OLIGO Primer Analysis Software was the first publicly-available software for DNA primer design.[1] The first papers describing this software were published in 1989 and 1990,[2][3] and have been cited together over 500 times in scientific journals and about 500 times in patents (according to Scopus). The program is a comprehensive real time PCR primer and probe search and analysis tool, and also does other tasks such as siRNA and molecular beacon searches, open reading frame and restriction enzyme analysis etc. It has been created and maintained by Wojciech Rychlik and Piotr Rychlik,[1][4][5] and distributed through the Internet. The OLIGO was cited already in 1991 in a review in Critical Reviews in Biochemistry and Molecular Biology as a recommended software to calculate primer's characteristics,[6] and this opinion, held throughout the consecutive upgrades (with OLIGO 7 being the latest one in 2009), is widespread until now.[7][8]
Oligo Primer Analysis Software has been used in various scientific studies (as cited by examples of recent publications), among them for: real time PCR,[9][10][11] apoptosis studies,[12] antigen typing,[13][14] species identification,[15][16] studies on species evolution,[17] measuring mRNA expression levels,[18][19][20][21] oligonucleotide-based array hybridization studies,[22] degenerate primer studies,[23] microsatellite analysis,[24][25] DNA microarray detection,[26] inverse PCR,[27] genome walking,[8] nucleotide polymorphisms studies,[28][29] detection of microorganisms or viruses,[30][31] genotyping,[32] vector (gene) construction,[33][34] genome sequencing,[35] detection of mutants,[36] genetic disease studies,[37][38] siRNA and gene silencing,[39][40] FISH analysis (single cell expression study),[41] and scorpion probes.[42]
Oligo is a registered trademark of Molecular Biology Insights, Inc. (U.S.P.T.O. #3034446).
References
- ^ a b Wojciech Rychlik (2007). "OLIGO 7 Primer Analysis Software". Methods Mol. Biol. 402: 35–60. PMID 17951789.
- ^ Wojciech Rychlik and Robert E. Rhoads (1989) A Computer Program for Choosing Optimal Oligonucleotides for Filter Hybridization, Sequencing and in vitro Amplification of DNA; Nucleic Acids Research 17, 8543-8551.
- ^ Wojciech Rychlik, William J. Spencer, and Robert E. Rhoads (1990) Optimization of the Annealing Temperature for DNA Amplification in Vitro; Nucleic Acids Res. 18, 6409-6412.
- ^ www.biocompare.com/review/682/Oligo-Primer-Analysis-Software-From-Molecular-Biology-Insights.html
- ^ Wojciech Rychlik (1993) Selection of Primers for Polymerase Chain Reaction, in Methods in Molecular Biology Vol. 15: PCR Protocols: Current Methods and Applications; Ed. B.A. White; Humana Press Inc., Totowa, NJ. pp. 31-40.
- ^ Bej AK, Mahbubani MH, and Atlas RM (1991). "Amplification of Nucleic Acids by Polymerase Chain Reaction (PCR) and Other Methods and Their Applications". Crit. Rev. Biochem. Mol. Biol. 26 (3-4): 301–34. PMID 1718663.
- ^ Kamel A. Abd-Elsalam (2003) Bioinformatic Tools and Guideline for PCR Primer Design; African Journal of Biotechnology 2, 91-95.
- ^ a b Tokuji Tsuchiya, Nanako Kameya, and Ikuo Nakamura (2009). "Straight Walk: A modified method of ligation-mediated genome walking for plant species with large genomes". Analytical Biochemistry 388: 158–160.
- ^ Dmitry A. Khodakov, Natalia V. Zakharova, Dmitry A. Gryadunov, Felix P. Filatov, Alexander S. Zasedatelev, and Vladimir M. Mikhailovich (2008) An Oligonucleotide Microarray for Multiplex Real-Time PCR Identification of HIV-1, HBV, and HCV; BioTechniques 44, 241-248.
- ^ Andrea Francesconi, Miki Kasai, Susan M. Harrington, Mara G. Beveridge, Ruta Petraitiene, Vidmantas Petraitis, Robert L. Schaufele, and Thomas J. Walsh (2008) Automated and Manual Methods of DNA Extraction for Aspergillus Fumigatus and Rhizopus Oryzae Analyzed by Quantitative Real-Time PCR; Journal of Clinical Microbiology 46, 1978-1984.
- ^ Arneth Borros (2009) Following Ionic Activity by Electrochemistry During the Polymerase Chain Reaction; Analytical Biochemistry 385, 26-33.
- ^ Arabinda Das, Naren L. Banik, and Swapan K. Ray (2008) Modulatory Effects of Acetazolomide and Dexamethasone on Temozolomide Mediated Apoptosis in Human Glioblastoma T98G and U87MG Cells; Cancer Investigation 26, 352 - 358.
- ^ Svetlana Adamovic, Silja S. Amundssen, Benedicte A. Lie, Åsa Hellqvist, Audur H. Gudjonsdottir, Johan Ek, Staffan Nilsson, Jan Wahlström, Henry Ascher, Ludvig M Sollid, and Åsa Naluai (2008) Fine Mapping Study in Scandinavian Families Suggests Association Between Coeliac Disease and Haplotypes in Chromosome Region 5q32; Tissue Antigens 71, 27-34.
- ^ Sarah H. Haddock, Christine Quartararo, Patrick Cooley, and Dat D. Dao (2002) Low-Resolution Typing of HLA-DQA1 Using DNA Microarray, Methods in Molecular Biology 170, 201-210.
- ^ P. Rahimi, B. Sharifnabi, and M. Bahar (2008) Detection of Aflatoxin in Aspergillus Species Isolated from Pistachio in Iran; Journal of Phytopathology 156, 15 - 20.
- ^ Yu-Li Song, Naoki Kato, Cheng-Xu Liu, Yoshiko Matsumiya, Haru Kato, and Kunitomo Watanabe (2006) Rapid Identification of 11 Human Intestinal Lactobacillus Species by Multiplex PCR Assays Using Group- and Species-Specific Primers Derived from the 16S–23S rRNA Intergenic Spacer region and its Flanking 23S rRNA; FEMS Microbiology Letters 187, 167-173.
- ^ Arhat Abzhanov (2009) Darwin’s Finches: Analysis of Beak Morphological Changes During Evolution; Cold Spring Harbor Protocols; doi:10.1101/pdb.emo119.
- ^ Holger G Hass, Oliver Nehls, Juergen Jobst, Andrea Frilling, Ulrich Vogel, and Stephan Kaiser (2008) Identification of Osteopontin as the Most Consistently Over-Expressed Gene in Intrahepatic Cholangiocarcinoma: Detection by Oligonucleotide Microarray and Real-Time PCR Analysis; World J Gastroenterol 28, 2501-2510.
- ^ Arabinda Das, Amogh Belagodu, Russel J. Reiter, Swapan K. Ray, and Naren L. Banik (2008) Cytoprotective Effects of Melatonin on C6 Astroglial Cells Exposed to Glutamate Excitotoxicity and Oxidative Stress; Journal of Pineal Research 45, 117 - 124.
- ^ G.T. Shishkina, T.S. Kalinina, and N.N. Dygalo (2004) Attenuation of α2A-adrenergic Receptor Expression in Neonatal Rat Brain by RNA Interference or Antisense Oligonucleotide Reduced Anxiety in Adulthood; Neuroscience 129, 521-528.
- ^ Canhui Liu, Chitra Chauhan, Charles R. Katholi, and Thomas R. Unnasch (2009) The splice leader addition domain represents an essential conserved motif for heterologous gene expression in B. malayi; Molecular & Biochemical Parasitology 166, 15–21.
- ^ Daryl A. Scott, Merel Klaassens, Ashley M. Holder, Kevin P. Lally, Caraciolo J. Fernandes, Robert-Jan Galjaard, Dick Tibboel, Annelies de Klein, and Brendan Lee (2007) Genome-Wide Oligonucleotide-Based Array Comparative Genome Hybridization Analysis of Non-Isolated Congenital Diaphragmatic Hernia; Human Molecular Genetics. 16, 424-430.
- ^ Omar J. Jabado, Gustavo Palacios, Vishal Kapoor, Jeffrey Hui, Neil Renwick, Zhai Junhui, Thomas Briese, and W. Ian Lipkin (2006) Greene SCPrimer: a Rapid Comprehensive Tool for Designing Degenerate Primers from Multiple Sequence Alignments; Nucleic Acids Research. 34, 6605-6611.
- ^ Tommy L. F. Leung, Tania M. King, Robert Poulin, and Devon B. Keeney (2008) Ten Polymorphic Microsatellite Loci for the Trematode Curtuteria Australis (Echinostomatidae); Molecular Ecology Resources 8, 1046 - 1048.
- ^ Theodora Kopun, Kathrin A. Winkler, and Steven Weiss (2009) Eight new polymorphic microsatellite DNA markers for Sakhalin taimen Parahucho perryi; Conservation Genetics 10, 1089–1091.
- ^ Dmitry A. Khodakov, Natalia V. Zakharova, Dmitry A. Gryadunov, Felix P. Filatov, Alexander S. Zasedatelev, and Vladimir M. Mikhailovich (2008) An Oligonucleotide Microarray for Multiplex Real-Time PCR Identification of HIV-1, HBV, and HCV; BioTechniques 44, 241-248.
- ^ Kazutaka Yamada, Takeshi Terahara, Shinya Kurata, Toyokazu Yokomaku, Satoshi Tsuneda, and Shigeaki Harayama (2008) Retrieval of Entire Genes from Environmental DNA by Inverse PCR with Pre-Amplification of Target Genes Using Primers Containing Locked Nucleic Acids; Environmental Microbiology 10, 978 - 987.
- ^ Hai-Gang Qi, Xiao Liu, and Guo-Fan Zhang (2008) Characterization of 12 Single Nucleotide Polymorphisms (SNPs) in Pacific Abalone, Haliotis Discus Hannai; Molecular Ecology Resources 8, 974-976.
- ^ O. A. Gra, A. S. Glotov, Zh. M. Kozhekbayeva, O. V. Makarova, and T. V. Nasedkina (2008) Genetic Polymorphism of GST, NAT2 , and MTRR and Susceptibility to Childhood Acute Leukemia; Molecular Biology 42, 187-197.
- ^ Laura F. Lalonde and Alvin A. Gajadhar (2008) Highly Sensitive and Specific PCR Assay for Reliable Detection of Cyclospora Cayetanensis Oocysts; Applied and Environmental Microbiology 74, 4354-4358.
- ^ T. Wei, G. Lu, and G. R. G. Clover (2009) A Multiplex RT-PCR for the Detection of Potato Yellow Vein Virus, Tobacco Rattle Virus and Tomato Infectious Chlorosis Virus in Potato with a Plant Internal Amplification Control; Plant Pathology 58, 203-209.
- ^ Kristel Van Laethema, Yoeri Schrootena, Kris Covensa, Nathalie Dekeersmaekera, Paul De Munterc, Eric Van Wijngaerdenc, Marc Van Ransta, and Anne-Mieke Vandamme (2008) A Genotypic Assay for the Amplification and Sequencing of Integrase from Diverse HIV-1 Group M Subtypes; Journal of Virological Methods 153, 176-181.
- ^ Guozheng Conga, Jianhua Zhoua, Shandian Gaoa, Junzheng Dua, Junjun Shaoa, Tong Lina, Huiyun Chang, and Qingge Xie (2008) Construction of Recombinant Retroviral Vector Carrying Lab Gene of Foot-and-Mouth Disease Virus and Its Expression in Bovine Kidney (MDBK) Cells; Chinese Journal of Biotechnology 24, 740-745.
- ^ Faranak Ghazi Sherbaf, Zohreh Hojati, and Majid Motovali-Bashi (2009) Construction of recombinant vectors containing clavulanic acid antibiotic regulatory gene, claR, isolated of Streptomyces clavuligerus strains; Iranian Journal of Biotechnology 7, 112-116.
- ^ Lei Wei, Xiaobing Wu, and Zhigang Jiang (2009) The complete mitochondrial genome structure of snow leopard Panthera uncia; Molecular Biology Reports 36, 871–878.
- ^ David S. Perlin, Sergey Balashov, and Steven Park (2008) Multiplex Detection of Mutations; Methods in Molecular Biology 429, 23-31.
- ^ Michele Salemi, Corrado Romano, Concetta Barone, Francesco Cali, Filippo Caraci, Carmelo Romano, Cataldo Scavuzzo, Francesco Scillato, Maria Grazia Salluzzo, Maria Piccione, Manuela Martines, Giovanni Corsello, Ferdinando Nicoletti, and Paolo Bosco (2009) SPANX-B and SPANX-C (Xq27 region) gene dosage analysis in Down’s syndrome subjects with undescended testes; Journal of Genetics 88, 93-97.
- ^ Carmen Palomino, M. D. Fernández-Romero, J. Rubio, A. Torres, M. T. Moreno, and T. Millán (2009) Integration of new CAPS and dCAPS-RGA markers into a composite chickpea genetic map and their association with disease resistance; Theoretical and Applied Genetics 118, 671–682.
- ^ Baoshan Xu, Chao Wang, Jie Yang, Guanping Mao, Cheng Zhang, Dan Liu, Ping Tai, Bo Zhou, Guoliang Xia, and Meijia Zhang (2008) Silencing of Mouse Hepatic Lanosterol 14-α Demethylase Down-Regulated Plasma Low-Density Lipoprotein Cholesterol Levels by Short-Term Treatment of siRNA; Biol. Pharm. Bull. 31, 1182-1191.
- ^ Anastasia Khvorova, Angela Reynolds, and Sumedha D. Jayasena (2003) Functional siRNA and miRNAs Exhibit Strand Bias; Cell, 115, 209-216.
- ^ Rossanna C. Pezo, Saumil J. Gandhi, L. Andrew Shirley, Richard G. Pestell, Leonard H. Augenlicht, and Robert H. Singer (2008) Single-Cell Transcription Site Activation Predicts Chemotherapy Response in Human Colorectal Tumors; Cancer Research 68, 4977-4982.
- ^ Rachael Carters, Jennifer Ferguson, Rupert Gaut, Paul Ravetto, Nicola Thelwell, and David Whitcombe (2008) Design and Use of Scorpions Fluorescent Signaling Molecules; Methods in Molecular Biology 429, 99-115.
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