A method is provided for amplifying and detecting specific GC-rich nucleic acid sequences contained in a nucleic acid or in a mixture of nucleic acids, which includes treating a separate nucleic acid containing the specific sequence with a molar excess of primers and a polymerase and extending the primers in the presence of dATP, dCTP, TTP, and an analogue of dGTP. In one application of the present invention, individuals who are carriers for, or afflicted by, the fragile X syndrome are detected.
The first mRNA transcript isolated for this gene was part of an artificial chimera derived from two distinct gene transcripts and a primer used in the cloning process (see Genbank accession M29204). A positively charged amino terminus present only in the chimera was determined to bind GC-rich DNA, thus mistakenly thought to identify a transcription factor gene. [provided by RefSeq, Jul 2008 ...
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The GC percent track shows the percentage of G (guanine) and C (cytosine) bases in 5-base windows. High GC content is typically associated with gene-rich areas. This track may be configured in a variety of ways to highlight different apsects of the displayed information. Click the Graph configuration help link for an explanation of the configuration options ...
The GC percent track shows the percentage of G (guanine) and C (cytosine) bases in 5-base windows. High GC content is typically associated with gene-rich areas. This track may be configured in a variety of ways to highlight different apsects of the displayed information. Click the Graph configuration help link for an explanation of the configuration options ...
The theory of self-reproductive molecular systems involves the consequence that translation must have started from a selected distribution of RNA molecules, that comprised GC-rich sequences of a lengt
Hi, The following references discuss the use of Betaine (and other additives) in PCR. Basically, using a 5M stock solution of Betaine, adjust to a final concentration of 0.5-1.5M in your PCR reaction. Nucleic Acids Research 25(19)3957-3958, 1997 Betaine improves the PCR amplification of GC-rich DNA sequences W Henke, K Herdel, K Jung, D Schnorr, S Loening BioTechniques 21(6)1102-1108, 1996 December Strategy for controlling preferential amplification and avoiding false negatives on PCR typing T Weissensteiner, J Lanchbury Genome Research 6:633-638, 1996 Uniform amplification of a mixture of deoxyribonucleic acids with a varying GC content N Baskaran, R Kandpal, A Bhargava, M Glynn, A Bale, S Weissman **************************************************************** Bradley Turner Beth Israel Deaconess Medical Center Harvard Medical School 617-667-1215 phone Division of Gastroenterology 617-667-2767 fax Room Dana 536 bsturner at biosun.harvard.edu 330 Brookline Avenue bturner at bidmc.harvard.edu ...
We show that although the currently available isochore mapping methods agree on the isochore classification of about two-thirds of the human DNA, they produce significantly different results with regard to the location of isochore boundaries and isochore length distribution. We present a new consensus isochore assignment method based on majority voting and provide IsoBase, a comprehensive on-line database of isochore maps for all completely sequenced vertebrate genomes.
There are at least 16 genes within the common overlapping region. A few of these genes are expressed in the central nervous system and/or likely to be dosage sensitive, or reported to be associated with disease by animal studies. These genes could be candidate genes for patients with deletion or duplication in this region.. The transcription factor gene (SP1) is most likely to be dosage sensitive (haploinsufficiency score: 0.81%) [DECIPHER]. The protein encoded by the SP1 gene is a zinc finger transcription factor that binds to GC-rich motifs of many promoters and is then involved in a variety of cellular processes such as cell growth, apoptosis, differentiation and immune responses, DNA damage response, and chromatin remodeling (provided by RefSeq, Nov 2014). The SP7 gene (haploinsufficiency score: 14.4%) encodes a bone specific transcription factor (osterix) which regulates osteogenesis and bone formation during embryonic development [8]. Niger et al. [9] reported that the activity of osterix ...
PCR amplification of GC-rich templates is often hindered by formation of secondary structures and the requirement for high melting temperatures. PrimeSTAR GXL DNA Polymerase is a high fidelity PCR enzyme that allows efficient amplification of the most challenging templates. With this enzyme, amplification of GC-rich templates is possible without reaction optimization or inclusion of additives such as DMSO or Betaine.. In this experiment, PrimeSTAR GXL DNA polymerase was compared to other commercially available enzymes for the amplification of a target with high GC content. Only the PrimeSTAR GXL enzyme was able to efficiently amplify the GC-rich template without additives or special reaction conditions. ...
... definition, Physics.. Also, isochor. Also called isometric, isometric line. for a given substance, a curve graphing temperature against pressure, when the volume of the substance is held constant. See more.
Sequence related amplification polymorphism (SRAP) marker technique was used to assess genetic relationships and diversity among genotypes of Saccharum and allied genera. In the SRAP technique, the primers were arbitrarily designed with an AT- and GC-rich motif to anneal introns and exons, respectively. The level of polymorphism observed proved that the SRAP system was robust and amplified markers across species and genera and established evolutionary history interconnecting members of the Saccharum complex. The resolving power of the SRAP markers coupled with the fact that some of the amplicons could be amplifying gene-rich regions from diverse loci of the genome, was indicative of its potential usefulness for linkage and quantitative trait loci (QTLs) mapping in sugarcane. S. spontaneuam has been the most important source of wild germplasm for sugarcane cultivar development in Louisiana. Genetic diversity and structure of 51 S. spontaneum genotypes in the local collection (USDA, Houma, LA) was
Some DNA sequencing technologies arent very good at sequencing and assembling DNA thats rich in GC base pairs. What this means is that some sequenced genomes could be missing stretches of GC-rich DNA if they rely exclusively on those techniques. This difficult-to-sequence DNA was called "dark DNA" in a paper published last summer (July 2017).. The paper looked at some missing genes in the genome of the sand rat Psammomys obesus. The authors initially used a standard shotgun strategy in order to sequence the sand rat genome. They combined millions of short reads (<200 bp) to assemble a complete genome. A large block of genes seemed to be missing-genes that were conserved and present in the genomes of related species (Hargraves et al., 2017). They knew the genes were present because they could detect the mRNAs corresponding to those genes ...
The Genetics Society of America (GSA), founded in 1931, is the professional membership organization for scientific researchers and educators in the field of genetics. Our members work to advance knowledge in the basic mechanisms of inheritance, from the molecular to the population level.. Online ISSN: 1943-2631. ...
Background. Bacterial genomes possess varying GC content (total guanines (Gs) and cytosines (Cs) per total of the four bases within the genome) but within a given genome, GC content can vary locally along the chromosome, with some regions significantly more or less GC rich than on average. We have examined how the GC content varies within microbial genomes to assess whether this property can be associated with certain biological functions related to the organisms environment and phylogeny. We utilize a new quantity GCVAR, the intra-genomic GC content variability with respect to the average GC content of the total genome. A low GCVAR indicates intra-genomic GC homogeneity and high GCVAR heterogeneity.. Results. The regression analyses indicated that GCVAR was significantly associated with domain (i.e. archaea or bacteria), phylum, and oxygen requirement. GCVAR was significantly higher among anaerobes than both aerobic and facultative microbes. Although an association has previously been found ...
The species page of Empusa sp. IRT-2002. Also know as (German: große Mantiden). Information about genome files, completeness, GC-content, size, N50-values, and sequencing methods are listed.
The species page of Magnaporthe sp. MG12. . Information about genome files, completeness, GC-content, size, N50-values, and sequencing methods are listed.
An industrial approach to protein production demands maximization of cloned gene expression, balanced with the recombinant hosts viability. Expression of toxic genes from thermophiles poses particular difficulties due to high GC content, mRNA secondary structures, rare codon usage and impairing the hosts coding plasmid replication. TaqII belongs to a family of bifunctional enzymes, which are a fusion of the restriction endonuclease (REase) and methyltransferase (MTase) activities in a single polypeptide. The family contains thermostable REases with distinct specificities: TspGWI, TaqII, Tth111II/TthHB27I, TspDTI and TsoI and a few enzymes found in mesophiles. While not being isoschizomers, the enzymes exhibit amino acid (aa) sequence homologies, having molecular sizes of ~120 kDa share common modular architecture, resemble Type-I enzymes, cleave DNA 11/9 nt from the recognition sites, their activity is affected by S-adenosylmethionine (SAM). We describe the taqIIRM gene design, cloning and expression
TY - JOUR. T1 - Protein elemental sparing and codon usage bias are correlated among bacteria. AU - Bragg, Jason G.. AU - Quigg, Antonietta. AU - Raven, John A.. AU - Wagner, Andreas. PY - 2012/5. Y1 - 2012/5. N2 - Highly expressed proteins can exhibit relatively small material costs, in terms of the quantities of carbon (C), nitrogen (N) or sulphur (S) atoms they contain. This elemental sparing probably reflects selection to reduce the quantities of potentially growth-limiting elements in abundant proteins, but the evolutionary mechanisms for adaptive elemental sparing are still poorly understood. Here, we predict that the extent of elemental sparing in highly expressed proteins will vary among organisms, according to the effectiveness of selection in determining the fate of mutations. We test this hypothesis in bacteria by asking whether elemental sparing is correlated with codon usage bias. Bacteria exhibit extraordinary variation in their life histories and demography and consequently in the ...
Codon usage pattern and relative synonymous codon usage (RSCU) of mtDNA of Meloidogyne graminicola.Numbers on the Y-axis refer to the total number of codons (A)
An important unanswered question in evolutionary genomics is the source of considerable variation of genomic base composition (GC content) even among organisms that share one habitat. Evolution toward GC-poor genomes has been considered a major adaptive pathway in the oligotrophic ocean, but GC-rich bacteria are also prevalent and highly successful in this environment. We quantify the contribution of multiple factors to the change of genomic GC content of Ruegeria pomeroyi DSS-3, a representative and GC-rich member in the globally abundant Roseobacter clade, using an agent-based model ...
Expression breadth and synonymous substitution patterns are most probably due to gene length effects: The above results are suggestive of selection possibly playing a role in codon usage bias in humans. However, as stated earlier, genes of different length are likely to have different MCB values owing to the nature of the method. Indeed, if we randomize our sequences and measure the mean MCB for 1000 simulants for each of our genes, we find that the MCB, on average, is higher for shorter genes. This is to be expected of any statistic that employs a multinomial distribution and applies equally to the method of Karlin and Mrazek.. Importantly, it so happens that in our data set longer genes have a slightly higher rate of synonymous substitutions and are not expressed in as broad a range of tissues. Therefore, plotting mean MCB for the randomized genes against breadth of expression for the real gene, we still find a weak positive correlation of the order of magnitude reported for the real genes (P ...
Specificity protein 1 gene is mapped on chromosome 12q13.1 that contains 785 amino acids with a molecular weight of 81kDa encodes a transcription factors which upregulates or downregulates in response to physiological and pathological stimuli. It has three transcript variants encoding in different isoforms found in this gene. Specificity protein 1 binds with high affinity to GC rich sequence that regulates expression of an arrangement of genes drawn in various cellular processes such as growth, differentiation, immune response and apoptosis which in turn modulates cell responses to DNA damage implicated in chromatin remodeling. It binds to the PDGFR-alpha G-box promoter that modulates the cell response to DNA damage as well as functions in the recruitment of SMARCA4 on the c-FOS promoter and necessary in the regulation of FE65 gene expression. Specificity protein 1 is extremely regulated by post translational modification like phosphorylation, proteolytic cleavage, sumoylation, acetylation and ...
chai_z at wehi.edu.au wrote: : 1). Does the A,C rich sequence mean anything? : Zhonglin Chai Ive seen a lot of ACACACACAC and GTGTGTGTGT (pyrimidine-purine) repeats in non-coding DNA and there is a lot of literature about them. But sorry I dont have the references in front of me. Other than that, I cant help you. -- ******************************************************************** * Brian Foley * If we knew what we were doing * * Molecular Genetics Dept. * it wouldnt be called research * * University of Vermont ...
Molecular Cloning, also known as Maniatis, has served as the foundation of technical expertise in labs worldwide for 30 years. No other manual has been so popular, or so influential.
GC-rich regions of the DNA are of special interest, as they generally occur within transcribed or control regions of the genome. However, the high GC-content makes these sequences prone to the formation of hairpin structures, which may persist even at th
The most concerning issue is a dropout of GC rich regions in clustering. This has been an on-again off-again issue with Illumina that we have addressed over a year ago by improvements in amplification cycling conditions and enzyme selection. Some time, several months ago (we do not have a precise window), Illumina appears to have changed the chemistry of one of their clustering components and that caused a major change in performance on GC rich areas. This can be seen as an absence of reads from very GC rich areas but, because these areas are rare in most genomes, they cannot be seen on the flowcell wide metrics. This issue is found on current HiSeq and MiSeqV2 kits but not on MiSeqV1 kits nor, we suspect, on the GAII. We have been able to address this problem by adding a brief boiling step during NaOH denaturation of the samples and have implemented this as SOP starting about two weeks ago. This drop out of regions can cause significant issues for several studies - most notably ChIP analyses - ...
Brachypodium distachyon has been proposed as a new model for the temperate grass because it is related to the major cereal grain species (such as wheat, barley, oat, maize, rice, and sorghum) and many forage and turf species. In this study, a multivariate statistical analysis was performed to investigate the characteristics of codon bias and the main factors affecting synonymous codon usage in Brachypodium. We found that low- and high-GC content genes with different codon usage occur frequently in the genome.
The completion of the genome sequence of Mycobacterium tuberculosis strain H37Rv revealed that 10% of the coding capacity is devoted to two, large multigene families that are characterised by repeat sequences. These are the PE and PPE families that code for acidic, glycine rich proteins. A subgroup of the PE family is the polymorphic GC rich sequence (PGRS) gene subfamily. Genome comparisons of clinical isolates of M. tuberculosis have confirmed the polymorphic character of some of these genes suggesting they may be analogous to the contingency loci found in other pathogenic bacteria. Certain PE-PGRS proteins play a direct role in virulence in M. marinum, other PE-PGRS genes are cell surface associated, and some PE-PGRS proteins are variable surface antigens, supporting a potential role in host pathogen interactions. A reporter assay designed to investigate mutations in a PE-PGRS repeat-containing sequence was used to assess mutation rates in various M. smegmatis host strains by fluctuation ...
Approximately 10 % of the Mycobacterium tuberculosis genome is made up of two families of genes that are poorly characterized due to their high GC content and highly repetitive nature. The PE and PPE families are typified by their highly conserved N-terminal domains that incorporate proline-glutamate (PE) and proline-proline-glutamate (PPE) signature motifs. They are hypothesised to be important virulence factors involved with host-pathogen interactions, but their high genetic variability and complexity of analysis means they are typically disregarded in genome studies ...
GC Application #17848: European PAH Mix # 2 on ZB-50. Column used: Zebron™ ZB-50, GC Cap. Column 30 m x 0.25 mm x 0.25 µm, Ea Part#: 7HG-G004-11
In molecular biology and genetics, GC-content (or guanine-cytosine content) is the percentage of nitrogenous bases on a DNA molecule that are either guanine or cytosine (from a possibility of four different ones, also including adenine and thymine).[1] This may refer to a specific fragment of DNA or RNA, or that of the whole genome. When it refers to a fragment of the genetic material, it may denote the GC-content of part of a gene (domain), single gene, group of genes (or gene clusters), or even a non-coding region. G (guanine) and C (cytosine) undergo a specific hydrogen bonding, whereas A (adenine) bonds specifically with T (thymine). The GC pair is bound by three hydrogen bonds, while AT pairs are bound by two hydrogen bonds. DNA with high GC-content is more stable than DNA with low GC-content; however, the hydrogen bonds do not stabilize the DNA significantly, and stabilization is due mainly to stacking interactions.[2] In spite of the higher thermostability conferred to the genetic ...
LA Taq DNA Polymerase enables efficient amplification of large DNA templates (up to 48 kb) and longer and more accurate genomic DNA PCR amplification. GC buffers for efficient amplification of templates that are GC rich or have secondary structure.
TY - JOUR. T1 - Preliminary aqnalysis of length and GC content variation in the ribosomal first internal transcribed spacer (ITS1) of marine animals. AU - Chow, S.. AU - Ueno, Y.. AU - Toyokawa, M.. AU - Oohara, I.. AU - Takeyama, Haruko. PY - 2009/6. Y1 - 2009/6. N2 - Length and guanine-cytosine (GC) content of the ribosomal first internal transcribed spacer (ITS1) were compared across a wide variety of marine animal species, and its phylogenetic utility was investigated. From a total of 773 individuals representing 599 species, we only failed to amplify the ITS1 sequence from 87 individuals by polymerase chain reaction with universal ITS1 primers. No species was found to have an ITS1 region shorter than 100 bp. In general, the ITS1 sequences of vertebrates were longer (318 to 2,318 bp) and richer in GC content (56.8% to 78%) than those of invertebrates (117 to 1,613 bp and 35.8% to 71.3%, respectively). Specifically, gelatinous animals (Cnidaria and Ctenophora) were observed to have short ITS1 ...
(2017) B. Miller et al. Biomedical Genetics and Genomics. It is well-documented that codon usage biases affect gene translational efficiency; however, it is less known if viruses share their hosts codon usage motifs. We determined that human-infecting viruses share similar codon usage biases as ...