A tool for design of primers for microRNA-specific quantitative RT-qPCR

BMC Bioinformatics

Volumn 15, Issue 1, 2014, Pages

  Busk, Peter K ^a  

^a AALBORG UNIVERSITY   (Denmark)

Author keywords

MicroRNA; Primer design; Quantitative PCR; Software

Indexed keywords

AUTOMATIC DESIGN; COMMERCIAL ASSAYS; MICRORNAS; PRIMER DESIGN; QUANTITATIVE PCR; SECONDARY STRUCTURES; STAND-ALONE SOFTWARE; WINDOWS PLATFORM;

APPLICATION PROGRAMS; COMPUTER SOFTWARE; DESIGN; MAMMALS; POLYMERASE CHAIN REACTION;

RNA;

MAMMALIA;

MICRORNA; PRIMER DNA;

ALGORITHM; ARTICLE; BIOLOGY; CHEMISTRY; COMPUTER PROGRAM; GENETICS; METHODOLOGY; REAL TIME POLYMERASE CHAIN REACTION; RNA PROBE;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DNA PRIMERS; MICRORNAS; REAL-TIME POLYMERASE CHAIN REACTION; RNA PROBES; SOFTWARE;

EID: 84892932112     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-15-29     Document Type: Article

References (24)

1. Farazi TA, Hoell JI, Morozov P, Tuschl T. MicroRNAs in human cancer. Adv Exp Med Biol 2013, 774:1-20. 3704221, 23377965.
2. Sun G. MicroRNAs and their diverse functions in plants. Plant Mol Biol 2012, 80:17-36. 10.1007/s11103-011-9817-6, 21874378.
3. Yates LA, Norbury CJ, Gilbert RJC. The long and short of microRNA. Cell 2013, 153:516-519. 10.1016/j.cell.2013.04.003, 23622238.
4. Kolbert CP, Feddersen RM, Rakhshan F, Grill DE, Simon G, Middha S, Jang JS, Simon V, Schultz DA, Zschunke M, Lingle W, Carr JM, Thompson EA, Oberg AL, Eckloff BW, Wieben ED, Li P, Yang P, Jen J. Multi-platform analysis of microRNA expression measurements in RNA from fresh frozen and FFPE tissues. PLoS ONE 2013, 8:e52517. 10.1371/journal.pone.0052517, 3561362, 23382819.
5. van Rooij E. The Art of MicroRNA Research. Circ Res 2011, 108:219-234. 10.1161/CIRCRESAHA.110.227496, 21252150.
6. De Planell-Saguer M, Rodicio MC. Detection methods for microRNAs in clinic practice. Clin Biochem 2013, 46:869-878. 10.1016/j.clinbiochem.2013.02.017, 23499588.
7. Benes V, Castoldi M. Expression profiling of microRNA using real-time quantitative PCR, how to use it and what is available. Methods 2010, 50:244-249. 10.1016/j.ymeth.2010.01.026, 20109550.
8. Chen C, Ridzon DA, Broomer AJ, Zhou Z, Lee DH, Nguyen JT, Barbisin M, Xu NL, Mahuvakar VR, Andersen MR, Lao KQ, Livak KJ, Guegler KJ. Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res 2005, 33:e179. 10.1093/nar/gni178, 1292995, 16314309.
9. Balcells I, Cirera S, Busk PK. Specific and sensitive quantitative RT-PCR of miRNAs with DNA primers. BMC Biotechnol 2011, 11:70. 10.1186/1472-6750-11-70, 3135530, 21702990.
10. Busk PK. Method For Quantification Of Small RNA Species 2010, WO2010085966 (A2).
11. Cirera S, Busk PK. Quantification of miRNAs by a simple and specific qPCR method. Methods Mol Biol In press.
12. SantaLucia J. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc Natl Acad Sci USA 1998, 95:1460-1465. 10.1073/pnas.95.4.1460, 19045, 9465037.
13. Rozen S, Skaletsky H. Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 2000, 132:365-386.
14. Shi R, Chiang VL. Facile means for quantifying microRNA expression by real-time PCR. Biotechniques 2005, 39:519-525. 10.2144/000112010, 16235564.
15. Innis MA, Gelfand DH. Optimization of PCRs. PCR Protocols: A Guide to Methods and Applications 1990, 3-12. San Diego: Academic Press, Innis MA, Gelfand DH, Sninsky JJ, White TJ.
16. Husted S, Søkilde R, Rask L, Cirera S, Busk PK, Eriksen J, Litman T. MicroRNA expression profiles associated with development of drug resistance in Ehrlich ascites tumor cells. Mol Pharm 2011, 8:2055-2062. 10.1021/mp200255d, 21899346.
17. Podolska A, Anthon C, Bak M, Tommerup N, Skovgaard K, Heegaard PM, Gorodkin J, Cirera S, Fredholm M. Profiling microRNAs in lung tissue from pigs infected with Actinobacillus pleuropneumoniae. BMC Genomics 2012, 13:459. 10.1186/1471-2164-13-459, 3465251, 22953717.
18. Skovgaard K, Cirera S, Vasby D, Podolska A, Breum S, Dürrwald R, Schlegel M, Heegaard PM. Expression of innate immune genes, proteins and microRNAs in lung tissue of pigs infected experimentally with influenza virus (H1N2). Innate Immun. 2013, 19:531-544. 10.1177/1753425912473668, 23405029.
19. Timoneda O, Balcells I, Córdoba S, Castelló A, Sánchez A. Determination of reference microRNAs for relative quantification in porcine tissues. PLoS ONE 2012, 7:e44413. 10.1371/journal.pone.0044413, 3438195, 22970213.
20. Timoneda O, Balcells I, Núñez JI, Egea R, Vera G, Castelló A, Tomàs A, Sánchez A. miRNA expression profile analysis in kidney of different porcine breeds. PLoS ONE 2013, 8:e55402. 10.1371/journal.pone.0055402, 3555835, 23372853.
21. Onodera K. Selection for 3′-end triplets for polymerase chain reaction primers. Methods Mol Biol 2007, 402:61-74. 10.1007/978-1-59745-528-2_3, 17951790.
22. Miura F, Uematsu C, Sakaki Y, Ito T. A novel strategy to design highly specific PCR primers based on the stability and uniqueness of 3′-end subsequences. Bioinformatics 2005, 21:4363-4370. 10.1093/bioinformatics/bti716, 16234322.
23. Mann T, Humbert R, Dorschner M, Stamatoyannopoulos J, Noble WS. A thermodynamic approach to PCR primer design. Nucleic Acids Res 2009, 37:e95. 10.1093/nar/gkp443, 2715258, 19528077.
24. Goldrick M, Busk PK, Lepovitz L. Reduce microRNA RT-qPCR Assay Costs by More Than 10-fold Without Compromising Results 2013, Bioo Scientific, http://www.biooscientific.com/Portals/0/White%20Papers/Reduce%20microRNA%20RTqPCR%20Assay%20Costs%20by%20More%20Than%2010-fold%20Without%20Compromising%20Results.pdf.