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Protospacer Adjacent Motif
A protospacer adjacent motif (PAM) is a 2–6-base pair DNA sequence immediately following the DNA sequence targeted by the Cas9 nuclease in the CRISPR bacterial adaptive immune system. The PAM is a component of the invading virus or plasmid, but is not found in the bacterial host genome and hence is not a component of the bacterial CRISPR locus. Cas9 will not successfully bind to or cleave the target DNA sequence if it is not followed by the PAM sequence. PAM is an essential targeting component which distinguishes bacterial self from non-self DNA, thereby preventing the CRISPR locus from being targeted and destroyed by the CRISPR-associated nuclease. Spacers/protospacers In a bacterial genome, CRISPR loci contain "spacers" (viral DNA inserted into a CRISPR locus) that in type II adaptive immune systems were created from invading viral or plasmid DNA (called "protospacers"). Upon subsequent invasion, a CRISPR-associated nuclease such as Cas9 attaches to a tracrRNA– crRNA comple ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Base Pair
A base pair (bp) is a fundamental unit of double-stranded nucleic acids consisting of two nucleobases bound to each other by hydrogen bonds. They form the building blocks of the DNA double helix and contribute to the folded structure of both DNA and RNA. Dictated by specific hydrogen bonding patterns, "Watson–Crick" (or "Watson–Crick–Franklin") base pairs (guanine–cytosine and adenine–thymine) allow the DNA helix to maintain a regular helical structure that is subtly dependent on its nucleotide sequence. The Complementarity (molecular biology), complementary nature of this based-paired structure provides a Redundancy (information theory), redundant copy of the genetic information encoded within each strand of DNA. The regular structure and data redundancy provided by the DNA double helix make DNA well suited to the storage of genetic information, while base-pairing between DNA and incoming nucleotides provides the mechanism through which DNA polymerase replicates DNA and ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Guanine
Guanine () (symbol G or Gua) is one of the four main nucleotide bases found in the nucleic acids DNA and RNA, the others being adenine, cytosine, and thymine ( uracil in RNA). In DNA, guanine is paired with cytosine. The guanine nucleoside is called guanosine. With the formula C5H5N5O, guanine is a derivative of purine, consisting of a fused pyrimidine- imidazole ring system with conjugated double bonds. This unsaturated arrangement means the bicyclic molecule is planar. Properties Guanine, along with adenine and cytosine, is present in both DNA and RNA, whereas thymine is usually seen only in DNA, and uracil only in RNA. Guanine has multiple tautomeric forms. For the imidazole ring, the proton can reside on either nitrogen. For the pyrimidine ring, the ring N-H can center can reside on either of the ring nitrogens. The latter tautomer does not apply to nucleoside or nucleotide versions of guanine. It binds to cytosine through three hydrogen bonds. In cytosine, t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Nature Biotechnology
''Nature Biotechnology'' is a monthly peer-reviewed scientific journal published by Nature Portfolio. The editor-in-chief is Barbara Cheifet who heads an in-house team of editors. The focus of the journal is biotechnology including research results and the commercial business sector of this field. Coverage includes the related biological, biomedical, agricultural and environmental sciences. Also of interest are the commercial, political, legal, and societal influences that affect this field. The journal continues serial publication of the title "Bio/Technology", which had a publication period of 1983 to 1996. Abstracting and indexing This journal is indexed in Accessed 2012-06-29 * BIOBASE * BIOSIS * Chemical Abstracts Service * CSA Illumina * CAB Abstracts * EMBASE * Scopus * Current Contents * Science Citation Index * Medline (PubMed) A ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
GUIDE-Seq
GUIDE-Seq (Genome-wide, Unbiased Identification of DSBs Enabled by Sequencing) is a molecular biology technique that allows for the unbiased in vitro detection of off-target genome editing events in DNA caused by CRISPR/Cas9 as well as other RNA-guided nucleases in living cells. Similar to LAM-PCR, it employs multiple PCRs to amplify regions of interest that contain a specific insert that preferentially integrates into double-stranded breaks. As gene therapy is an emerging field, GUIDE-Seq has gained traction as a cheap method to detect the off-target effects of potential therapeutics without needing whole genome sequencing. __TOC__ Principles Conceived to work in concert with next-gen sequencing platforms such as Illumina dye sequencing, GUIDE-Seq relies on the integration of a blunt, double-stranded oligodeoxynucleotide (dsODN) that has been phosphothioated on two of the phosphate linkages on the 5' end of both strands. The dsODN cassette integrates into any site in the genome ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
CRISPR/Cpf1
Cas12a (CRISPR-associated protein 12a, previously known as Cpf1) is an RNA-guided endonuclease-exonuclease that forms an essential component of the CRISPR systems found in some bacteria and archaea. In its natural context, Cas12a targets and destroys the genetic material of viruses and other foreign mobile genetic elements, thereby protecting the host cell from infection. Like other Cas enzymes, Cas12a binds to a "guide" RNA (termed a crRNA, or CRISPR RNA) which targets it to a DNA sequence in a specific and programmable matter. In the host organism, the crRNA contains a constant region that is recognized by the Cas12a protein and a "spacer" region that is complementary to a piece of foreign nucleic acid (e.g. a portion of a phage genome) that previously infected the cell. As with Cas9 and other Cas proteins, the programmable DNA-targeting activity of Cas12a makes it a useful tool for biotechnology and biological research applications. By modifying the spacer sequence in the crR ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cell (journal)
''Cell'' is a peer-reviewed scientific journal publishing research papers across a broad range of disciplines within the life sciences. Areas covered include molecular biology, cell biology, systems biology, stem cells, developmental biology, genetics and genomics, proteomics, cancer research, immunology, neuroscience, structural biology, microbiology, virology, physiology, biophysics, and computational biology. The journal was established in 1974 by Benjamin LewinElsevier: ''Cell'': Home (accessed 12 December 2008) and is published twice monthly by Cell Press, owned by . |
Pyrimidine
Pyrimidine (; ) is an aromatic, heterocyclic, organic compound similar to pyridine (). One of the three diazines (six-membered heterocyclics with two nitrogen atoms in the ring), it has nitrogen atoms at positions 1 and 3 in the ring. The other diazines are pyrazine (nitrogen atoms at the 1 and 4 positions) and pyridazine (nitrogen atoms at the 1 and 2 positions). In nucleic acids, three types of nucleobases are pyrimidine derivatives: cytosine (C), thymine (T), and uracil (U). Occurrence and history The pyrimidine ring system has wide occurrence in nature as substituted and ring fused compounds and derivatives, including the nucleotides cytosine, thymine and uracil, thiamine (vitamin B1) and alloxan. It is also found in many synthetic compounds such as barbiturates and the HIV drug zidovudine. Although pyrimidine derivatives such as alloxan were known in the early 19th century, a laboratory synthesis of a pyrimidine was not carried out until 1879, when Grimaux repor ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Francisella Novicida
''Francisella novicida'' is a bacterium of the Francisellaceae family, which consist of Gram-negative pathogenic bacteria. These bacteria vary from small Coccus, cocci to rod-shaped, and are most known for their intracellular parasitic capabilities. In this family, six species have been identified; however, the species ''F. novicida'' is under intense scrutiny. Though some believe it should be classified with its own species designation, others argue it should be reclassified as a subspecies under ''F. tularensis''. If it were to be classified as a subspecies, ''F. novicida'' would join the other known subspecies including ''F. t. tularensis'' (type A) and ''F. t. holarctica'' (type B). Biochemical assays for identifying ''F. tularensis'' subtypes and strains are not ideal because the results are often non-definitive and subject to variation, therefore these assays should only be considered as supplementary tests for identification of ''Francisella'' species and subspecies. Several ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Scientific Reports
''Scientific Reports'' is a peer-reviewed open-access scientific mega journal published by Nature Portfolio, covering all areas of the natural sciences. The journal was established in 2011. The journal states that their aim is to assess solely the scientific validity of a submitted paper, rather than its perceived importance, significance, or impact. In September 2016, the journal became the largest in the world by number of articles, overtaking '' PLOS ONE''. Abstracting and indexing The journal is abstracted and indexed in the Chemical Abstracts Service, the Science Citation Index Expanded, and selectively in Index Medicus/MEDLINE/PubMed. According to the ''Journal Citation Reports'', the journal has a 2023 impact factor 3.8. Reviewing policy The ''Guide to Referees'' states that to be published, "a paper must be scientifically valid and technically sound in methodology and analysis", and reviewers have to ensure manuscripts "are not assessed based on their perceived impor ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Streptococcus Thermophilus
''Streptococcus thermophilus'' formerly known as ''Streptococcus salivarius ''subsp.'' thermophilus'' is a gram-positive bacteria, gram-positive bacterium, and a lactic acid fermentation, fermentative facultative anaerobic organism, facultative anaerobe, of the ''Streptococcus viridans, viridans'' group. It tests negative for cytochrome, oxidase, and catalase, and positive for alpha-hemolytic activity. It is motility, non-motile and does not form endospores. ''S. thermophilus'' is fimbria (bacteriology), fimbriated. It is also classified as a lactic acid bacteria, lactic acid bacterium. ''S. thermophilus'' is found in fermented milk products and is generally used in the production of yogurt, alongside Lactobacillus delbrueckii subsp. bulgaricus, ''Lactobacillus delbrueckii'' subsp. ''bulgaricus''. The two species are synergistic, and ''S. thermophilus'' probably provides ''L. d. bulgaricus'' with folic acid and formic acid, which it uses for purine synthesis. ''S. thermophil ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Treponema Denticola
''Treponema denticola'' is a Gram-negative, obligate anaerobic, motile and highly proteolytic spirochete bacterium. It is one of four species of oral spirochetes to be reliably cultured, the others being ''Treponema pectinovorum, Treponema socranskii'' and '' Treponema vincentii''''. T. denticola'' dwells in a complex and diverse microbial community within the oral cavity and is highly specialized to survive in this environment. ''T. denticola'' is associated with the incidence and severity of human periodontal disease. ''Treponema denticola'' is one of three bacteria that form the Red Complex, the other two being '' Porphyromonas gingivalis'' and '' Tannerella forsythia''. Together they form the major virulent pathogens that cause chronic periodontitis. Having elevated ''T. denticola'' levels in the mouth is considered one of the main etiological agents of periodontitis. ''T. denticola'' is related to the syphilis-causing obligate human pathogen, ''Treponema pallidum'' su ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
