Pyrosequencing 1154853 225775728 2008-07-15T10:12:25Z 61.16.169.12 /* Procedure */ {{context}} [[Image:Pyrogram1.jpg|thumb|right|Example of a pyrogram showing the nucleotide sequence in a specific section of DNA. The tops represent light emission and nucleotide binding.]] '''Pyrosequencing''' is a method of [[DNA sequencing]] (determining the order of [[nucleotides]] in DNA) based on the "sequencing by synthesis" principle. The technique was developed by [[Mostafa Ronaghi]] and [[Pål Nyrén]] at the [[Royal Institute of Technology]] in Stockholm in the 1990s.<ref name=RonachiScience> {{cite journal| author=Ronaghi et al. |title=A sequencing method based on real-time pyrophosphate | journal=Science |date=1998-07-17|volume=281|page=363 |url=http://www.sciencemag.org/cgi/content/full/281/5375/363 |pmid=9705713| pages=363| doi=10.1126/science.281.5375.363}} </ref> <ref>{{cite journal|author=Ronaghi et al.|title=Real-time DNA sequencing using detection of pyrophosphate release| journal=Analytical Biochemistry|date=1996 |volume=242 |page=84-89 |pmid=8923969|pages=84|doi=10.1006/abio.1996.0432}}</ref><ref>{{cite journal|author=Nyrén, P. |title=The History of Pyrosequencing|journal=Methods Mol Biology |date=2007|volume=373| pmid=17185753|pages=1–14}}</ref> ==Procedure== "Sequencing by synthesis" involves taking a single strand of the DNA to be sequenced and then synthesizing it's complementary strand enzymatically. The Pyrosequencing method is based on detecting the activity of [[DNA polymerase]] (a DNA synthesizing enzyme) with another [[chemiluminescent]] [[enzyme]]. Essentially, the method allows sequencing of a single strand of [[DNA]] by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step. The template DNA is immobilized, and solutions of A, C, G, and T [[nucleotides]] are added and removed after the reaction, sequentially. Light is produced only when the nucleotide solution complements the first unpaired base of the template. The sequence of solutions which produce chemiluminescent signals allows the determination of the sequence of the template. [[ssDNA]] template is hybridized to a sequencing [[primer]] and incubated with the enzymes [[DNA polymerase]], [[ATP sulfurylase]], [[luciferase]] and [[apyrase]], and with the substrates [[adenosine 5´ phosphosulfate]] (APS) and [[luciferin]]. # The addition of one of the four [[deoxynucleotide triphosphate]]s ([[dNTP]]s)(in the case of ATP we add ATPαS which is not a substrate for a luciferase) initiates the second step. DNA polymerase incorporates the correct, complementary dNTPs onto the template. This incorporation releases [[pyrophosphate]] (PPi) stoichiometrically. # ATP sulfurylase quantitatively converts PPi to [[Adenosine triphosphate|ATP]] in the presence of adenosine 5´ phosphosulfate. This ATP acts as fuel to the luciferase-mediated conversion of luciferin to oxyluciferin that generates visible light in amounts that are proportional to the amount of ATP. The light produced in the luciferase-catalyzed reaction is detected by a camera and analyzed in a program. # Unincorporated nucleotides and ATP are degraded by the apyrase, and the reaction can restart with another nucleotide. Currently, a limitation of the method is that the lengths of individual reads of DNA sequence are in the neighborhood of 300-500 nucleotides, shorter than the 800-1000 obtainable with [[DNA sequencing#Chain-termination methods|chain termination]] methods (e.g. Sanger sequencing). This can make the process of [[genome assembly]] more difficult, particularly for sequence containing a large amount of [[repetitive DNA]]. As of 2007, pyrosequencing is most commonly used for resequencing or sequencing of genomes for which the sequence of a close relative is already available. The templates for pyrosequencing can be made both by solid phase template preparation (Streptavidin coated magnetic beads) and enzymatic template preparation (Apyrase+Exonuclease). ==Licensing== Pyrosequencing AB was started to commercialize the machine and reagent for sequencing of short stretches of DNA. Pyrosequencing AB was renamed to Biotage in 2003. Pyrosequencing technology was further licensed to [[454 Life Sciences]]. 454 developed an array-based Pyrosequencing which has emerged as a rapid platform for large-scale DNA sequencing. Most notable are the applications for genome sequencing and metagenomics. ''GS FLX'', the latest pyrosequencing platform by 454 Life Sciences (owned by Roche), can generate 100 million nucleotide data in a 7 hour run with a single machine. It is anticipated that the throughput would increase by 5-10 fold with the next release. Each run would cost about 5,000-6,000 USD, pushing de novo sequencing of mammalian genomes into the million dollar range. ==Use in research== In September 2007, 454 pyrosequencing was used in a study implicating [[Israel acute paralysis virus]] in honeybee [[Colony Collapse Disorder]] <ref>[http://www.washingtonpost.com/wp-dyn/content/article/2007/09/06/AR2007090601471.html?tid=informbox AP, Virus May Be Cause of Honeybees' Deaths. The Washington Post, September 6th, 2007.]</ref>. ==External links and references== * http://www.454.com *{{cite journal| author=Ronaghi M. |url=http://www.genome.org/cgi/content/full/11/1/3 |title=Pyrosequencing sheds light on DNA sequencing|journal=[[Genome Research]]|date=2001 Jan|volume=11 |pmid=11156611|pages=3–11 |doi=10.1101/gr.11.1.3}} * {{cite journal|author=Ronaghi et al.|title=Improved performance of Pyrosequencing using single-stranded DNA-binding protein| journal= Analytical Biochemistry |date=2000 |pmid=11067751 |volume=286 |page=282-288|pages=282|doi=10.1006/abio.2000.4808}} * {{cite journal| author=Elahi et al.| title=Pyrosequencing: a tool for DNA sequencing analysis |journal=Methods Mol Biol |date=2004 |volume=255 |pmid=15020827 |pages=211–219}} * {{cite journal|author=Gharizadeh et al.|title=Long-read pyrosequencing using pure 2'-deoxyadenosine-5'-O'-(1-thiotriphosphate) Sp-isomer|journal=Anal Biochem|date=2002 |volume=301| page=82-90 |pmid=11811970 |pages=82|doi=10.1006/abio.2001.5494}} * {{cite journal|author=Fakhrai-Rad et al.|title=Pyrosequencing: an accurate detection platform for single nucleotide polymorphisms|journal=Hum Mutat. |date=2002| pmid=11968080|volume=19|pages=479|doi=10.1002/humu.10078}} ==References== {{reflist}} [[Category:Molecular biology]] [[Category:Biotechnology]] [[Category:DNA sequencing]] [[sv:Pyrosekvensering]]