mutagenesis Primer ... The DNA polymerase incorporates nucleotides to fill in any gaps.. *The DNA ligase covalently joins the DNA of adjacent segments ... It requires that the DNA fragments contain ~20-40 base pair overlap with adjacent DNA fragments. These DNA fragments are mixed ... This DNA assembly method has many advantages compared to conventional restriction enzyme/ligation cloning of recombinant DNA. ...
Je odličen primer neoklasične arhitekture tega območja. Po odločilnem obdobju za Grčijo leta 1912-1922 je Pirej doživel ... pristanišče je bilo tudi dopolnjeno in posodobljeno s poglabljanjem dna, gradnjo Kraljevega pristanišča, Trumba Pier, in ...
Primer so ustnače[1]. Pri sesalcih[uredi , uredi kodo]. Pri višjih vretenčarjih lahko pojav razdelimo na genetsko pogojen - ... Vzrok je kritični izbris 11,7-kb elementa DNA, ki vsebuje predvsem ponavljajoča zaporedja. Interseksualnost je recesivna dedna ... Primer je oranžna klovnovska ribica (Amphiprion ocellaris), ki zivi v majhnih skupinah z eno samico. Če ta pogine, eden od ...
S kislinami tvori Pb2+ soli, ki nastanejo preko klastrov, na primer [Pb6O(OH)6]4+. Z močnimi bazami tvori soli plumbite:[8] ... Zmes PbO in glicerina se strdi v trden vodoodporen cement, ki se je včasih uporabljal za tesnenje stranic in dna akvarijev in ...
Disease Primers. 2: 16090. doi:10.1038/nrdp.2016.90. PMC 5539539. PMID 27976670.. ... The examination of preserved museum specimens has found Borrelia DNA in an infected Ixodes ricinus tick from Germany that dates ... Except for one study in Europe,[229] much of the data implicating lizards is based on DNA detection of the spirochete and has ... Polymerase chain reaction (PCR) tests for Lyme disease have also been developed to detect the genetic material (DNA) of the ...
The genome of an organism is the whole of its hereditary information encoded in its DNA (or, for some viruses, RNA). This ... A primer of genome science. 2nd ed. Sinauer Assoc.. *Gregory T.R. (ed) 2005. The evolution of the genome. Elsevier. ... Note: The DNA from a single human cell has a length of ~1.8 m (but at a width of ~2.4 nanometers). ... However, no single haploid chromosome set defines even the DNA of a species. Because of the huge variety of alleles carried by ...
Repetitive DNA sequences must be blocked by adding short fragments of DNA to the sample. The probe is then applied to the ... Bacterial FISH probes are often primers for the 16s rRNA region. FISH is widely used in the field of microbial ecology, to ... Preparation and hybridization process - DNA[edit]. Scheme of the principle of the FISH Experiment to localize a gene in the ... Preparing DNA probes for one species and performing FISH with this probe allows one to visualize the distribution of this ...
Two bands of DNA, at 106bps and 112bps, are resolved if both the AMELX and AMELY versions of the gene are present (i.e. the ... Mutation in regions of AMELY intron 1 commonly used as primer annealing sites may disable PCR amplification. A 6bp insertion to ... sample is from a male) or one band of DNA, at 106bps, if the AMELX version only is present (i.e. the sample is from a female).[ ...
2004). Geometric Morphometrics for Biologists: A Primer. Academic Press. ISBN 0127784608.. *↑ Meijer, G. A.; et al. (1997). " ... 1993) A Hidden Markov Model that finds genes in E. coli DNA ... Circular SV40 DNA Molecules Containing Lambda Phage Genes and ... "PRIMER: Genomics and Its Impact on Science and Society: The Human Genome Project and Beyond" (pdf) (en inglés). Consultado o 1 ... "DNA sequencing with chain-terminating inhibitors". Proceedings of National Academy of Sciences 74 (12). ...
Virus RNA polymerases use VPg as primer. VPg as primer uses both minus and plus strand RNA synthesis. Picornavirus replication ... and a poliovirus clone was the first infectious DNA clone made of an RNA virus in animals. Along with rhinovirus, poliovirus ... end that is used as a primer for transcription by RNA polymerase.This primer is called VPg genome range between 2-3 kb. VPg ... The VPgpUpUOH primer is transferred to the 3' end of the RNA template for elongation, which can continue by addition of ...
... www.intechopen.com/books/dna-repair/meiosis-as-an-evolutionary-adaptation-for-dna-repair (页面存档备份,存于互联网档案馆) ... A primer for the perimenopausal. The North American Menopause Society. [2013-04-11]. (原始内容存档于2013-04-10).. ... Harris Bernstein, Carol Bernstein and Richard E. Michod (2011). Meiosis as an Evolutionary Adaptation for DNA Repair. Chapter ... Impairment of BRCA1-related DNA double-strand break repair leads to ovarian aging in mice and
For this process the cell goes through the steps of the cell cycle and development which involves cell growth, DNA replication ... "Science Primer".. *^ "Cell Biology , Learn Science at Scitable". www.nature.com. Retrieved 2018-06-10 ... DNA replication, damage and repair - are considered to be the interphase portion of the cycle. While the M phase (mitosis and ...
මෙහිදී RNA, DNA (මෙම විෂයේ දී complementary DNA හෝ cDNA නමින් හැඳින්වේ) බවට reverse transcription කිරීම සහ අවශ්‍ය DNA ඉලක්ක ... Database of validated PCR primer sets (website critique). *Animation to illustrate RT-PCR procedure, from Cold Spring Harbor ...
The 3' end includes 3 regions, which are PPT (polypurine tract), U3, and R. The PPT is a primer for plus-strand DNA synthesis ... This DNA can be incorporated into host genome as a provirus that can be passed on to progeny cells. The retrovirus DNA is ... PBS (primer binding site) consists of 18 bases complementary to 3' end of tRNA primer. L region is an untranslated leader ... It has been speculated that the RNA to DNA transcription processes used by retroviruses may have first caused DNA to be used as ...
Sitosina (C) merupakan salah satu daripada bes nitrogen dalam DNA dan RNA bersama adenina, guanina dan timina serta urasil ... 4.45 (sekunder), 12.2 (primer)[1] Kerentanan magnetik (χ). -55.8·10−6 cm3/mol ...
Main articles: RNA and DNA. The major difference between RNA and DNA is the presence of a hydroxyl group at the 2'-position of ... The longest primer extension performed by a ribozyme polymerase was 20 bases.[29] In 2016, researchers reported the use of in ... This forces an RNA double helix to change from a B-DNA structure to one more closely resembling A-DNA. ... DNA and proteins seemed the dominant macromolecules in the living cell, with RNA only aiding in creating proteins from the DNA ...
Disease Primers. 3 (17071): 17071. doi:10.1038/nrdp.2017.71. PMID 28980624.. *^ a b c d e f g h i j k l m n o p q r s t u v van ... The zebrafish has transparent embryos that can be injected with DNA or RNA and has a lifespan of up to two years.[79] Induced ...
2017). "Environmental DNA in subterranean biology: range extension and taxonomic implications for Proteus". Scientific Reports ... kot primer za redukcijo telesnih struktur zaradi neuporabe.[35] ... Using Environmental DNA". PLoS ONE. Vol. 12 no. 1. str. ...
Primer: Študija na 23 pacientih s kroničnim srčnim popuščanjem. Kontrolna skupina je prejemala 100 mg CoQ10 4 tedne. VO2 in od ... CoQ10 je prav tako zelo učinkovit pri zaščiti celic (keratinocitov) pred oksidativnimi poškodbami DNA, ki so inducirane z ... Signifikantno je upadla oksidativna poškodba DNA v keratinocitih. Ubikinon lahko upočasni izgubo hialuronske kisline in vpliva ... pri MPTP modelnih miših ter zmanjšala lipidno peroksidacijo in oksidativne poškodbe DNA v striatumu pri podganah z 3- ...
Pelagični sedimenti, ki vsebujejo ostanke organizmov, ki so se potopili do dna oceana, vključujejo rdeče gline in globigerine, ... Več lokalnih posebnih vremenskih primerov je mogoče najti kot je na primer Azorski anticiklon, Benguelski tok in Nor'easter. ... Zajema večino oceanskega dna in sega v debelini od 60-3.300 metrov, so najdebelejši v konvergenčnih pasovih, predvsem na ... Glavna značilnost batimetrije (meritve oceanskega dna) je podmorsko gorovje imenovano Srednjeatlantski hrbet. [3] Ta sega od ...
順鉑,又稱順式-二氯二氨合鉑(II),是含鉑(II)、呈平面正方形結構的化療藥物。同類藥物還包括卡鉑(Carboplatin)和奧沙利鉑。這些化合物能夠交叉鏈接DNA,並通過相似的反應路徑產生烷化劑,殺死細胞。[37] ... Platinum primer. Diamond Cutters International. [2011-06-18].. *^ Unknown Facts
primer. A short strand of RNA or DNA that serves as a starting point for DNA synthesis.. progeny. Any genetic descendant or ... DNA. See deoxyribonucleic acid.. DNA replication. The chemical duplication or copying of a DNA molecule; the process of ... DNA sequencing. The process of determining the precise order of nucleotides within a DNA molecule.. drug. Any substance that ... One of the four nucleobases used in the nucleic acid DNA (but not in RNA). It is represented in DNA sequences by the letter T. ...
3% require a reverse transcriptase enzyme to convert between RNA and DNA. 17% of plant viruses are ssDNA and very few are dsDNA ... 2001). "In vivo analysis of the TSWV cap-snatching mechanism: single base complementarity and primer length requirements". The ...
Primer Premier. *List of software for protein model error verification. *List of protein secondary structure prediction ... Comparison of DNA melting prediction software. *COMPLEAT (Bioinformatics tool). *Computational Resource for Drug Discovery ...
DNA-based tests[edit]. These are based on detecting a leukaemic specific DNA sequence. Generally this is achieved through the ... From this sequence, PCR primers are designed that will only amplify the specific leukemic clone from the patient. ... Both the DNA and RNA based tests require that a pathologist examine the bone marrow to determine which leukaemic specific ... The DNA sequence chosen may contribute to the genesis of the leukaemia, or may simply be linked to it. ...
Na primer, zaporedje DNK, ki kodira insulin za človeka, prav tako kodira inzulin, če ga vstavimo v druge organizme, kot so to ... Eden od njih so primerjave zaporedij DNA, kjer sodeluje z molekularno biologijo in genomiko, po drugi pa s primerjavo fosilov ...
RT-PCR using nested primer pairs is used to amplify several chikungunya-specific genes from whole blood, generating thousands ... a nonstructural protein that degrades RBP1 and turns off the host cell's ability to transcribe DNA.[51] NS2 interferes with the ...
The 60kDa DNA/RNA binding protein and 52kDa T-cell regulatory protein are the best characterised antigens of anti-Ro antibodies ... by R. A. (2000). Immunofluorescence in clinical immunology : a primer and atlas. Basel [u.a.]: Birkhäuser. ISBN 978-3764361822 ... Presence of high DNA-binding and low C3 levels have been shown to have extremely high predictive value (94%) for the diagnosis ... Anti-double stranded DNA (anti-dsDNA) antibodies are highly associated with SLE. They are a very specific marker for the ...
... and DNA-dependent-DNA-polymerase activity (used to create cccDNA from pdsDNA in the first step of the replication cycle). ... or 4-nucleotide primer.[5] Most hepadnaviruses will only replicate in specific hosts, and this makes experiments using in vitro ... Based on the presence of viral genomes in bird DNA it appears that the Hepatoviruses evolved ,82 million years ago.[6] Birds ... HBV was identified as a new DNA virus in the 1960s, followed a couple of decades later by the discovery of the flavivirus ...
PCR amplification of megabase DNA with tagged random primers (T-PCR).. Grothues D1, Cantor CR, Smith CL. ...
Breaking (shearing) DNA by Alkali Hydrolysis Suitable for BAC clones before labelling using random-primer (random priming, ... 300 ng DNA + 6.5 ul 4M NaOH made up to 155 ul, final NaOH 200 mM ... autoclaving of syringing the DNA requires too much volume). ...
The present invention provides these E. suis primers and a method to use these primers in a PCR protocol to provide a highly ... suis specific primers in PCR with DNA from swine blood increases the sensitivity of current DNA hybridization protocols for ... These primers are capable of effectively hybridizing and serving as primers for the thermostable DNA polymerase used in the ... Saiki, Randall K., Primer Directed Enzymatic Amplification of DNA With a Thermostable DNA Polymerase, Science 239:487 491 (1988 ...
Template and primer requirements for DNA Pol θ-mediated end joining Message Subject (Your Name) has sent you a message from ... Template and primer requirements for DNA Pol θ-mediated end joining. Peng He and Wei Yang ... Polθ requires a minimum of 2 bp and optimally 4 bp between a template/primer pair for efficient and processive DNA synthesis. ... DNA Pol θ shares structural homology with the high-fidelity replicases, and its polymerase domain (Polθ) has been shown to ...
... region are shown in the Forward primer and Reverse Primer boxes.. In the Primer Parameters section, we set the Minimum PCR ... those primers are. Therefore, you need to make a special note of the primer data from the Primer-BLAST results.. ... see the sequences of the primers, as well as other data on the PCR primers. For comparison, results for Primer pairs 2 and 3 ... How does Primer-BLAST work?. The search for primers is essentially a 2-step process:. 1. Use the Primer3 program to design ...
... including random primers and hexamers, oligo (dT) primers, and sequencing primers. These products are commonly used in a ... Learn about the different pre-synthesized DNA primers and oligos that are available, ... pre-designed DNA primers and oligos. These products include random primers, Oligo (dT) primers, gene specific primers for ... Sequencing primers. Short RNA or DNA oligonucleotides are often used as primers in PCR reactions to amplify a specific target ...
In this study we designed a set of PCR primers for the mitochondrial 12S ribosomal DNA sequence based on 64 complete ... Conclusions/Significance Newly designed 12S ribosomal DNA primers have considerable potential for metazoan metagenetic analysis ... These regions were used to design a primer pair that flanks a more variable region in the gene. Then all of the complete ... Unlike microbial studies, where analysis of the 16S ribosomal DNA sequence is standard, the best gene for metazoan metagenetics ...
Big peaks for a short time, then nothing - too much DNA.. Nothing - bad primer, loss of DNA, bad cycling conditions.. If your ... Plasmid DNA Sequencing with Universal Primers - (Mar/08/2007 ). Hi all, Ive been having some trouble with sequencing. The gene ... The next important thing the amount of DNA and Big Dye terminator in used. The amount of DNA I use is about 400- 500ng.. ... The DNA has to be the cleanest you can possibly get it to be. No RNA , no proteins, removal of phenol must be complete, if your ...
We recommend designing long (~26-35) oligonucleotide primers to amplify bisulfite treated/deaminated DNA. Because bisulfite DNA ... Home FAQs What are the general recommendations for designing primers for bisulfite-treated/deaminated DNA? ... Note that since the DNA strands are no longer complementary after bisulfite-treatment/deamination, an individual primer set ... The first primer should be designed to anneal to the converted target sequence. The second primer should be designed to anneal ...
It will degrade a secondary primer if bound to the same strand (e.g. a mutagenesis primer). ... The exonuclease will only degrade double stranded DNA that it encounters while extending a DNA fragment. ... Taq DNA Polymerase with Standard Taq (Mg-free) Buffer, Taq DNA Polymerase with ThermoPol® II (Mg-free) Buffer, Crimson Taq DNA ... Crimson Taq DNA Polymerase with (Mg-free) Buffer, Taq DNA Polymerase with ThermoPol® Buffer, Taq DNA Polymerase with Standard ...
... vijay at ust.hk vijay at ust.hk Mon Sep 2 04:29:48 EST 2002 *Next ... Would anyone please suggest me the three primers for the TAIL reactions or the protocol from their own lab. Here is the vector ... student working now to clone a T-DNA insertion mutant of Cis-cinnamic acid.The mutant is isolated from Ecker and Alonso ... insertional line CS75100.I would like to design the primers for both Left and Right borders of the vector pROK2 for TAIL-PCR. ...
... primer annealing and primer extension (Figure 1). The initial step denatures the target DNA by heating it to 94°C or higher. ... serving as primers for the DNA polymerase. Finally, the synthesis of new DNA begins as the reaction temperature is raised to ... and the DNA polymerase can extend the annealed primers to produce primer dimer, which often appears as a diffuse band of ... A typical amplification reaction includes target DNA, a thermostable DNA polymerase, two oligonucleotide primers, ...
Our custom DNA oligos are made to your specifications, with rigorous quality control and quick turnaround. They can be used in ...
Molecular basis for stool-based DNA tests for colorectal cancer: a primer for clinicians.. Boland CR1. ... Tumor cells and DNA are shed into the fecal stream, and uniquely mutated genes can be identified that would indicate the likely ...
These primers are going to be the death of me. Im using MethPrimer to design them, but the primer dimer problem is endless, ... Is there ever a point where you just deal with primer dimers? I saw some posts about formamide but wasnt sure if it applied. ... posted in DNA Methylation and Epigenetics: designing MSP for a USF site in my gene of interest. ... Primer dimmer is a big issue for MSP or any bisulfite based PCR because the low sequence complexity of the modified DNA. You ...
... relating to PCR-DNA amlification it refers to the DNA primer. First of all why is this the case - DNA relpication:RNA primer, ... No DNA polymerase can. But they could start with DNA primers if such thing was available (and they do when repairing DNA). When ... DNA primer? Secondly when I look at the definition for a primer - it states that it is an RNA stand...so whats with the DNA ... RNA primers could be used but they are unstable and Rnases are frequent and really hard to get rid of, while DNA is easy to ...
This page illustrates high molecular weight calf thymus DNA in a liquid crystalline phase viewed under a combination of crossed ... Liquid Crystalline DNA. DNA undergoes a series of liquid crystalline phase transitions when it is compressed in vivo into ... DNA is a very unusual molecule that is shaped like a very long piece of string. The diameter of the DNA molecule is about 25-30 ... In addition, it is important to the cell to be able to access the DNA molecule for the purposes of genetic control, routine ...
This technique involves a one-step PCR reaction utilizing genomic DNA and sequence-specific primers to determine the ... specificity of each allele and to produce a larger primer data base ideal for serological analysis. The application of this ... Chiu, Angela Chen-Yen. DNA Typing of HLA-B by PCR with Primer Mixes Utilizing Sequence-Specific Primers, thesis, August 1997; ... DNA Typing of HLA-B by PCR with Primer Mixes Utilizing Sequence-Specific Primers ...
BcaBEST DNA Labeling Kit. The BcaBEST DNA Labeling Kit is a novel random primer labeling system that uses longer primers (9- ... Unlike E. coli Klenow fragment or modified T7 DNA polymerase, Bca polymerase allows stable polymerization of DNA even for ... Lambda DNA digested with Hind III, 25 ng/µL). Note. The kit name has been changed from "Ladderman Labeling Kit" to "BcaBEST ... In general, probes with specific activities of ,109 dpm/mg DNA obtained with [32P]-alpha-dCTP (~3,000 Ci/mmol, 111 TBq/mmol). ...
Here we developed a new set of 100 primer pairs optimized for amplification in Monocotyledons. Primer pairs amplify coding ( ... we demonstrated that this new set of primers is of great interest for population genetics and we anticipate that it will also ... Chloroplast DNA sequences are of great interest for population genetics and phylogenetic studies. However, only a small set of ... Chloroplast DNA Is the Subject Area "Chloroplast DNA" applicable to this article? Yes. No. ...
... H. Förster and J. E. ... To detect early brown rot infections in fruit, two primer sets that were developed from DNA sequences of either ribosomal DNA ( ... This primer set, however, only detected DNA from some of the California isolates of M. fructicola. This genetic diversity was ... Primers X-09intF3 and X-09R were more sensitive and reliable for detecting small amounts of target DNA either extracted from ...
Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. By RK Saiki, DH Gelfand, S Stoffel, SJ ... Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. By RK Saiki, DH Gelfand, S Stoffel, SJ ... Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase Message Subject. (Your Name) has forwarded a ... A thermostable DNA polymerase was used in an in vitro DNA amplification procedure, the polymerase chain reaction. The enzyme, ...
Home/ Forums/ DNA (PCR, Real Time PCR): Primers and Oligonucleotides. DNA (PCR, Real Time PCR): Primers and Oligonucleotides. ... PCR primers for mycoplasma 16S rRNA gene? (Page: 1, 2, 3, 4) by Jason King » Fri, 11/20/2009 - 12:30 194. by Rahul Date. Sat, ... Exon exon junction primers for RT-PCR by Haritha » Sat, 08/17/2013 - 02:39 2. by elhamzeinali. Wed, 02/10/2016 - 06:19 ... Long Primers not working? by Crystal Ramirez » Tue, 06/14/2016 - 11:51 8. by Ivan Delgado. Thu, 06/16/2016 - 13:10 ...
Primer-BLAST. You are here. Home » Products » Sequencher » Sequencher Features » Connections » Primer-BLAST ... Your new primers are automatically tagged with a GenBank style feature key that makes them easier to see in an alignment. The ... Use Primer-BLAST to analyze sequences and check specificity.. Parallelize your analyses - use several different sets of ... If you want to learn more about Primer-BLAST, check out the Sequencher Connections tutorial. ...
A recent approach to detecting genetic polymorphism involves the amplification of genomic DNA using single primers of arbitrary ... Use of single-primer DNA amplifications in genetic studies of peanut (Arachis hypogaea L.). ... Williams JGK, Kubelik AR, Livak KJ, Rafalski JA, Tingey SV: DNA polymorphisms amplified by arbitrary primers are useful as ... A recent approach to detecting genetic polymorphism involves the amplification of genomic DNA using single primers of arbitrary ...
OH with a photolabile protecting group which can temporarily cease DNA strand growth and can smoothly reinitia ... Photo-cleavable nucleotides for primer free enzyme mediated DNA synthesis A. S. Mathews, H. Yang and C. Montemagno, Org. Biomol ... The synthesised nucleotides are employed for terminating and reinitiating template-less DNA synthesis, using primer independent ... The use of this photolabile nucleotide in one step stop-start DNA synthesis is a novel strategy towards the precise assembly of ...
The primers sequences were from EcoRI J fragment of Ad169. The first primer set was selected to amplify a 242 bp fragment and ... Cytomegalovirus DNA detection of an immediate early protein gene with nested primer oligonucleotides J Virol Methods. 1991 May; ... The first primer set was selected to amplify a 242 bp fragment and the next primer set was nested within the first and ... With the single PCR system it was possible to detect 100 fg HCMV DNA but with double PCR 5-10 fg were detectable. Specific ...
Antibodies / Assay Kits / Biology Cells / cDNA / Clia Kits / Culture Cells / Devices / DNA / DNA Templates / DNA Testing / ... Copyright © 2020 Primers, 16s Ribosomal DNA - François Lutzonis Lab - OnePress theme by FameThemes ...
Mitochondrial DNA Sequencing Primers mtDNA sequencing is useful in evolutionary studies, single nucleotide polymorphism (SNP) ... within the D-loop region of human mitochondrial DNA (mtDNA). ...
How should I store my targeted DNA sequencing library prep assay primers?. Primer pools are stable for up to one year at -20 °C ...
  • The following FAQ contains frequently asked questions and answers about the 'A Magnetic Primer Designer' Project Idea and/or Project Kit ( http://www.sciencebuddies.org/science-fair-projects/project_ideas/BioChem_p017.shtml?from=AAE ). (sciencebuddies.org)
  • Q: I added 60 pennies to the cup, but the primer strand did not fall off of the DNA template strand. (sciencebuddies.org)
  • In this case, we suggest cutting a strip of felt that can be placed between the two strands and testing all of the primers with this strip of felt placed between them and the DNA template strand. (sciencebuddies.org)
  • When you pair the primer strand up with the DNA template strand, make sure that the primer strand is not flipping over on itself and creating more than 1 match with the DNA template strand (or the primer strand). (sciencebuddies.org)
  • Because magnets like to bond with each other, the primer strand will try to find ways to create extra matches with the DNA template strand (and the primer strand). (sciencebuddies.org)
  • The primer strand should be hanging flat against the DNA template strand. (sciencebuddies.org)
  • 5 x HOT FIREPol® Blend Master Mix Ready to Load is a premixed ready-to-use solution containing all reagents required for PCR (except template, primers and water). (medibena.at)
  • The user simply needs to add water, template and primers. (medibena.at)
  • You will get better results when testing seven different primers compared to testing fewer primers. (sciencebuddies.org)
  • Testing seven different primers should let you easily see a trend in your results. (sciencebuddies.org)
  • Testing each primer at least three times will help you make sure that your results are repeatable and reproducible. (sciencebuddies.org)
  • You may actually notice a little variation in the amount of pennies needed to make the primer fall off when testing a given primer three different times, which is why you will use the average of your results when making a graph. (sciencebuddies.org)
  • Even after 18 years, our first batch of FIREPol ® DNA Polymerase gives satisfactory results in PCR. (medibena.at)