"the Nobel prizes awarded for research on RNA in 2009 it was awarded for the elucidation of the atomic structure of the ribosome to Venki Ramakrishnan, Tom Steitz, and Ada Yonath. In 1967, Carl Woese hypothesized that RNA might be catalytic and suggested that the earliest forms of life (self-replicating molecules) could have relied on RNA both to carry genetic information and to catalyze biochemical reactions—an RNA world. In March 2015, complex DNA and RNA nucleotides, including uracil, cytosine and thymine, were reportedly formed in the laboratory under outer space conditions, using starter chemicals, such as pyrimidine, an organic compound"
"derivatives are more often used as antiphotosynthetic herbicides, destroying weeds in cotton, sugar beet, turnips, soya, peas, sunflower crops, vineyards, berry plantations, and orchards. In yeast, uracil concentrations are inversely proportional to uracil permease. Mixtures containing uracil are also commonly used to test reversed-phase HPLC columns. As uracil is essentially unretained by the non-polar stationary phase, this can be used to determine the dwell time (and subsequently dwell volume, given a known flow rate) of the system. Uracil Uracil (; U) is one of the four nucleobases in the nucleic acid of RNA that are represented by the letters A,"
"of UDG is to remove mutations in DNA, more specifically removing uracil. These proteins have a 3-layer alpha/beta/alpha structure. The polypeptide topology of UDG is that of a classic alpha/beta protein. The structure consists primarily of a central, four-stranded, all parallel beta sheet surrounded on either side by a total of eight alpha helices and is termed a parallel doubly wound beta sheet. Uracil-DNA glycosylases are DNA repair enzymes that excise uracil residues from DNA by cleaving the N-glycosydic bond, initiating the base excision repair pathway. Uracil in DNA can arise either through the deamination of cytosine to form mutagenic"
"Thymine Thymine (T, Thy) is one of the four nucleobases in the nucleic acid of DNA that are represented by the letters G–C–A–T. The others are adenine, guanine, and cytosine. Thymine is also known as 5-methyluracil, a pyrimidine nucleobase. In RNA, thymine is replaced by the nucleobase uracil. Thymine was first isolated in 1893 by Albrecht Kossel and Albert Neumann from calves' thymus glands, hence its name. As its alternate name (5-methyluracil) suggests, thymine may be derived by methylation of uracil at the 5th carbon. In RNA, thymine is replaced with uracil in most cases. In DNA, thymine (T) binds"
"bacteria from infection by viruses. This does not appear to be the entire story. Four modifications to the cytosine residues in human DNA have been reported. These modifications are the addition of methyl (CH)-, hydroxymethyl (CHOH)-, formyl (CHO)- and carboxyl (COOH)- groups. These modifications are thought to have regulatory functions. Uracil is found in the centromeric regions of at least two human chromosomes (6 and 11). Seventeen non canonical bases are known to occur in DNA. Most of these are modifications of the canonical bases plus uracil. Twin helical strands form the DNA backbone. Another double helix may be found"
"Uracil-DNA glycosylase Uracil-DNA glycosylase, also known as UNG or UDG, is an enzyme. The human gene is well researched and orthologs exist ubiquitously among prokaryotes and eukaryotes and even in some DNA viruses. The first uracil DNA-glycosylase was isolated from ""Escherichia coli"". The human gene encodes one of several uracil-DNA glycosylases. Alternative promoter usage and splicing of this gene leads to two different isoforms: the mitochondrial UNG1 and the nuclear UNG2. One important function of uracil-DNA glycosylases is to prevent mutagenesis by eliminating uracil from DNA molecules by cleaving the N-glycosylic bond and initiating the base-excision repair (BER) pathway. Uracil"
"of uracil is not known. The negative charge is placed on the oxygen anion and produces a p""K"" of less than or equal to 12. The basic p""K"" = -3.4, while the acidic p""K"" = 9.38. In the gas phase, uracil has 4 sites that are more acidic than water. Uracil is rarely found in DNA, and this may have been an evolutionary change to increase genetic stability. This is because cytosine can deaminate spontaneously to produce uracil through hydrolytic deamination. Therefore, if there were an organism that used uracil in its DNA, the deamination of cytosine (which undergoes base"
"bases occur from cytosine deamination or misincorporation of dUMP residues. After a mutation occurs, the mutagenic threat of uracil propagates through any subsequent DNA replication steps. Once unzipped, mismatched guanine and uracil pairs are separated, and DNA polymerase inserts complementary bases to form a guanine-cytosine (GC) pair in one daughter strand and an adenine-uracil (AU) pair in the other. Half of all progeny DNA derived from the mutated template inherit a shift from GC to AU at the mutation site. UDG excises uracil in both AU and GU pairs to prevent propagation of the base mismatch to downstream transcription and"
"glycosylases remove uracil from DNA, which can arise either by spontaneous deamination of cytosine or by the misincorporation of dU opposite dA during DNA replication. The prototypical member of this family is E. coli UDG, which was among the first glycosylases discovered. Four different uracil-DNA glycosylase activities have been identified in mammalian cells, including UNG, SMUG1, TDG, and MBD4. They vary in substrate specificity and subcellular localization. SMUG1 prefers single-stranded DNA as substrate, but also removes U from double-stranded DNA. In addition to unmodified uracil, SMUG1 can excise 5-hydroxyuracil, 5-hydroxymethyluracil and 5-formyluracil bearing an oxidized group at ring C5. TDG"
"RNA. They then added 1 radioactively labeled amino acid, the building blocks of proteins, and 19 unlabeled amino acids to the extract, varying the labeled amino acid in each sample. Only in the extract containing the radioactively labeled phenylalanine, was the resulting protein also radioactive. This implied that the genetic code for phenylalanine on RNA consisted of a repetition of uracil bases. Indeed, as we know now, it is UUU (three uracil bases in a row). This was the first step in deciphering the codons of the genetic code and the first demonstration of messenger RNA (""see Nirenberg and Matthaei"
"permits base pairing by providing complementarity between the two bases, and which is essential for replication of or transcription of the encoded information found in DNA. DNA and RNA also contain other (non-primary) bases that have been modified after the nucleic acid chain has been formed. In DNA, the most common modified base is 5-methylcytosine (mC). In RNA, there are many modified bases, including those contained in the nucleosides pseudouridine (Ψ), dihydrouridine (D), inosine (I), and 7-methylguanosine (mG). Hypoxanthine and xanthine are two of the many bases created through mutagen presence, both of them through deamination (replacement of the amine-group"
"are some rare cases where thymine does occur in RNA and uracil in DNA. Here are the 4 major ribonucleotides (ribonucleoside 5'-monophosphate) which are the structural units of RNAs. In ribonucleotides, the sugar component is ribose while in deoxyribonucleotides, the sugar component is deoxyribose. Instead of a hydroxyl group at the second carbon in the ribose ring, it is replaced by a hydrogen atom. Both types of pentoses in DNA and RNA are in their β-furanose (closed five-membered ring) form and they define the identity of a nucleic acid. DNA is defined by containing 2'-deoxy-ribose nucleic acid while RNA is"
"consequence of the presence of the 2'-hydroxyl group is that in conformationally flexible regions of an RNA molecule (that is, not involved in formation of a double helix), it can chemically attack the adjacent phosphodiester bond to cleave the backbone. RNA is transcribed with only four bases (adenine, cytosine, guanine and uracil), but these bases and attached sugars can be modified in numerous ways as the RNAs mature. Pseudouridine (Ψ), in which the linkage between uracil and ribose is changed from a C–N bond to a C–C bond, and ribothymidine (T) are found in various places (the most notable ones"
"and J segment is chosen to be spliced together to form the final gene, which is catalyzed by RAG1 and RAG2 recombinases. Activation-Induced Cytidine Deaminase (AID) then converts cytidine into uracil. Uracil normally does not exist in DNA, and thus the base is excised and the nick is converted into a double-stranded break which is repaired by non-homologous end joining (NHEJ). This procedure is very error-prone and leads to somatic hypermutation. This genomic instability is crucial in ensuring mammalian survival against infection. V, D, J recombination can ensure millions of unique B-cell receptors; however, random repair by NHEJ introduces variation"
"repairing DNA damage. Supporting this view is the finding that single base lesions of the type dU:dG in the DNA of ""S. pombe"" stimulate meiotic recombination. This recombination requires uracil-DNA glycosylase, an enzyme that removes uracil from the DNA backbone and initiates base excision repair. On the basis of this finding, it was proposed that base excision repair of either a uracil base, an abasic site, or a single-strand nick is sufficient to initiate recombination in S. pombe. Other experiments with ""S. pombe"" indicated that faulty processing of DNA replication intermediates, i.e. Okazaki fragments, causes DNA damages such as single-strand"
"it can act as a co-factor to enzymes, and can transfer a phosphate to convert adenosine diphosphate (ADP) to adenosine triphosphate (ATP). In DNA and RNA, cytosine is paired with guanine. However, it is inherently unstable, and can change into uracil (spontaneous deamination). This can lead to a point mutation if not repaired by the DNA repair enzymes such as uracil glycosylase, which cleaves a uracil in DNA. When found third in a codon of RNA, cytosine is synonymous with uracil, as they are interchangeable as the third base. When found as the second base in a codon, the third"
"Artificial nucleotides (""Unnatural Base Pairs"" (UBPs) named ""d5SICS UBP"" and ""dNaM UBP"") have been inserted into bacterial DNA but these genes did not template mRNA or induce protein synthesis. The artificial nucleotides featured two fused aromatic rings which formed a (d5SICS–dNaM) complex mimicking the natural (dG–dC) base pair. One of the most common base analogs is 5-bromouracil (5BU), the abnormal base found in the mutagenic nucleotide analog BrdU. When a nucleotide containing 5-bromouracil is incorporated into the DNA, it is most likely to pair with adenine; however, it can spontaneously shift into another isomer which pairs with a different nucleobase,"
"This and many other examples set forth in the research demonstrated a trend toward guanine and cytosine in the genome and that these bases were evolutionarily superior and that held constant across all genomes. Wobble base pair A wobble base pair is a pairing between two nucleotides in RNA molecules that does not follow Watson-Crick base pair rules. The four main wobble base pairs are guanine-uracil (G-U), hypoxanthine-uracil (I-U), hypoxanthine-adenine (I-A), and hypoxanthine-cytosine (I-C). In order to maintain consistency of nucleic acid nomenclature, ""I"" is used for hypoxanthine because hypoxanthine is the nucleobase of inosine; nomenclature otherwise follows the names"
"the DNA polymerase used in PCR from proceeding past the site of damage, while these abasic sites also directly weakened the DNA and made it more likely to fragment upon heating. In this way, the researchers were able to show evidence of ongoing DNA repair in high-GC Gram-positive bacteria up to 600,000 years old. Uracil-DNA glycosylase has been shown to interact with RPA2. Uracil-DNA glycosylase Uracil-DNA glycosylase, also known as UNG or UDG, is an enzyme. The human gene is well researched and orthologs exist ubiquitously among prokaryotes and eukaryotes and even in some DNA viruses. The first uracil DNA-glycosylase"
"in RNA contains a ribose sugar, with carbons numbered 1' through 5'. A base is attached to the 1' position, in general, adenine (A), cytosine (C), guanine (G), or uracil (U). Adenine and guanine are purines, cytosine and uracil are pyrimidines. A phosphate group is attached to the 3' position of one ribose and the 5' position of the next. The phosphate groups have a negative charge each, making RNA a charged molecule (polyanion). The bases form hydrogen bonds between cytosine and guanine, between adenine and uracil and between guanine and uracil. However, other interactions are possible, such as a"
"Base J β--Glucopyranosyloxymethyluracil or base J is a hypermodified nucleobase found in the DNA of kinetoplastids including the human pathogenic trypanosomes. It was discovered in 1993, in the trypanosome ""Trypanosoma brucei"" and was the first hypermodified nucleobase found in eukaryotic DNA; it has since been found in other kinetoplastids, including ""Leishmania"". Within these organism Base J acts as a RNA polymerase II transcription terminator, with its removal in knockout cells being accompanied by a massive read-through at RNA polymerase II termination sites, which ultimately proves lethal to the cell. Base J is formed by the initial hydroxylation of thymidine and"
"the subsequent glycosylation by an as yet unidentified glycosyltransferase. Base J β--Glucopyranosyloxymethyluracil or base J is a hypermodified nucleobase found in the DNA of kinetoplastids including the human pathogenic trypanosomes. It was discovered in 1993, in the trypanosome ""Trypanosoma brucei"" and was the first hypermodified nucleobase found in eukaryotic DNA; it has since been found in other kinetoplastids, including ""Leishmania"". Within these organism Base J acts as a RNA polymerase II transcription terminator, with its removal in knockout cells being accompanied by a massive read-through at RNA polymerase II termination sites, which ultimately proves lethal to the cell. Base J"
"DNA, enzymes need to repair any damage. There are many types of DNA repair. Base excision repair utilizes base flipping to flip the damaged base out of the double helix and into the specificity pocket of a glycosylase which hydrolyzes the glycosidic bond and removes the base. DNA glycosylases interact with DNA, flipping bases to determine a mismatch. An example of base excision repair occurs when a cytosine base is deaminated and becomes a uracil base. This causes a U:G mispair which is detected by Uracil DNA glycosylase. The uracil base is flipped out into the glycosylase active pocket where"
"properties of known glycosylases in commonly studied model organisms. DNA glycosylases can be grouped into the following categories based on their substrate(s): In molecular biology, the protein family, Uracil-DNA glycosylase (UDG) is an enzyme that reverts mutations in DNA. The most common mutation is the deamination of cytosine to uracil. UDG repairs these mutations. UDG is crucial in DNA repair, without it these mutations may lead to cancer. This entry represents various uracil-DNA glycosylases and related DNA glycosylases (EC), such as uracil-DNA glycosylase, thermophilic uracil-DNA glycosylase, G:T/U mismatch-specific DNA glycosylase (Mug), and single-strand selective monofunctional uracil-DNA glycosylase (SMUG1). Uracil DNA"
"defined by containing ribose nucleic acid. In some occasions, DNA and RNA may contain some minor bases. Methylated forms of the major bases are most common in DNA. In viral DNA, some bases may be hydroxymethylated or glucosylated. In RNA, minor or modified bases occur more frequently. Some examples include hypoxanthine, dihydrouracil, methylated forms of uracil, cytosine, and guanine, as well as modified nucleoside pseudouridine. Nucleotides with phosphate groups in positions other than on the 5' carbon have also been observed. Examples include ribonucleoside 2',3'-cyclic monophosphates which are isolatable intermediates, and ribonucleoside 3'-monophosphates which are end products of the hydrolysis"
"5-Bromouracil 5-Bromouracil (5-BrU, 5BrUra, or br5Ura) is a brominated derivative of uracil that acts as an antimetabolite or base analog, substituting for thymine in DNA, and can induce DNA mutation in the same way as 2-aminopurine. It is used mainly as an experimental mutagen, but its deoxyriboside derivative (5-bromo-2-deoxy-uridine) is used to treat neoplasms. 5-BrU exists in three tautomeric forms that have different base pairing properties. The keto form (shown in the infobox) is complementary to adenine, so it can be incorporated into DNA by aligning opposite adenine residues during DNA replication (see below left). Alternatively, the enol (below right)"
"SHM involves deamination of cytosine to uracil in DNA by an enzyme called Activation-Induced (Cytidine) Deaminase, or AID. A cytosine:guanine pair is thus directly mutated to a uracil:guanine mismatch. Uracil residues are not normally found in DNA, therefore, to maintain the integrity of the genome, most of these mutations must be repaired by high-fidelity Base excision repair enzymes. The uracil bases are removed by the repair enzyme, uracil-DNA glycosylase. Error-prone DNA polymerases are then recruited to fill in the gap and create mutations. The synthesis of this new DNA involves error-prone DNA polymerases, which often introduce mutations at the position"
"in the aromatic bases of the DNA. In dsDNA, or even regions of RNA where double-stranded structure occurs, the bases are stacked parallel to each other, and the overlap of the base molecular orbitals leads to a decrease in absorbance of UV light. This phenomenon is called the hypochromic effect. When DNAse liberates nucleotides from dsDNA, the bases are no longer stacked as they are in dsDNA, so that orbital overlap is minimized and UV absorbance increases. This increase in absorbance underlies the basis of Kunitz unit of DNAse activity. One Kunitz unit is defined as the amount of enzyme"
"the bases. Common names of aminoallyl nucleosides are initially abbreviated with aa- or AA- to indicate aminoallyl. The 5-carbon sugar is indicated with or without the lowercase ""d"" indicating deoxyribose if included or ribose if not. Finally the nitrogenous base and number of phosphates are indicated (i.e. aa-UTP = aminoallyl uridine triphosphate). The goal of combining fluorescence and nucleic acids has been to provide a non-isotopic tag that is detectable to study DNA or RNA. This type of labeling allows scientists to study DNA or RNA in their structure, function, or formation with other nucleic acids. The first base modification"
"pathway that protects the bacterial chromosome from mutations by the spontaneous deamination of dCTP to dUTP. The dUTPase deficiency prevents the breakdown of dUTP, resulting in a high level of dUTP in the cell. The uracil deglycosidase deficiency prevents the removal of uracil from newly synthesized DNA. As the double-mutant ""E. coli"" replicates the phage DNA, its enzymatic machinery may, therefore, misincorporate dUTP instead of dTTP, resulting in single-strand DNA that contains some uracils (ssUDNA). The ssUDNA is extracted from the bacteriophage that is released into the medium, and then used as template for mutagenesis. An oligonucleotide containing the desired"
"viruses. Instead of thymidine, RNA contains uridine (uracil joined to ribose). Uracil is chemically very similar to thymine, which is also known as 5-methyluracil. Since thymine nucleotides are precursors of DNA (but not RNA), the prefix ""deoxy"" is often left out, i.e., deoxythymidine is often just called thymidine. Thymidine is listed as a chemical teratogen. Iododeoxyuridine is a radiosensitizer and increases the amount of DNA damage received from ionizing radiation. Azidothymidine (AZT) – used in the treatment of HIV infection. AZT inhibits the process of reverse transcription, a critical step in the viral life cycle. Radiolabeled thymidine (TdR), such as"
"as the 3' C/D box is represented by Small Cajal body specific RNA 18. The 3' C/D domain (U4-8) was also cloned previously by Darzacq and called U91. Both the doublet (U12-22/U4-8) and singlet (U4-8) forms of this snRNA have been purified from HeLa cells. The doublet form U12-22/U4-8 has been shown to localise to the nucleoplasm and is proposed to reside in the Cajal bodies whereas the U4-8 single domain appears to accumulate in the nucleolus. In humans the genomic location of U12-88/U4-8 is intergenic and the purified transcript has been shown to possess a methylated guanosine cap suggesting"
"RNA also contains the base uracil in place of thymine. RNA molecules are less stable than DNA and are typically single-stranded. Genes that encode proteins are composed of a series of three-nucleotide sequences called codons, which serve as the ""words"" in the genetic ""language"". The genetic code specifies the correspondence during protein translation between codons and amino acids. The genetic code is nearly the same for all known organisms. The total complement of genes in an organism or cell is known as its genome, which may be stored on one or more chromosomes. A chromosome consists of a single, very"