Pyrosequencing

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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. It differs from Sanger sequencing, in that it relies on the detection of pyrophosphate release on nucleotide incorporation, rather than chain termination with dideoxynucleotides.^[1] The technique was developed by Pål Nyrén and Mostafa Ronaghi at the Royal Institute of Technology in Stockholm in 1996.^[2][3][4] The desired DNA sequence is able to be determined by light emitted upon incorporation of the next complementary nucleotide by the fact that only one out of four of the possible A/T/C/G nucleotides are added and available at a time so that only one letter can be incorporated on the single stranded template (which is the sequence to be determined). The intensity of the light determines if there are more than one of these "letters" in a row. The previous nucleotide letter (one out of four possible dNTP) is degraded before the next nucleotide letter is added for synthesis: allowing for the possible revealing of the next nucleotide(s) via the resulting intensity of light (if the nucleotide added was the next complementary letter in the sequence). This process is repeated with each of the four letters until the DNA sequence of the single stranded template is determined.

Procedure

"Sequencing by synthesis" involves taking a single strand of the DNA to be sequenced and then synthesizing its 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 immobile, and solutions of A, C, G, and T nucleotides are sequentially added and removed from the reaction. 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.

1. The addition of one of the four deoxynucleoside triphosphates (dNTPs) (dATPαS, which is not a substrate for a luciferase, is added instead of dATP) initiates the second step. DNA polymerase incorporates the correct, complementary dNTPs onto the template. This incorporation releases pyrophosphate (PPi) stoichiometrically.
2. ATP sulfurylase quantitatively converts PPi to 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.
3. 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 chain termination methods (e.g. Sanger sequencing). This can make the process of genome assembly more difficult, particularly for sequences 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).

Commercialization

The company Pyrosequencing AB in Uppsala, Sweden commercialized machinery and reagents for sequencing short stretches of DNA using the pyrosequencing technique. Pyrosequencing AB was renamed to Biotage in 2003 which was acquired by Qiagen in 2008.^[5] Pyrosequencing technology was further licensed to 454 Life Sciences. 454 developed an array-based pyrosequencing technology which has emerged as a 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 (now owned by Roche Diagnostics), can generate 400 Mb in a 10 hour run with a single machine. Each run would cost about 5,000-7,000 USD.

References

Further reading

This article includes a list of references, related reading or external links, but its sources remain unclear because it lacks inline citations. Please improve this article by introducing more precise citations. (June 2010)

• Ronaghi M. (January 2001). "Pyrosequencing sheds light on DNA sequencing" (PDF). Genome Research 11 (1): 3–11. doi:10.1101/gr.11.1.3. PMID 11156611. http://genome.cshlp.org/cgi/reprint/11/1/3.pdf. 

• Ronaghi et al. (2000). "Improved performance of Pyrosequencing using single-stranded DNA-binding protein". Analytical Biochemistry 286 (2): 282–8. doi:10.1006/abio.2000.4808. PMID 11067751. 

• Elahi et al.; Ronaghi, M (2004). "Pyrosequencing: a tool for DNA sequencing analysis". Methods Mol Biol 255: 211–219. doi:10.1385/1-59259-752-1:211. PMID 15020827. 

• Gharizadeh et al.; Nordström, T; Ahmadian, A; Ronaghi, M; Nyrén, P (2002). "Long-read pyrosequencing using pure 2'-deoxyadenosine-5'-O'-(1-thiotriphosphate) Sp-isomer". Anal Biochem 301 (1): 82–90. doi:10.1006/abio.2001.5494. PMID 11811970. 

• Fakhrai-Rad et al.; Pourmand, N; Ronaghi, M (2002). "Pyrosequencing: an accurate detection platform for single nucleotide polymorphisms". Hum Mutat. 19 (5): 479–85. doi:10.1002/humu.10078. PMID 11968080. 

• Langaee T, Ronaghi M (June 2005). "Genetic variation analyses by Pyrosequencing". Mutat. Res. 573 (1-2): 96–102. doi:10.1016/j.mrfmmm.2004.07.023. PMID 15829240. 

• Metzker M. (2005). "Emerging Technologies in DNA Sequencing". Genome Research 15 (12): 1767–76. doi:10.1101/gr.3770505. PMID 16339375.