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46-743: L50 may refer to : N50, L50, and related statistics , used in genome assembly HMS Rochester (L50) , Royal Navy ship Daihatsu New Line#First generation (L50) , |Daihatsu compact truck model British L-class submarine#Group 3 (L50-class) , British submarine class Suzuki Carry#Fifth generation (L50/60) , Suzuki van Landing Craft L-50 , Swedish Navy landing craft Honduran lempira , Honduran banknote Suzuki FB series engine#L50 , Suzuki FB series engine model HMAS Tobruk (L 50) , Royal Australian Navy ship Kavango – Southwest Bantu languages , Bantu language List of Toyota transmissions , Toyota transmission [REDACTED] Topics referred to by

92-477: A (d5SICS–dNaM) complex or base pair in DNA. His team designed a variety of in vitro or "test tube" templates containing the unnatural base pair and they confirmed that it was efficiently replicated with high fidelity in virtually all sequence contexts using the modern standard in vitro techniques, namely PCR amplification of DNA and PCR-based applications. Their results show that for PCR and PCR-based applications,

138-635: A class of single-ringed chemical structures called pyrimidines . Purines are complementary only with pyrimidines: pyrimidine–pyrimidine pairings are energetically unfavorable because the molecules are too far apart for hydrogen bonding to be established; purine–purine pairings are energetically unfavorable because the molecules are too close, leading to overlap repulsion. Purine–pyrimidine base-pairing of AT or GC or UA (in RNA) results in proper duplex structure. The only other purine–pyrimidine pairings would be AC and GT and UG (in RNA); these pairings are mismatches because

184-437: A living organism passing along an expanded genetic code to subsequent generations. Romesberg said he and his colleagues created 300 variants to refine the design of nucleotides that would be stable enough and would be replicated as easily as the natural ones when the cells divide. This was in part achieved by the addition of a supportive algal gene that expresses a nucleotide triphosphate transporter which efficiently imports

230-467: A set of contigs, the N50 is defined as the sequence length of the shortest contig at 50% of the total assembly length. It can be thought of as the point of half of the mass of the distribution; the number of bases from all contigs longer than the N50 will be close to the number of bases from all contigs shorter than the N50 . For example, consider 9 contigs with the lengths 2,3,4,5,6,7,8,9, and 10; their sum

276-432: A small number of base mispairs within a long sequence of normal DNA base pairs. To repair mismatches formed during DNA replication, several distinctive repair processes have evolved to distinguish between the template strand and the newly formed strand so that only the newly inserted incorrect nucleotide is removed (in order to avoid generating a mutation). The proteins employed in mismatch repair during DNA replication, and

322-483: A third base pair, in addition to the two base pairs found in nature, A-T ( adenine – thymine ) and G-C ( guanine – cytosine ). A few research groups have been searching for a third base pair for DNA, including teams led by Steven A. Benner , Philippe Marliere , Floyd E. Romesberg and Ichiro Hirao . Some new base pairs based on alternative hydrogen bonding, hydrophobic interactions and metal coordination have been reported. In 1989 Steven Benner (then working at

368-501: A weighted median statistic such that 50% of the entire assembly is contained in contigs or scaffolds equal to or larger than this value. Given a set of contigs, each with its own length, the L50 is defined as count of smallest number of contigs whose length sum makes up half of genome size. From the example above the L50=3. The N90 statistic is less than or equal to the N50 statistic; it

414-433: Is (100 × (UG50/Length of reference genome). The UG50% , as a percentage-based metric, can be used to compare assembly results from different samples or studies. Consider two fictional, highly simplified genome assemblies, A and B, that are derived from two different species. Assembly A contains six contigs of lengths 80  kbp , 70 kbp, 50 kbp, 40 kbp, 30 kbp, and 20 kbp. The sum size of assembly A

460-532: Is 290 kbp, the N50 contig length is 70 kbp because 80 + 70 is greater than 50% of 290, and the L50 contig count is 2 contigs. The contig lengths of assembly B are the same as those of assembly A, except for the presence of two additional contigs with lengths of 10 kbp and 5 kbp. The size of assembly B is 305 kbp, the N50 contig length drops to 50 kbp because 80 + 70 + 50

506-514: Is 54, half of the sum is 27, and the size of the genome also happens to be 54. Then, 50% of this assembly would be 10 + 9 + 8 = 27 (half the length of the sequence). Thus the N50=8, which is the size of the contig which, along with the larger contigs, contain half of sequence of a particular genome. Note: When comparing N50 values from different assemblies, the assembly sizes must be the same size in order for N50 to be meaningful. N50 can be described as

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552-455: 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

598-410: Is also often used to imply distance along a chromosome, but the number of base pairs it corresponds to varies widely. In the human genome, the centimorgan is about 1 million base pairs. An unnatural base pair (UBP) is a designed subunit (or nucleobase ) of DNA which is created in a laboratory and does not occur in nature. DNA sequences have been described which use newly created nucleobases to form

644-456: Is contained in contigs of size U50 or larger. UL50 is the number of contigs whose length sum produces U50. UG50 is the length of the smallest contig such that 50% of the reference genome is contained in unique, target-specific contigs of size UG50 or larger. UG50% is the estimated percent coverage length of the UG50 in direct relation to the length of the reference genome. The calculation

690-425: Is different from Wikidata All article disambiguation pages All disambiguation pages N50, L50, and related statistics To provide a better assessment of assembly output for viral and microbial datasets, a new metric called U50 should be used. The U50 identifies unique, target-specific contigs by using a reference genome as baseline, aiming at circumventing some limitations that are inherent to

736-484: Is estimated to be about 3.2 billion base pairs long and to contain 20,000–25,000 distinct protein-coding genes. A kilobase (kb) is a unit of measurement in molecular biology equal to 1000 base pairs of DNA or RNA. The total number of DNA base pairs on Earth is estimated at 5.0 × 10 with a weight of 50 billion tonnes . In comparison, the total mass of the biosphere has been estimated to be as much as 4  TtC (trillion tons of carbon ). Hydrogen bonding

782-475: Is greater than 50% of 305, and the L50 contig count is 3 contigs. This example illustrates that one can sometimes increase the N50 length simply by removing some of the shortest contigs or scaffolds from an assembly. If the estimated or known size of the genome from the fictional species A is 500 kbp then the NG50 contig length is 30 kbp because 80 + 70 + 50 + 40 + 30

828-568: Is greater than 50% of 500. In contrast, if the estimated or known size of the genome from species B is 350 kbp then it has an NG50 contig length of 50 kbp because 80 + 70 + 50 is greater than 50% of 350. N50 can be found mathematically for a list L of positive integers as follows: For example: If L = (2, 2, 2, 3, 3, 4, 8, 8), then L' consists of six 2's, six 3's, four 4's, and sixteen 8's. That is, L' has twice as many 2s as L ; it has three times as many 3s as L ; it has four times as many 4s; etc. The median of

874-412: Is minimal, but its role in the specificity underlying complementarity is, by contrast, of maximal importance as this underlies the template-dependent processes of the central dogma (e.g. DNA replication ). The bigger nucleobases , adenine and guanine, are members of a class of double-ringed chemical structures called purines ; the smaller nucleobases, cytosine and thymine (and uracil), are members of

920-465: Is the chemical interaction that underlies the base-pairing rules described above. Appropriate geometrical correspondence of hydrogen bond donors and acceptors allows only the "right" pairs to form stably. DNA with high GC-content is more stable than DNA with low GC-content. Crucially, however, stacking interactions are primarily responsible for stabilising the double-helical structure; Watson-Crick base pairing's contribution to global structural stability

966-411: Is the length for which the collection of all contigs of that length or longer contains at least 90% of the sum of the lengths of all contigs. Note that N50 is calculated in the context of the assembly size rather than the genome size. Therefore, comparisons of N50 values derived from assemblies of significantly different lengths are usually not informative, even if for the same genome. To address this,

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1012-475: The N50 metric. The use of the U50 metric allows for a more accurate measure of assembly performance by analyzing only the unique, non-overlapping contigs. Most viral and microbial sequencing have high background noise (i.e., host and other non-targets), which contributes to having a skewed, misrepresented N50 value - this is corrected by U50 . N50 statistic defines assembly quality in terms of contiguity . Given

1058-746: The Swiss Federal Institute of Technology in Zurich) and his team led with modified forms of cytosine and guanine into DNA molecules in vitro . The nucleotides, which encoded RNA and proteins, were successfully replicated in vitro . Since then, Benner's team has been trying to engineer cells that can make foreign bases from scratch, obviating the need for a feedstock. In 2002, Ichiro Hirao's group in Japan developed an unnatural base pair between 2-amino-8-(2-thienyl)purine (s) and pyridine-2-one (y) that functions in transcription and translation, for

1104-407: The 32-element set L' is the average of the 16th smallest element, 4, and 17th smallest element, 8, so the N50 is 6. We can see that the sum of all values in the list L that are smaller than or equal to the N50 of 6 is 16 = 2+2+2+3+3+4 and the sum of all values in the list L that are larger than or equal to 6 is also 16 = 8+8. For comparison with the N50 of 6, note that

1150-459: The DNA helix to maintain a regular helical structure that is subtly dependent on its nucleotide sequence . The complementary nature of this based-paired structure provides a 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

1196-653: The GC content. Higher GC content results in higher melting temperatures; it is, therefore, unsurprising that the genomes of extremophile organisms such as Thermus thermophilus are particularly GC-rich. On the converse, regions of a genome that need to separate frequently — for example, the promoter regions for often- transcribed genes — are comparatively GC-poor (for example, see TATA box ). GC content and melting temperature must also be taken into account when designing primers for PCR reactions. The following DNA sequences illustrate pair double-stranded patterns. By convention,

1242-441: The N50 statistic. The D50 statistic (also termed D50 test ) is similar to the N50 statistic in definition though it is generally not used to describe genome assemblies. The D50 statistic is the lowest value d for which the sum of the lengths of the largest d lengths is at least 50% of the sum of all of the lengths. U50 is the length of the smallest contig such that 50% of the sum of all unique, target-specific contigs

1288-422: The amino acid sequence of proteins via the genetic code . The size of an individual gene or an organism's entire genome is often measured in base pairs because DNA is usually double-stranded. Hence, the number of total base pairs is equal to the number of nucleotides in one of the strands (with the exception of non-coding single-stranded regions of telomeres ). The haploid human genome (23 chromosomes )

1334-532: The authors of the Assemblathon competition came up with a new measure called NG50 . The NG50 statistic is the same as N50 except that it is 50% of the known or estimated genome size that must be of the NG50 length or longer. This allows for meaningful comparisons between different assemblies. In the typical case that the assembly size is not more than the genome size, the NG50 statistic will not be more than

1380-404: The best-performing UBP Romesberg's laboratory had designed and inserted it into cells of the common bacterium E. coli that successfully replicated the unnatural base pairs through multiple generations. The transfection did not hamper the growth of the E. coli cells and showed no sign of losing its unnatural base pairs to its natural DNA repair mechanisms. This is the first known example of

1426-551: The clinical significance of defects in this process are described in the article DNA mismatch repair . The process of mispair correction during recombination is described in the article gene conversion . The following abbreviations are commonly used to describe the length of a D/R NA molecule : For single-stranded DNA/RNA, units of nucleotides are used—abbreviated nt (or knt, Mnt, Gnt)—as they are not paired. To distinguish between units of computer storage and bases, kbp, Mbp, Gbp, etc. may be used for base pairs. The centimorgan

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1472-526: The d5SICS–dNaM unnatural base pair is functionally equivalent to a natural base pair, and when combined with the other two natural base pairs used by all organisms, A–T and G–C, they provide a fully functional and expanded six-letter "genetic alphabet". In 2014 the same team from the Scripps Research Institute reported that they synthesized a stretch of circular DNA known as a plasmid containing natural T-A and C-G base pairs along with

1518-411: The formation of short double-stranded helices, and a wide variety of non–Watson–Crick interactions (e.g., G–U or A–A) allow RNAs to fold into a vast range of specific three-dimensional structures . In addition, base-pairing between transfer RNA (tRNA) and messenger RNA (mRNA) forms the basis for the molecular recognition events that result in the nucleotide sequence of mRNA becoming translated into

1564-573: The gap between adjacent bases on a single strand and induce frameshift mutations by "masquerading" as a base, causing the DNA replication machinery to skip or insert additional nucleotides at the intercalated site. Most intercalators are large polyaromatic compounds and are known or suspected carcinogens . Examples include ethidium bromide and acridine . Mismatched base pairs can be generated by errors of DNA replication and as intermediates during homologous recombination . The process of mismatch repair ordinarily must recognize and correctly repair

1610-673: The genetic alphabet expansion significantly augment DNA aptamer affinities to target proteins. In 2012, a group of American scientists led by Floyd Romesberg, a chemical biologist at the Scripps Research Institute in San Diego, California, published that his team designed an unnatural base pair (UBP). The two new artificial nucleotides or Unnatural Base Pair (UBP) were named d5SICS and dNaM . More technically, these artificial nucleotides bearing hydrophobic nucleobases , feature two fused aromatic rings that form

1656-514: The mean of the list L is 4 while the median is 3. To recapitulate in a more visual way, we have: Values of the list       L =  (2,    2,    2,    3,       3,       4,          8,                      8) Values of

1702-505: The mechanism through which DNA polymerase replicates DNA and RNA polymerase transcribes DNA into RNA. Many DNA-binding proteins can recognize specific base-pairing patterns that identify particular regulatory regions of genes. Intramolecular base pairs can occur within single-stranded nucleic acids. This is particularly important in RNA molecules (e.g., transfer RNA ), where Watson–Crick base pairs (guanine–cytosine and adenine– uracil ) permit

1748-536: The new list   L' = (2  2  2  2  2  2  3  3  3  3  3  3  4  4  4  4   8   8  8  8  8  8  8  8  8  8  8  8  8  8  8  8) Ranks of L' values =           1  2  3  4  5  6  7  8  9  10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 Kilobase A base pair ( bp )

1794-409: The number of amino acids which can be encoded by DNA, from the existing 20 amino acids to a theoretically possible 172, thereby expanding the potential for living organisms to produce novel proteins . The artificial strings of DNA do not encode for anything yet, but scientists speculate they could be designed to manufacture new proteins which could have industrial or pharmaceutical uses. Experts said

1840-448: The patterns of hydrogen donors and acceptors do not correspond. The GU pairing, with two hydrogen bonds, does occur fairly often in RNA (see wobble base pair ). Paired DNA and RNA molecules are comparatively stable at room temperature, but the two nucleotide strands will separate above a melting point that is determined by the length of the molecules, the extent of mispairing (if any), and

1886-447: The same term This disambiguation page lists articles associated with the same title formed as a letter–number combination. If an internal link led you here, you may wish to change the link to point directly to the intended article. Retrieved from " https://en.wikipedia.org/w/index.php?title=L50&oldid=684636510 " Category : Letter–number combination disambiguation pages Hidden categories: Short description

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1932-578: The site-specific incorporation of non-standard amino acids into proteins. In 2006, they created 7-(2-thienyl)imidazo[4,5-b]pyridine (Ds) and pyrrole-2-carbaldehyde (Pa) as a third base pair for replication and transcription. Afterward, Ds and 4-[3-(6-aminohexanamido)-1-propynyl]-2-nitropyrrole (Px) was discovered as a high fidelity pair in PCR amplification. In 2013, they applied the Ds-Px pair to DNA aptamer generation by in vitro selection (SELEX) and demonstrated

1978-463: The synthetic DNA incorporating the unnatural base pair raises the possibility of life forms based on a different DNA code. In addition to the canonical pairing, some conditions can also favour base-pairing with alternative base orientation, and number and geometry of hydrogen bonds. These pairings are accompanied by alterations to the local backbone shape. The most common of these is the wobble base pairing that occurs between tRNAs and mRNAs at

2024-519: The third base position of many codons during transcription and during the charging of tRNAs by some tRNA synthetases . They have also been observed in the secondary structures of some RNA sequences. Additionally, Hoogsteen base pairing (typically written as A•U/T and G•C) can exist in some DNA sequences (e.g. CA and TA dinucleotides) in dynamic equilibrium with standard Watson–Crick pairing. They have also been observed in some protein–DNA complexes. In addition to these alternative base pairings,

2070-542: The top strand is written from the 5′-end to the 3′-end ; thus, the bottom strand is written 3′ to 5′. Chemical analogs of nucleotides can take the place of proper nucleotides and establish non-canonical base-pairing, leading to errors (mostly point mutations ) in DNA replication and DNA transcription . This is due to their isosteric chemistry. One common mutagenic base analog is 5-bromouracil , which resembles thymine but can base-pair to guanine in its enol form. Other chemicals, known as DNA intercalators , fit into

2116-402: The triphosphates of both d5SICSTP and dNaMTP into E. coli bacteria. Then, the natural bacterial replication pathways use them to accurately replicate a plasmid containing d5SICS–dNaM. Other researchers were surprised that the bacteria replicated these human-made DNA subunits. The successful incorporation of a third base pair is a significant breakthrough toward the goal of greatly expanding

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