Specific and sensitive quantitative RT-PCR of miRNAs with DNA primers

BMC Biotechnology

Volumn 11, Issue , 2011, Pages

  Balcells, Ingrid ^a   Cirera, Susanna ^b   Busk, Peter K ^c  

^a UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

^b UNIVERSITY OF COPENHAGEN   (Denmark)

^c AALBORG UNIVERSITY   (Denmark)

Author keywords

[No Author keywords available]

Indexed keywords

ANNEALING TEMPERATURES; BIOLOGICAL PROCESS; BIOLOGICAL SAMPLES; DNA TAIL; EXPRESSION LEVELS; LOCKED NUCLEIC ACID; MICRORNAS; ORDERS OF MAGNITUDE; PCR METHOD; POST-TRANSCRIPTIONAL; QUANTITATIVE RT-PCR; REAL-TIME PCR; REVERSE TRANSCRIPTION; SINGLE NUCLEOTIDES;

DNA; GENES; TRANSCRIPTION;

POLYMERASE CHAIN REACTION;

MICRORNA; NUCLEIC ACID; PRIMER DNA;

ACCURACY; ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; GENE AMPLIFICATION; GENE EXPRESSION; NONHUMAN; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; SINGLE NUCLEOTIDE POLYMORPHISM; CHEMISTRY; GENETICS; METHODOLOGY; STANDARD; TEMPERATURE;

DNA PRIMERS; MICRORNAS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; TEMPERATURE;

EID: 79959425811     PISSN: None     EISSN: 14726750     Source Type: Journal    
DOI: 10.1186/1472-6750-11-70     Document Type: Article

References (29)

1. Schetter AJ, Heegaard NHH, Harris CC. Inflammation and cancer: interweaving microRNA, free radical, cytokine and p53 pathways. Carcinogenesis 2010, 31:37-49. 10.1093/carcin/bgp272, 2802675, 19955394.
2. Fabbri M. miRNAs as molecular biomarkers of cancer. Expert Rev Mol Diagn 2010, 10:435-444. 10.1586/erm.10.27, 20465498.
3. Ferracin M, Veronese A, Negrini M. Micromarkers: miRNAs in cancer diagnosis and prognosis. Expert Rev Mol Diagn 2010, 10:297-308. 10.1586/erm.10.11, 20370587.
4. Mitchell PS, Parkin RK, Kroh EM, Fritz BR, Wyman SK, Pogosova-Agadjanyan EL, Peterson A, Noteboom J, O'Briant KC, Allen A, Lin DW, Urban N, Drescher CW, Knudsen BS, Stirewalt DL, Gentleman R, Vessella RL, Nelson PS, Martin DB, Tewari M. Circulating microRNAs as stable blood-based markers for cancer detection. Proc Natl Acad Sci USA 2008, 105:10513-10518. 10.1073/pnas.0804549105, 2492472, 18663219.
5. Heneghan HM, Miller N, Lowery AJ, Sweeney KJ, Newell J, Kerin MJ. Circulating microRNAs as novel minimally invasive biomarkers for breast cancer. Ann Surg 2010, 251:499-505. 10.1097/SLA.0b013e3181cc939f, 20134314.
6. Fichtlscherer S, De Rosa S, Fox H, Schwietz T, Fischer A, Liebetrau C, Weber M, Hamm CW, Röxe T, Müller-Ardogan M, Bonauer A, Zeiher AM, Dimmeler S. Circulating microRNAs in patients with coronary artery disease. Circ Res 2010, 107:677-684. 10.1161/CIRCRESAHA.109.215566, 20595655.
7. Zhang Y, Jia Y, Zheng R, Guo Y, Wang Y, Guo H, Fei M, Sun S. Plasma MicroRNA-122 as a Biomarker for Viral-, Alcohol-, and Chemical-Related Hepatic Diseases. Clin Chem 2010, 56:1830-1838. 10.1373/clinchem.2010.147850, 20930130.
8. Vasilescu C, Rossi S, Shimizu M, Tudor S, Veronese A, Ferracin M, Nicoloso MS, Barbarotto E, Popa M, Stanciulea O, Fernandez MH, Tulbure D, Bueso-Ramos CE, Negrini M, Calin GA. MicroRNA fingerprints identify miR-150 as a plasma prognostic marker in patients with sepsis. PLoS ONE 2009, 4:e7405. 10.1371/journal.pone.0007405, 2756627, 19823581.
9. Liu C, Kao S, Tu H, Tsai M, Chang K, Lin S. Increase of microRNA miR-31 level in plasma could be a potential marker of oral cancer. Oral Dis 2010, 16:360-364. 10.1111/j.1601-0825.2009.01646.x, 20233326.
10. 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.
11. Mestdagh P, Feys T, Bernard N, Guenther S, Chen C, Speleman F, Vandesompele J. High-throughput stem-loop RT-qPCR miRNA expression profiling using minute amounts of input RNA. Nucleic Acids Res 2008, 36:e143. 10.1093/nar/gkn725, 2588502, 18940866.
12. Kumar P, Johnston BH, Kazakov SA. miR-ID: A novel, circularization-based platform for detection of microRNAs. RNA 2011, 17:365-380. 10.1261/rna.2490111, 21169480.
13. Wang H, Ach RA, Curry B. Direct and sensitive miRNA profiling from low-input total RNA. RNA 2007, 13:151-159. 1705746, 17105992.
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. Busk PK. Method for Quantification of Small RNA Species. 2010, WO/2010/085966.
16. Veedu RN, Vester B, Wengel J. Enzymatic incorporation of LNA nucleotides into DNA strands. Chembiochem 2007, 8:490-492. 10.1002/cbic.200600501, 17315250.
17. Bustin SA, Benes V, Garson JA, Hellemans J, Huggett J, Kubista M, Mueller R, Nolan T, Pfaffl MW, Shipley GL, Vandesompele J, Wittwer CT. The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem 2009, 55:611-622. 10.1373/clinchem.2008.112797, 19246619.
18. Pfaffl MW, Horgan GW, Dempfle L. Relative expression software tool (REST) for group-wise comparison and statistical analysis of relative expression results in real-time PCR. Nucleic Acids Res 2002, 30:e36. 10.1093/nar/30.9.e36, 113859, 11972351.
19. Tichopad A, Dilger M, Schwarz G, Pfaffl MW. Standardized determination of real-time PCR efficiency from a single reaction set-up. Nucleic Acids Res 2003, 31:e122. 10.1093/nar/gng122, 219490, 14530455.
20. Ruijter JM, Ramakers C, Hoogaars WMH, Karlen Y, Bakker O, van den Hoff MJB, Moorman AFM. Amplification efficiency: linking baseline and bias in the analysis of quantitative PCR data. Nucleic Acids Res 2009, 37:e45. 10.1093/nar/gkp045, 2665230, 19237396.
21. Rutledge RG, Stewart D. A kinetic-based sigmoidal model for the polymerase chain reaction and its application to high-capacity absolute quantitative real-time PCR. BMC Biotechnol 2008, 8:47. 10.1186/1472-6750-8-47, 2397388, 18466619.
22. Bustin SA. A-Z of Quantitative PCR (IUL Biotechnology, No. 5) 2004, International University Line.
23. Raymond CK, Roberts BS, Garrett-Engele P, Lim LP, Johnson JM. Simple, quantitative primer-extension PCR assay for direct monitoring of microRNAs and short-interfering RNAs. RNA 2005, 11:1737-1744. 10.1261/rna.2148705, 1370860, 16244135.
24. Nielsen KE, Singh SK, Wengel J, Jacobsen JP. Solution structure of an LNA hybridized to DNA: NMR study of the d(CT(L)GCT(L)T(L)CT(L)GC):d(GCAGAAGCAG) duplex containing four locked nucleotides. Bioconjug Chem 2000, 11:228-238. 10.1021/bc990121s, 10725100.
25. Chen Y, Gelfond JAL, McManus LM, Shireman PK. Reproducibility of quantitative RT-PCR array in miRNA expression profiling and comparison with microarray analysis. BMC Genomics 2009, 10:407. 10.1186/1471-2164-10-407, 2753550, 19715577.
26. Arora A, Kaur H, Wengel J, Maiti S. Effect of locked nucleic acid (LNA) modification on hybridization kinetics of DNA duplex. Nucleic Acids Symp Ser 2008, 52:417-418.
27. Sambrook J, Russell DW. Molecular Cloning: A Laboratory Manual 2001, Cold Spring Harbor Laboratory Press.
28. Latorra D, Arar K, Hurley JM. Design considerations and effects of LNA in PCR primers. Mol Cell Probes 2003, 17:253-259. 10.1016/S0890-8508(03)00062-8, 14580400.
29. 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.