align none style margin left 1em align center valign bottom Nucleobase Image Adenine chemical structure.png ... bottom Nucleobase Image Hypoxanthine.png 70px Chemical structure of hypoxanthine br Hypoxanthine ... cellspacing 0 align none style margin left 1em align center valign bottom Nucleobase Image Dihydrouracil.PNG ... bases main Nucleic acid analogues A vast number of nucleobase analogues exist. The most common applications ... it Base azotata la Basis nucleici acidi nl Nucleobase ro Baz azotat ru sr Nukleobaza vi Nucleobase zh ... more details
Pfam box Symbol Transp cyt pur Name Permease for cytosine purines, uracil, thiamine, allantoin image width caption Pfam PF02133 InterPro IPR001248 SMART Prosite SCOP TCDB 2.A.39 OPM family 67 OPM protein 2x79 PDB The Nucleobase Cation Symporter 1 NCS1 family consists of bacterial and yeast transporters for nucleobases including purines and pyrimidines . Members of this family possess twelve transmembrane a helical spanners TMSs . At least some of them have been shown to function in uptake by substrate H symport mechanism. See also InterPro IPR012681 and InterPro IPR012732 . Category Protein domains Category Protein families Category Membrane proteins membrane protein stub InterPro content IPR001248 ... more details
A base analog is a chemical that can substitute for a normal nucleobase in nucleic acid s. A common example would be 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 , guanine . If this happens during DNA replication, a guanine will be inserted opposite the base analog, and in the next DNA replication, that guanine will pair with a cytosine. This results in a change in one base pair of DNA, specifically a Transition genetics transition mutation . Image 5bu 2.gif center thumb 500px Mutagenesis by 5BU See also Antimetabolite References Griffiths AJ, Wessler SR, Lewontin RC, Gelbart WM, Suzuki DT, Miller JH. Introduction to Genetic Analysis , 8th ed. New York W.H.Freeman and Co, 2005. Category DNA Category Genetics de Basenanaloga zh ... more details
About a notation method for the notation of genetic information multiple video card technology by Diamond Multimedia xDNA multi graphics for other alterantive nucleic acid coding systems nucleic acid analogues lowercase xDNA is a modified form of DNA with 8 nucleobase s the four natural bases adenine A , cytosine C , guanine G , and thymine T , and four artificial modifications of these made longer by the addition of an extra benzene ring xA, xC, xG, and xT. ref cite journal last Lynch first Stephen R. coauthors Haibo Liu, Jianmin Gao, and Eric T. Kool year 2006 month October title Toward a Designed, Functioning Genetic System with Expanded Size Base Pairs Solution Structure of the Eight Base xDNA Double Helix journal Journal of the American Chemical Society volume 128 issue 45 pages 14704 14711 doi 10.1021 ja065606n pmid 17090058 pmc 2519095 ref A pairs with xT, C pairs with xG, G pairs with xC, and T pairs with xA, so the distance between the two halves of the double helix is consistently greater. The double helix is thus wider and has a longer pitch. Experiments with xDNA are expected to provide new insight into the behavior of natural DNA. Also, the extended bases xA, xC, xG, and xT are fluorescence fluorescent , and single strands composed of only extended bases can recognize and bind to single strands of natural DNA, which could make them useful tools for studying biological systems. The same research group also constructed widened DNA, called yDNA . border 1 cellpadding 2 cellspacing 0 align none style margin left 1em align center File Adenin.svg 55px Chemical structure of dxA File Thymine skeletal.svg 65px Chemical structure of dxT File Cytosin.svg 50px Chemical structure of dxC File Guanine.svg 80px Chemical structure of dxG align center Adenine Thymine Cytosine Guanine align center File modified nucleobase dxA.svg 85px File modified nucleobase dxT.svg 85px File modified nucleobase dxC.svg 75px File modified nucleobase dxG.svg 110px align center Size expand ... more details
Wiktionarypar triplet A triplet is a set of three items. It may refer to Science A series of three Nucleobase nucleotide base s that form Genetic code J coupling as part of NMR spectroscopy Opal in preparation to be a gemstone Spin triplet in quantum mechanics as in triplet oxygen , or simply triplet state in general. Tuple of length 3 in mathematics Technologies Photography triplet or paint triplet Triplet lens , optical device consisting of three single lenses Tandem bicycle with three seats Other uses Binghamton Triplets , a minor league baseball team One of three babies in a multiple birth The Triplets , a Catalan children s book The Triplets band , a Latin pop group Troy Aikman , Emmitt Smith , and Michael Irvin of NFL fame from 1990 1999 See also First Hurwitz triplet Les Triplettes de Belleville , a 2003 french animated film by Sylvain Chomet Tercet in poetry Triad disambiguation , another general term for a group of three Triptych , a work of art which is divided into three sections Tuplet in music disambig de Triplett fr Triplet hsb Triplet nl Triplet pl Triplett ru sk Triplet ... more details
Nucleic acid structure refers to the Biomolecular structure structure of nucleic acid s such as DNA and RNA It is often divided into four different levels Nucleic acid primary structure Primary structure &mdash the raw sequence of nucleobase s of each of the component DNA strands Nucleic acid secondary structure Secondary structure &mdash the set of interactions between bases, i.e., which parts of which strands are bound to each other Nucleic acid tertiary structure Tertiary structure &mdash the locations of the atoms in three dimensional space, taking into consideration geometrical and steric constraints and Nucleic acid quaternary structure Quaternary structure &mdash the higher level organization of DNA in chromatin, or to the interactions between separate RNA units in the ribosome or spliceosome . See also Nucleic acid double helix Nucleic acid structure determination experimental Nucleic acid structure prediction computational DNA nanotechnology Nucleic acid design Nucleic acid thermodynamics Crosslinking of DNA DNA supercoil molecular biology stub Biomolecular structure Category DNA Category RNA ca Estructura de l ADN es Estructura del cido nucleico tr DNA n n yap s zh DNA ... more details
File TsDNA.png thumb right 110px Schematic of triple stranded DNA. A triple stranded DNA is a structure of DNA in which three oligonucleotides wind around each other and form a triple helix . In this structure, one strand binds to a DNA B form DNA double helix through Hoogsteen base pair Hoogsteen or reversed Hoogsteen hydrogen bonds . For example, a nucleobase T binds to a Base pair Watson Crick base pairing of T A by Hoogsteen base pair Hoogsteen hydrogen bonds between an AxT pair x represents a Hoogsteen base pair . An N 3 protonated cytosine , represented as C , can also form a base triplet with a C G pair through the Hoogsteen base pair Hoogsteen base pairing of an GxC . Thus, the triple helical DNAs using these Hoogsteen base pair Hoogsteen pairing s consist of two homo pyrimidine s and one homo purine , and the homo pyrimidine third strand is parallel to the homo purine strand. A homo purine third strand can also bind to a homo purine homo pyrimidine duplex using reversed Hoogsteen base pair Hoogsteen pattern s. In this triplex, a nucleobase A binds to a T A base pair and a G to a C G pair. Since the nucleobase s on the third strand have to be reversed, the homo purine third strand is antiparallel to the homo purine strand of the original duplex. Triple stranded DNA was a common hypothesis in the 1950s when scientists were struggling to discover DNA s true structural from. Watson and Crick who later won the Nobel Prize for their double helix model originally considered a triple helix model, as did Linus Pauling Pauling and Robert Corey Corey , who published a proposal for their triple helix model in the 1953 scientific journal Nature , as well as fellow scientist Fraser. However, Watson and Crick soon identified several problems with these models Negatively charged phosphates near the axis will repel each other, leaving the question as to how the three chain structure would stay together. In a triple helix model specifically Pauling and Corey s model , some o ... more details
Refimprove auto yes date December 2009 Image Cytosine chemical structure.png Cytosine 100px right Cytosine Image Thymine chemical structure.png Thymine 100px right Thymine Image Uracil chemical structure.png Uracil 100px right Uracil Image Adenine chemical structure.png Adenine 100px right Adenine Image Guanine chemical structure.png Guanine 100px right Guanine A nitrogenous nitrogen containing base is a nitrogen containing molecule having the chemical properties of a base. It is an organic compound that owes its property as a Base chemistry base to the lone pair of electron s of a nitrogen atom . In biological science s, nitrogenous bases are typically classified as the derivatives of two parent compounds, pyrimidine and purine . ref Nelson and Cox 2008, p. 272. ref They are non polar and due to their aromaticity , planar. Both pyrimidines and purines resemble pyridine and are thus weak bases and relatively unreactive towards electrophilic aromatic substitution . ref Carey 2006, p. 1206. ref Their flat shape is particularly important when considering their roles in nucleic acids as nucleobase s building blocks of DNA and RNA adenine , guanine , thymine , cytosine , and uracil . These nitrogenous bases hydrogen bond between opposing DNA strands to form the rungs of the twisted ladder or double helix of DNA or a biological catalyst that is found in the nucleotides. Adenine is always paired with thymine, and guanine is always paired with cytosine. Notes Reflist 2 References Nelson, David L. and Michael M. Cox 2008 . Principles of Biochemstry , ed. 5, W.H. Freeman and Company. Carey, Francis A. 2008 . Organic Chemistry , ed. 6, Mc Graw Hill. DEFAULTSORT Nitrogenous Base Category Biochemistry Biochemistry stub ar ca Base nitrogenada es Base nitrogenada eo Nitrogena bazo gl Base nitroxenada lt Nukleobaz pt Base nitrogenada th tr Azotlu baz zh ... more details
chembox verifiedrevid 428766450 ImageFile dTDP chemical structure.png ImageSize 197 IUPACName 2R,3S,5R 3 hydroxy br 5 5 methyl 2,4 dioxopyrimidin br 1 yl oxolan 2 yl methyl phosphono hydrogen phosphate OtherNames Section1 Chembox Identifiers CASNo 1861 44 5 PubChem 164628 SMILES CC1 CN C O NC1 O C H 2C C H C H O2 COP O O OP O O O O MeSHName Section2 Chembox Properties Formula C sub 10 sub H sub 16 sub N sub 2 sub O sub 12 sub P sub 2 sub MolarMass 402.19 Appearance Density MeltingPt BoilingPt Solubility Section3 Chembox Hazards MainHazards FlashPt Autoignition Thymidine diphosphate , abbreviated dTDP , is a nucleoside diphosphate . It is an ester of pyrophosphoric acid with the nucleoside thymidine . dTDP consists of the pyrophosphate Functional group group , the pentose sugar ribose , and the nucleobase thymine . Unlike the other deoxyribonucleotide s, thymidine diphosphate does not contain the deoxy prefix in its name. ref cite book title The ACS style guide effective communication of scientific diphosphates information year 2006 publisher American Chemical Society location Washington, D.C. isbn 9780841239999 edition 3rd editor Coghill, Anne M. Garson, Lorrin R. page 244 ref clear See also Nucleoside Nucleotide DNA RNA Oligonucleotide Thymidine diphosphate glucose dTDP glucose Reference reflist External links Nucleobases, nucleosides, and nucleotides Category Nucleotides biochem stub ca Difosfat de timidina nl Thymidinedifosfaat ja sr Timidin difosfat zh ... more details
Unreferenced stub auto yes date December 2009 Chembox Verifiedfields changed verifiedrevid 417404599 ImageFile Uridindiphosphat protoniert.svg ImageSize IUPACName Uridine 5 trihydrogen diphosphate OtherNames Section1 Chembox Identifiers CASNo 58 98 0 CASNo Ref cascite correct CAS PubChem 1158 ChEMBL Ref ebicite changed EBI ChEMBL 130266 IUPHAR ligand 1749 ChemSpiderID Ref chemspidercite changed chemspider ChemSpiderID 19952429 StdInChI Ref stdinchicite changed chemspider StdInChI 1S C9H12N2O6.2H3O4P c12 3 4 6 14 7 15 8 17 4 11 2 1 5 13 10 9 11 16 2 1 5 2,3 4 h1 2,4,6 8,12,14 15H,3H2, H,10,13,16 2 H3,1,2,3,4 t4 ,6 ,7 ,8 m1.. s1 StdInChIKey Ref stdinchicite changed chemspider StdInChIKey PMPFLUWUGZHTOK WFIJOQBCSA N SMILES MeSHName Uridine diphosphate Section2 Chembox Properties Formula C sub 9 sub H sub 14 sub N sub 2 sub O sub 12 sub P sub 2 sub MolarMass 404.161 Appearance Density MeltingPt BoilingPt Solubility Section3 Chembox Hazards MainHazards FlashPt Autoignition Uridine diphosphate , abbreviated UDP , is a nucleoside diphosphate . It is an ester of pyrophosphoric acid with the nucleoside uridine . UDP consists of the pyrophosphate Functional group group , the pentose sugar ribose , and the nucleobase uracil . See also Nucleoside Nucleotide DNA RNA Oligonucleotide UGGT Nucleobases, nucleosides, and nucleotides DEFAULTSORT Uridine Diphosphate Category Nucleotides Category Pyrimidinediones Biochem stub ca Difosfat d uridina da Uridindifosfat de Uridindiphosphat es Uridina difosfato fr Uridine diphosphate gl Urid n difosfato it Uridina difosfato nl Uridinedifosfaat ja pl Urydynodifosforan sr Uridin difosfat fi Uridiinidifosfaatti zh ... more details
chembox verifiedrevid 443555075 ImageFile Cytidindiphosphat protoniert.svg ImageSize IUPACName OtherNames Section1 Chembox Identifiers ChemSpiderID Ref chemspidercite correct chemspider ChemSpiderID 5902 InChI 1 C9H15N3O11P2 c10 5 1 2 12 9 15 11 5 8 7 14 6 13 4 22 8 3 21 25 19,20 23 24 16,17 18 h1 2,4,6 8,13 14H,3H2, H,19,20 H2,10,11,15 H2,16,17,18 t4 ,6 ,7 ,8 m1 s1 InChIKey ZWIADYZPOWUWEW XVFCMESIBF ChEMBL Ref ebicite correct EBI ChEMBL 425252 StdInChI Ref stdinchicite correct chemspider StdInChI 1S C9H15N3O11P2 c10 5 1 2 12 9 15 11 5 8 7 14 6 13 4 22 8 3 21 25 19,20 23 24 16,17 18 h1 2,4,6 8,13 14H,3H2, H,19,20 H2,10,11,15 H2,16,17,18 t4 ,6 ,7 ,8 m1 s1 StdInChIKey Ref stdinchicite correct chemspider StdInChIKey ZWIADYZPOWUWEW XVFCMESISA N CASNo 63 38 7 CASNo Ref cascite correct CAS CASOther br 34393 59 4 disodium salt NOT CAS verified PubChem 290 ChEBI Ref ebicite correct EBI ChEBI 17239 SMILES O P O O OP O O OC C H 2O C H N 1C O N C N C C 1 C H O C H 2O Section2 Chembox Properties Formula C sub 9 sub H sub 15 sub N sub 3 sub O sub 11 sub P sub 2 sub MolarMass 403.176422 Appearance Density MeltingPt BoilingPt Solubility Section3 Chembox Hazards MainHazards FlashPt Autoignition Cytidine diphosphate , abbreviated CDP , is a nucleoside diphosphate . It is an ester of pyrophosphoric acid with the nucleoside cytidine . CDP consists of the pyrophosphate Functional group group , the pentose sugar ribose , and the nucleobase cytosine . See also Nucleoside Nucleotide DNA RNA Oligonucleotide External links Nucleobases, nucleosides, and nucleotides Category Nucleotides Category Pyrimidones biochem stub ca Difosfat de citidina da Cytidindifosfat de Cytidindiphosphat fr Cytidine diphosphate gl Citid n difosfato it Citosindifosfato nl Cytidinedifosfaat ja sr Citidin difosfat zh ... more details
protein Name guanosine monophosphate reductase caption image width HGNCid 4376 Symbol GMPR AltSymbols EntrezGene 2766 OMIM 139265 RefSeq NM 006877 UniProt P36959 PDB ECnumber 1.7.1.7 Chromosome 6 Arm p Band 23 LocusSupplementaryData protein Name guanosine monophosphate reductase 2 caption image width HGNCid 4377 Symbol GMPR2 AltSymbols EntrezGene 51292 OMIM 610781 RefSeq NM 016576 UniProt Q9P2T1 PDB ECnumber Chromosome 14 Arm q Band 11.2 LocusSupplementaryData GMP reductase EC number 1.7.1.7 Guanosine 5 monophosphate oxidoreductase is an enzyme that catalyses the irreversible and NADPH dependent reductive deamination of Guanosine monophosphate GMP into Inosine monophosphate IMP . ref name pmid2904262 cite journal author Andrews SC, Guest JR title Nucleotide sequence of the gene encoding the GMP reductase of Escherichia coli K12 journal Biochem. J. volume 255 issue 1 pages 35 43 year 1988 month October pmid 2904262 pmc 1135187 doi url ref NADPH Guanosine monophosphate guanosine 5 phosphate NADP sup sup Inosine monophosphate inosine 5 phosphate NH sub 3 sub It converts nucleobase, nucleoside and nucleotide derivatives of G to A nucleotides, and maintains intracellular balance of A and G nucleotide nucleotides . In melanocytic cells, GMP reductase gene expression may be regulated by Microphthalmia associated transcription factor MITF . ref name pmid19067971 cite journal author Hoek KS, Schlegel NC, Eichhoff OM, et al. title Novel MITF targets identified using a two step DNA microarray strategy journal Pigment Cell Melanoma Res. volume 21 issue 6 pages 665 76 year 2008 pmid 19067971 doi 10.1111 j.1755 148X.2008.00505.x issn ref See also Purine metabolism References reflist External links MeshName GMP reductase Nitrogenous donor oxidoreductases Nucleotide metabolism InterPro content IPR001093 biochemistry stub it GMP reduttasi ja GMP ... more details
for the nucleic base Adenine Adenine Notability date February 2011 Adenine , named after the nucleobase adenine , is a script language , which is developed in the context of the Haystack PIM Haystack project and the Project Oxygen Oxygen project of the Massachusetts Institute of Technology MIT Computer Science and Artificial Intelligence Laboratory CSAIL in collaboration with Nippon Telegraph and Telephone NTT . A substantial characteristic of Adenine is that this language possesses native support for the Resource Description Framework RDF . The language constructs of Adenine are derived from Python programming language Python and Lisp programming language LISP . The language is written in RDF and thus also can be represented and written with RDF based Syntaxes such as Notation 3 N3 . Also, as well as RDF, Adenine can be extended. The data type system corresponds to the data type system from RDF and XML Schema, and can be extended. As a script language, Adenine is platform independent. External links http haystack.csail.mit.edu developers adenine.html Adenine Tutorial PDF http groups.csail.mit.edu haystack documents papers 2002 sow2002 adenine.pdf Adenine A Metadata Programming Language 17.3 KB Overview of Adenine PDF http web.archive.org web 20060902101312 http haystack.lcs.mit.edu documentation adenine.pdf Metadata Programming in Adenine Draft More detailed explanation of Adenine and its usage. http www.ifcx.org wiki Adenine.html Adenine page at IFCX.org Category Semantic Web Category RDF data access Category Scripting languages Category Extensible syntax programming languages Category Data structured programming languages Category Dynamic programming languages Category Statically typed programming languages both static and dynamic Category Functional languages Category Lisp programming language family Category Multi paradigm programming languages Category Object oriented programming languages Category Term rewriting programming languages de Adenine ... more details
Chembox ImageFile 7 Methylguanosine.svg ImageSize 180px IUPACName 7 Methylguanosine OtherNames N7 Methylguanosine 2 Amino 1,6 dihydro 7 methyl 6 oxo 9 small D small ribofuranosylpurinium Section1 Chembox Identifiers Abbreviations m7G m sup 7 sup G CASNo 20244 86 4 CASNo Ref cascite correct PubChem 445404 ChemSpiderID 393054 SMILES O C3 N C N Nc1c3n c n 1 C H 2O C H C H O C H 2O CO C InChI 1 C11H15N5O5 c1 15 3 16 8 5 15 9 20 14 11 12 13 8 10 7 19 6 18 4 2 17 21 10 h3 4,6 7,10,17 19H,2H2,1H3, H2 ,12,13,14,20 p 1 t4 ,6 ,7 ,10 m1 s1 InChIKey OGHAROSJZRTIOK UJMNIJGGBX StdInChI 1S C11H15N5O5 c1 15 3 16 8 5 15 9 20 14 11 12 13 8 10 7 19 6 18 4 2 17 21 10 h3 4,6 7,10,17 19H,2H2,1H3, H2 ,12,13,14,20 p 1 t4 ,6 ,7 ,10 m1 s1 StdInChIKey OGHAROSJZRTIOK KQYNXXCUSA O Section2 Chembox Properties C 11 H 16 N 5 O 5 Appearance Density MeltingPt BoilingPt Solubility Section3 Chembox Hazards MainHazards FlashPt Autoignition 7 Methylguanosine is a modified purine nucleobase . It is a methylation methylated version of guanosine and when found in human urine, it may be a biomarker of some types of cancer. ref cite journal pmid 1739950 year 1992 last1 Reynaud first1 C last2 Bruno first2 C last3 Boullanger first3 P last4 Grange first4 J last5 Barbesti first5 S last6 Niveleau first6 A title Monitoring of urinary excretion of modified nucleosides in cancer patients using a set of six monoclonal antibodies volume 61 issue 3 pages 255 62 journal Cancer letters ref References reflist External links http www.hmdb.ca metabolites HMDB01107 Metabocard for 7 Methylguanosine HMDB01107 , Human Metabolome Database, University of Alberta DEFAULTSORT Methylguanosine, 7 Category Nucleosides Category Purines organic compound stub ... more details
chembox verifiedrevid 445712220 ImageFile Guanosintriphosphat protoniert.svg ImageSize 200px IUPACName 2 R ,3 S ,4 R ,5 R 5 2 amino 6 oxo 3 H purin 9 yl 3,4 dihydroxyoxolan 2 yl methyl hydroxy phosphonooxyphosphoryl hydrogen phosphate OtherNames guanosine triphosphate, 9 small D small ribofuranosylguanine 5 triphosphate, 9 small D small ribofuranosyl 2 amino 6 oxo purine 5 triphosphate Section1 Chembox Identifiers ChemSpiderID Ref chemspidercite correct chemspider ChemSpiderID 6569 InChI 1 C10H16N5O14P3 c11 10 13 7 4 8 18 14 10 12 2 15 7 9 6 17 5 16 3 27 9 1 26 31 22,23 29 32 24,25 28 30 19,20 21 h2 3,5 6,9,16 17H,1H2, H,22,23 H,24,25 H2,19,20,21 H3,11,13,14,18 t3 ,5 ,6 ,9 m1 s1 InChIKey XKMLYUALXHKNFT UUOKFMHZBF StdInChI Ref stdinchicite correct chemspider StdInChI 1S C10H16N5O14P3 c11 10 13 7 4 8 18 14 10 12 2 15 7 9 6 17 5 16 3 27 9 1 26 31 22,23 29 32 24,25 28 30 19,20 21 h2 3,5 6,9,16 17H,1H2, H,22,23 H,24,25 H2,19,20,21 H3,11,13,14,18 t3 ,5 ,6 ,9 m1 s1 StdInChIKey Ref stdinchicite correct chemspider StdInChIKey XKMLYUALXHKNFT UUOKFMHZSA N CASNo Ref cascite correct CAS CASNo 86 01 1 PubChem 6830 IUPHAR ligand 1742 ChEBI Ref ebicite correct EBI ChEBI 15996 SMILES c1nc2c n1 C H 3 C H C H C H O3 CO P O O O P O O OP O O O O O nH c nc2 O N MeSHName Guanosine triphosphate Section2 Chembox Properties C 10 H 16 N 5 O 14 P 3 Appearance Density MeltingPt BoilingPt Section3 Chembox Hazards Solubility MainHazards FlashPt Autoignition Guanosine 5 triphosphate GTP is a purine nucleoside triphosphate . It can act as a substrate for the synthesis of RNA during the transcription genetics transcription process. Its structure is similar to that of the guanine nucleobase , the only difference being that nucleotides like GTP have a ribose sugar and three phosphate s, with the nucleobase attached to the 1 and the triphosphate moiety attached to the 5 carbons of the ribose. It also has the role of a source of energy or an activator of substrates in metabolic reactions, like that ... more details
Phred base calling is a computer program for identifying a base nucleobase sequence from a fluorescence trace data generated by an automated DNA sequencer that uses electrophoresis and 4 fluorescent dye method. ref Ewing B, Hillier L, Wendl MC, Green P. 1998 Base calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8 3 175 185. PMID 9521921 http genome.cshlp.org content 8 3 175.long full article ref ref Ewing B, Green P. 1998 Base calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8 3 186 194. DOI 10.1101 gr.8.3.186 PMID 9521922 http genome.cshlp.org content 8 3 186.long fulll article ref When originally developed, Phred produced significantly fewer errors in the data sets examined than other methods, averaging 40 50 fewer errors. Phred quality score s have become widely accepted to characterize the quality of DNA sequences, and can be used to compare the efficacy of different sequencing methods. Background The fluorescent dye DNA sequencing is a molecular biology technique that involves labeling single strand DNA sequences of varied length with 4 fluorescent dyes corresponding to 4 different bases used in DNA and subsequently separating the DNA sequences by slab gel or capillary electrophoresis method see DNA Sequencing . The electrophoresis run is monitored by CCD on the DNA sequencer and this produces a time trace data or chromatogram of the fluorescent peaks that passed the CCD point. Examining the fluorescence peaks in the trace data, we can determine the order of individual bases nucleobase in the DNA . Since the intensity, shape and the location of a fluorescence peak are not always consistent or unambiguous, however, sometimes it is difficult or time consuming to determine or call the correct bases for the peaks accurately if it is done manually. Automated DNA sequencing techniques have revolutionized the field of molecular biology generating vast amounts of DNA sequence data. However, the sequence ... more details
chembox Verifiedfields changed verifiedrevid 461124476 ImageFile Guanosindiphosphat protoniert.svg ImageSize IUPACName OtherNames Section1 Chembox Identifiers CASNo Ref cascite changed ?? CASNo 146 91 8 ChEMBL Ref ebicite correct EBI ChEMBL 384759 PubChem 730 IUPHAR ligand 2410 ChemSpiderID Ref chemspidercite correct chemspider ChemSpiderID 8630 ChEBI Ref ebicite correct EBI ChEBI 17552 StdInChI Ref stdinchicite correct chemspider StdInChI 1S C10H15N5O11P2 c11 10 13 7 4 8 18 14 10 12 2 15 7 9 6 17 5 16 3 25 9 1 24 28 22,23 26 27 19,20 21 h2 3,5 6,9,16 17H,1H2, H,22,23 H2,19,20,21 H3,11,13,14,18 t3 ,5 ,6 ,9 m1 s1 StdInChIKey Ref stdinchicite correct chemspider StdInChIKey QGWNDRXFNXRZMB UUOKFMHZSA N SMILES C1 NC2 C N1C3C C C O3 COP O O OP O O O O O NC NC2 O N Section2 Chembox Properties Formula C sub 10 sub H sub 15 sub N sub 5 sub O sub 11 sub P sub 2 sub MolarMass 443.200522 Appearance Density MeltingPt BoilingPt Solubility Section3 Chembox Hazards MainHazards FlashPt Autoignition Guanosine diphosphate , abbreviated GDP , is a nucleoside diphosphate . It is an ester of pyrophosphoric acid with the nucleoside guanosine . GDP consists of the pyrophosphate Functional group group , the pentose sugar ribose , and the nucleobase guanine . GDP is the product of guanosine triphosphate GTP dephosphorylation by GTPase s, e.g., the G protein s that are involved in signal transduction . GDP is converted into GTP with the help of pyruvate kinase and phosphoenolpyruvate. See also Nucleoside Nucleotide DNA RNA Oligonucleotide Guanosine triphosphate Nucleobases, nucleosides, and nucleotides biochem stub Category Nucleotides Category Purines cs Guanosindifosf t da Guanosindifosfat de Guanosindiphosphat es Guanos n difosfato fr Guanosine diphosphate gl Guanos n difosfato it Guanosindifosfato nl Guanosinedifosfaat ja oc Guanosina difosfat pl Guanozynodifosforan pt Guanosina difosfato ru sr Guanozin difosfat fi Guanosiinidifosfaatti sv Guanosindifosfat uk ... more details
When referring to Transcription genetics DNA transcription , the coding strand is the DNA strand which has the same Nucleobase base sequence as the RNA transcript produced although with thymine replaced by uracil . It is this strand which contains codons , while the non coding strand contains anti codons. Alternative terms for strands Wherever a gene exists on a DNA molecule , one strand is the coding strand or sense strand or non template strand , and the other is the noncoding strand also called the antisense strand antisense is a general term for a sequence of DNA or RNA that is complementary to mRNA http books.google.com books?id BrNpbPkzoxAC&pg PA129&lpg PA129&dq coding strand antisense&source web&ots t6yUAob0Km&sig O3UVL8ZYlFi0ljVYax8hp695sRo PPA75,M1 , anticoding strand, template strand, or transcribed strand . Strands in transcription bubble During Transcription genetics transcription , RNA polymerase unwinds a short section of the DNA double helix near the start of the gene. This unwound section is known as the transcription bubble . The RNA polymerase, and therefore the transcription bubble, travels along the noncoding strand in the opposite, 3 to 5 , direction, as well as polymerizing a newly synthesized strand in 5 to 3 or Upstream and downstream DNA downstream direction. The DNA double helix is rewound by RNA polymerase at the rear of the transcription bubble Lewin, pp 235 http books.google.com books?id BrNpbPkzoxAC&pg PA129&lpg PA129&dq coding strand antisense&source web&ots t6yUAob0Km&sig O3UVL8ZYlFi0ljVYax8hp695sRo PPA75,M1 . Like how a zipper works, only it unzips it and rezips it without going back and forth. RNA DNA hybrid Where the helix is unwound, the coding strand consists of unpaired bases, whilst the template strand consists of an RNA DNA composite, followed by a number of unpaired bases at the rear. This hybrid consists of the most recently added nucleotides of the RNA transcript, complementary base paired to the template strand. The number ... more details
Unsourced image removed Image Hoogsteen base pair.png 160px right A Hoogsteen base pair is a variation of base pairing in nucleic acid s such as the A T pair. In this manner, two nucleobase s on each strand can be held together by hydrogen bond s in the major groove. A Hoogsteen base pair applies the N7 position of the purine base as a hydrogen bond acceptor and C6 amino group as a donor , which bind the Watson Crick N3&ndash N4 face of the pyrimidine base. History This term is named for Karst Hoogsteen , who, in 1963, first recognized the potential for these unusual pairings quoted from Lehninger Principles of Biochemistry by David Nelson and Michael Cox, 4th edition, published in 2005 by Freeman . Chemical properties Hoogsteen pairs have quite different properties from Base pair Watson Crick base pairs . The angle between the two glycosylic bonds ca. 80 in the A T pair is larger and the C1&prime &ndash C1&prime distance ca. 860 pm or 8.6 is smaller than in the regular geometry. In some cases, called reversed Hoogsteen base pairs, one base is rotated 180 with respect to the other. Triplex structures File Hoogsteen.png thumb right 200px Base triads in a DNA triple helix structure This non Watson Crick base pairing allows the third strands to wind around the duplexes, which are assembled in the Base pair Watson Crick pattern , and form triple stranded DNA triple stranded helices such as poly dA 2poly dT and poly rC 2poly rC . It can be also seen in three dimensional structures of transfer RNA . Quadruplex structures It also allows formation of secondary structures of single stranded DNA and RNA G rich called G quadruplex es G4 DNA and G4 RNA at least in vitro. It needs four triplets of G, separated by short spacers. This permits assembly of planar quartets which are composed of stacked associations of hoogsteen bonded guanines. ref In vivo veritas Using yeast to probe the biological functions of G quadruplexes. Johnson JE, Smith JS, Kozak ML, Johnson FB. Biochimie ... more details
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