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Microsatellite (SSR) amplification by PCR usually led to polymorphic bands: Evidence which shows replication slippage occurs in extend or nascent DNA strands | ||
| Molecular Biology Research Communications | ||
| مقاله 5، دوره 5، شماره 3، آذر 2016، صفحه 167-174 اصل مقاله (1.37 M) | ||
| نوع مقاله: Original article | ||
| شناسه دیجیتال (DOI): 10.22099/mbrc.2016.3789 | ||
| نویسندگان | ||
| Abasalt Hossienzadeh-Colagar* ؛ Mohammad Javad Haghighatnia؛ Zahra Amiri؛ Maryam Mohadjerani؛ Majid Tafrihi | ||
| Department of Molecular and Cell Biology, Faculty of Basic Sciences, University of Mazandaran, Babolsar, Mazandaran, Iran | ||
| چکیده | ||
| Microsatellites or simple sequence repeats (SSRs) are very effective molecular markers in population genetics, genome mapping, taxonomic study and other large-scale studies. Variation in number of tandem repeats within microsatellite refers to simple sequence length polymorphism (SSLP); but there are a few studies that are showed SSRs replication slippage may be occurred during in vitro amplification which are produced ‘stutter products’ differing in length from the main products. The purpose of this study is introducing a reliable method to realize SSRs replication slippage. At first, three unique primers designed to amplify SSRs loci in the great gerbil (Rhombomys opimus) by PCR. Crush and soak method used to isolate interesting DNA bands from polyacrylamide gel. PCR products analyzed using by sequencing methods. Our study has been shown that Taq DNA polymerase slipped during microsatellite in vitro amplification which led to insertion or deletion of repeats in sense or antisense DNA strands. It is produced amplified fragments with various lengths in gel electrophoresis showed as ‘stutter bands’. Thus, in population studies by SSRs markers recommend that replication slippage effects and stutter bands have been considered. | ||
| کلیدواژهها | ||
| Microsatellites؛ Taq polymerase slippage؛ Replication slippage | ||
| مراجع | ||
|
1. Schlötterer C. Evolutionary dynamics of microsatellite DNA. Chromosoma 2000;109: 365-371.
2. Ellegren H. Microsatellites: Simple sequences with complex evolution. Nat Rev Genet 2004;5:435-445.
3. Tóth G, Gáspári Z, Jurka J. Microsatellites in different eukaryotic genomes: survey and analysis. Genome res 2000;10:967-981.
4. Stolle E, Kidner JH, Moritz RF. Patterns of evolutionary conservation of microsatellites (SSRs) suggest a faster rate of genome evolution in Hymenoptera than in Diptera. Genome Biol Evol 2013;5:151-162.
5. Saavedra J, Silva TA, Mora F, Scapim CA. Bayesian analysis of the genetic structure of a Brazilian popcorn germplasm using data from simple sequence repeats (SSR). Chil J Agric Res 2013;73:99-107.
6. Olango TM, Tesfaye B, Pagnotta MA, Pè ME, Catellani M. Development of SSR markers and genetic diversity analysis in enset (Ensete ventricosum (Welw.) Cheesman), an orphan food security crop from Southern Ethiopia. BMC Genet 2015; 16:98-114.
7. Du X, Chen Z, Li W, Tan Y, Lu J, Zhu X et al. Development of novel microsatellite DNA markers by cross-amplification and analysis of genetic variation in gerbils. J Hered 2010;101:710-716.
8. Park YJ, Lee JK, Kim NS. Simple sequence repeat polymorphisms (SSRPs) for evaluation of molecular diversity and germplasm classification of minor crops. Molecules 2009;14:4546-4569.
9. Da Maia LC, Palmieri DA, De Souza VQ, Kopp MM, de Carvalho FI, Costa de Oliveira A. SSR locator: Tool for simple sequence repeat discovery integrated with primer design and PCR simulation. Int J Plant Genomics 2008;30:1071-1088.
10. De Boer M, Tzur S, van Leeuwen K, Dencher PC, Skorecki K, Wolach B, Gavrieli R, Nasidze I, Stoneking M, Tanck MW, Roos D. A founder effect for p47 phox Trp193Ter chronic granulomatous disease in Kavkazi Jews. Blood Cells Mol Dis 2015;55:320-327.
11. Fazekas AJ, Steeves R, Newmaster SG. Improving sequencing quality from PCR products containing long mononucleotide repeats. Biotechniques 2010;48 :277-285.
12. Castillo-Lizardo M, Henneke G, Viguera E. Replication slippage of the thermophilic DNA polymerases B and D from the Euryarchaeota Pyrococcus abyssi. Front Microbiol 2014;5:1-10.
13. Ananda G, Walsh E, Jacob KD, Krasilnikova M, Eckert KA, Chiaromonte F et al. Distinct mutational behaviors differentiate short tandem repeats from microsatellites in the human genome. Genome Biol Evol 2013;5:606-620.
14. Gemayel R, Vinces MD, Legendre M, Verstrepen KJ. Variable tandem repeats accelerate evolution of coding and regulatory sequences. Annu Rev Genet 2010; 44:445-477.
15. Brookes C, Bright JA, Harbison S, Buckleton J. Characterising stutter in forensic STR multiplexes. Forensic Sci Int Genet 2012;6:58-63.
16. Harr B, Zangerl B, Schlötterer C. Removal of microsatellite interruptions by DNA replication slippage: phylogenetic evidence from Drosophila. Mol Biol Evol 2000; 17:1001-1009.
17. Gaaib JN, Nassief AF, Al-Assi A. Simple salting-out method for genomic DNA extraction from whole blood. Tikrit J Pure Sci 2011;16:1813-1662.
18. Green MR, Sambrook J, Sambrook J. Molecular cloning: a laboratory manual 4 edition Cold Spring Harbor Laboratory Press. New York 2012.
19. Jennings TN, Knaus BJ, Mullins TD, Haig SM, Cronn RC. Multiplexed microsatellite recovery using massively parallel sequencing. Mol Ecol Resour 2011;11:1060-1067.
20. Majumder D, Rajesh T, Kipgen TL. Molecular approaches for detection of plant pathogens. Front Recent Develop Plant Sci 2012;1:116-136.
21. Shinde D, Lai Y, Sun F, Arnheim N. Taq DNA polymerase slippage mutation rates measured by PCR and quasi-likelihood analysis:(CA/GT) n and (A/T) n microsatellites. Nucleic Acids Res 2003;31:974-980.
22. Ellegren H. Microsatellite mutations in the germ line: implications for evolutionary inference. Trends Genet 2000;16:551-558.
23. Kunkel TA, Bebenek K. DNA replication fidelity. Annu Rev Biochem 2000;69:497-529. | ||
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