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.
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.[1] [2][3]

Contents

[edit] Procedure

The method is based on detecting the activity of DNA polymerase with a 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 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.

  1. The addition of one of the four deoxynucleotide triphosphates (dNTPs)(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.
  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 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).

[edit] 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.

[edit] Use in research

In September 2007, 454 pyrosequencing was used in a study implicating Israel acute paralysis virus in honeybee Colony Collapse Disorder [4].

[edit] External links and references

  • Elahi et al. (2004). "Pyrosequencing: a tool for DNA sequencing analysis". Methods Mol Biol 255: 211-219. PMID 15020827. 
  • Fakhrai-Rad et al. (2002). "Pyrosequencing: an accurate detection platform for single nucleotide polymorphisms". Hum Mutat. 19: 479. doi:10.1002/humu.10078. PMID 11968080. 

[edit] References

  1. ^ Ronaghi et al. (1998-07-17). "A sequencing method based on real-time pyrophosphate". Science 281: 363. doi:10.1126/science.281.5375.363. PMID 9705713. 
  2. ^ Ronaghi et al. (1996). "Real-time DNA sequencing using detection of pyrophosphate release". Analytical Biochemistry 242: 84. doi:10.1006/abio.1996.0432. PMID 8923969. 
  3. ^ Nyrén, P. (2007). "The History of Pyrosequencing". Methods Mol Biology 373: 1-14. PMID 17185753. 
  4. ^ AP, Virus May Be Cause of Honeybees' Deaths. The Washington Post, September 6th, 2007.
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