Amplicon

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Amplicon

An amplicon is a piece of DNA or RNA that is the source and/or product of natural or artificial amplification or replication events. It can be formed using various methods including polymerase chain reactions (PCR), ligase chain reactions (LCR), or natural gene duplication. In this context, "amplification" refers to the production of one or more copies of a genetic fragment or target sequence, specifically the amplicon. As the product of an amplification reaction, amplicon is used interchangeably with common laboratory terms, such as PCR product.

Artificial amplification is used in research,[1] forensics,[2] and medicine[1] for purposes that include detection and quantification of infectious agents,[3] identification of human remains,[4] and extracting genotypes from human hair.[2]

Natural gene duplication is implicated in several forms of human cancer including primary mediastinal B cell lymphoma and Hodgkin's lymphoma.[5] Amplicons in this context can refer both to sections of chromosomal DNA that have been excised, amplified, and reinserted elsewhere in the genome, and to extrachromasomal DNA known as double minutes, each of which can be composed of one or more genes. Amplification of the genes encoded by these amplicons generally increases transcription of those genes and ultimately the volume of associated proteins.[6]

Amplicon Structure[edit]

Amplicons in general are direct repeat (head-to-tail) or inverted repeat (head-to-head or tail-to-tail) genetic sequences, and can be either linear or circular in structure.[7] Circular amplicons consist of imperfect inverted duplications annealed into a circle[8] and are thought to arise from precursor linear amplicons.[9]

During artificial amplification, amplicon length is dictated by the experimental goals.[10]

Technology[edit]

Analysis of amplicons has been made possible by the development of amplification methods such as PCR, and increasingly by cheaper and more high-throughput technologies for DNA sequencing or next-generation sequencing, such as Ion semiconductor sequencing, popularly referred to as the brand of the developer, Ion Torrent.[11]

DNA sequencing technologies such as next-generation sequencing have made it possible to study amplicons in genome biology and genetics, including cancer genetics research,[12] phylogenetic research, and human genetics.[13]

Irrespective of the approach used to amplify the amplicons, some technique must be used to quantitate the amplified product.[14] Generally, these techniques incorporate a capture step and a detection step, although how these steps are incorporated depends on the individual assay.

Examples include the Amplicor HIV-1 Monitor Assay (RT-PCR), which has the capacity to recognize HIV in plasma; the HIV-1 QT (NASBA), which is used to measure plasma viral load by amplifying a segment of the HIV RNA; and Transcription Mediated Amplification, which employs a hybridization protection assay to distinguish Chlamydia trachomatis infections.[14] Various detection and capture steps are involved in each approach to assess the amplification product, or amplicon.

Applications[edit]

PCR can be used to determine sex from a human DNA sample.[15] The loci of Alu element insertion is selected, amplified and evaluated in terms of size of the fragment. The sex assay utilizes AluSTXa for the X chromosome, AluSTYa for the Y chromosome, or both AluSTXa and AluSTYa, to reduce the possibility of error to a negligible quantity. The inserted chromosome yields a large fragment when the homologous region is amplified. The males are distinguished as having two DNA amplicons present, while females have only a single amplicon. The kit adapted for carrying out the method includes a pair of primers to amplify the locus and optionally polymerase chain reaction reagents.[16]

LCR can be used to diagnose tuberculosis.[17] The sequence containing protein antigen B is targeted by four oligonucleotide primers—two for the sense strand, and two for the antisense strand. The primers bind adjacent to one another, forming a segment of double stranded DNA that once separated, can serve as a target for future rounds of replication. In this instance, the product can be detected via the microparticle enzyme immunoassay (MEIA).

See also[edit]

References[edit]

  1. ^ a b Meyers, Robert A., ed. (1995). Molecular Biology and Biotechnology: A Comprehensive Desk Reference. New York, NY: VCH Publishers. pp. 53, 585. ISBN 1-56081-925-1. 
  2. ^ a b Walsh, PS; Metzger, DA; Higuchi, R (1991). "Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material". BioTechniques 10 (4): 506–13. PMID 1867860. 
  3. ^ Consumer Affairs Branch (2010-08-17). "Roche Amplicor HIV-1 Monitor Test". FDA. Retrieved 2012-10-16. 
  4. ^ Gill, Peter; Ivanov, Pavel L.; Kimpton, Colin; Piercy, Romelle; Benson, Nicola; Tully, Gillian; Evett, Ian; Hagelberg, Erika; Sullivan, Kevin (1994). "Identification of the remains of the Romanov family by DNA analysis". Nature Genetics 6 (2): 130–5. doi:10.1038/ng0294-130. PMID 8162066. 
  5. ^ Rui, Lixin; Emre, N.C. Tolga; Kruhlak, Michael J.; Chung, Hye-Jung; Steidl, Christian; Slack, Graham; Wright, George W.; Lenz, Georg et al. (2010). "Cooperative Epigenetic Modulation by Cancer Amplicon Genes". Cancer Cell 18 (6): 590–605. doi:10.1016/j.ccr.2010.11.013. PMC 3049192. PMID 21156283. 
  6. ^ Bignell, G. R.; Santarius, T.; Pole, J. C.M.; Butler, A. P.; Perry, J.; Pleasance, E.; Greenman, C.; Menzies, A. et al. (2007). "Architectures of somatic genomic rearrangement in human cancer amplicons at sequence-level resolution". Genome Research 17 (9): 1296–303. doi:10.1101/gr.6522707. PMC 1950898. PMID 17675364. 
  7. ^ Cohn, Waldo E.; Moldave, Kivie, eds. (1996). Progress in Nucleic Acid Research and Molecular Biology. Academic Press. pp. 280–287. ISBN 978-0-12-540054-1. 
  8. ^ Grodin, K; Roy, G; Ouellette, M (1996). "Formation of extrachromosomal circular amplicons with direct or inverted duplications in drug-resistant Leishmania tarentolae.". Mol.Cell.Biol. 16 (7): 3587–3595. PMC 231354. PMID 8668175. 
  9. ^ Grodin, K; Küding; Roy, G; Ouellette, M (1998). "Linear amplicons as precursors of amplified circles in methotrexate-resistant Leishmania tarentolae.". Nucleic Acids Res. 26 (14): 3372–3378. doi:10.1093/nar/26.14.3372. PMC 147699. PMID 9649621. 
  10. ^ PCR Primer Design Guidelines. Premier Biosoft: Accelerating Research in Life Sciences. Retrieved from: http://www.premierbiosoft.com/tech_notes/PCR_Primer_Design.html
  11. ^ Ion Torrent Official Webpage
  12. ^ International Cancer Genome Consortium Official Website
  13. ^ National Human Genome Research Institute
  14. ^ a b Stanley, J. (2002). Essentials of Immunology & Serology by Jacqueline Stanley. Albany, NY: Delmar.
  15. ^ Mannucci, Armando; Sullivan, Kevin M.; Ivanov, Pavel L.; Gill, Peter (1994). "Forensic application of a rapid and quantitative DNA sex test by amplification of the X-Y homologous gene amelogenin". International Journal of Legal Medicine 106 (4): 190–3. doi:10.1007/BF01371335. PMID 8038111. 
  16. ^ Hedges, Dale J; Walker, Jerilyn A; Callinan, Pauline A; Shewale, Jaiprakash G; Sinha, Sudhir K; Batzer, Mark A (2003). "Mobile element-based assay for human gender determination". Analytical Biochemistry 312 (1): 77–9. doi:10.1016/S0003-2697(02)00430-X. PMID 12479838. 
  17. ^ O'Connor, T M (1 November 2000). "The ligase chain reaction as a primary screening tool for the detection of culture positive tuberculosis". Thorax 55 (11): 955–957. doi:10.1136/thorax.55.11.955. PMC 1745641. PMID 11050266. 

Further reading[edit]

External links[edit]

"What is an amplicon? See examples of the different applications.". Youtube video.