Abstract
Methods allowing sensitive and accurate quantitative analysis of defined RNA species are required in a wide variety of gene expression studies. Unlike the traditional hybridization methods, RNase protection or SI nuclease assays, the methods based on reverse transcription (RT) and polymerase chain reaction (PCR) provide an essentially unlimited sensitivity of detection. A drawback of the PCR-based methods is, however, that they do not allow direct quantification of a sequence present in a sample, because the efficiency of the PCR depends on the amount of the template sequence, and the amplification is exponential only at low concentrations of the template (1). Due to this “plateau effect” of the PCR, the amount of the amplification product does not reflect directly the original amount of the template. Moreover, subtle differences in the reaction conditions may cause significant sample-to-sample variation in the final yield of the PCR. The efficiency of amplification is also affected by the sequence of the PCR primers, as well as the size and, to some extent, the sequence of the PCR product. For these reasons a prerequisite for an accurate quantitative PCR analysis is that an internal standard is coamplified in the same reaction with the target sequence. The standard sequence should be as similar to the target sequence as possible to ensure that the target-to-standard ratio remains constant throughout the amplification. An ideal PCR standard differs from the target sequence only at one nucleotide position, by which the two sequences can be identified and quantified after the amplification. For quantification of RNA the optimal internal standard is RNA, to be able to control not only the efficiency of the PCR, but also that of the cDNA synthesis.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Syvänen, A.-C., Bengtström, M., Tenhunen, J., and Söderlund, H. (1988) Quantification of polymerase chain reaction products by affinity-based hybrid collection. Nucleic Acid Res. 16, 11,327–11,338.
Chelly, J., Kaplan, J.-C., Maire, P., Gautron, S., and Kahn, A. (1988) Transcription of the dystrophin gene in human muscle and non-muscle tissues. Nature 333, 858–860.
Wang, A. M., Doyle, M. V., and Mark, D. F. (1989) Quantitation of mRNA by the polymerase chain reaction. Proc. Natl. Acad. Sci. USA 86, 9717–9721.
Gilliland, G., Perrin, S., Blanchard, K., and Bunn, H. F. (1990) Analysis of cytokine mRNA and DNA: detection and quantitation by competitive polymerase chain reaction. Proc. Natl. Acad. Sci. USA 87, 2725–2729.
Syvänen, A.-C., Aalto-Setälä, K., Harju, L., Kontula, K., and Söderlund, H. (1990) A primer-guided nucleotide incorporation assay in the genotyping of apolipoprotein E. Genomics 8, 684–692.
Syvänen, A.-C., Sajantila, A., and Lukka, M. (1993) Identification of individuals by analysis of biallelic DNA markers, using PCR and solid-phase minisequencing. Am. J. Hum. Genet. 52, 46–59.
Karttunen, L., Lönnqvist, L., Godfrey, M., Peltonen, L., and Syvänen, A.-C. (1996) An accurate method for comparing transcript levels of two alleles or highly homologous genes: application to fibrillin transcripts in Marfan patients fibroblasts. Genome Res. 6, 392–403.
Ikonen, E., Manninen, T., Peltonen, L., and Syvänen, A.-C. (1992) Quantitative determination of rare mRNA species by PCR and solid-phase minisequencing. PCR Methods Appl. 1, 234–240.
Suomalainen, A., Majander, A., Pihko, H., Peltonen, L., and Syvänen, A.-C (1993) Quantification of tRNA3243 Leu point mutation of mitochondrial DNA in MELAS patients and its effects on mitochondrial transcription. Hum. Mol. Genet. 2, 525–534.
Melton, D. A., Krieg, P. A., Rebagliati, M. R., Maniatis, T., Zinn, K., and Green, M. R. (1984) Efficient in vitro synthesis of biologically active RNA and RNA hybridization probes from plasmids containing a bacteriophage SP6 promoter. Nucleic Acids Res. 12, 7035–7056.
Syvänen, A.-C. and Söderlund, H. (1993) Quantification of polymerase chain reaction products by affinity-based collection. Meth. Enzymol. 218, 474–490.
Syvänen, A.-C., Söderlund, H., Laaksonen, E., Bengtström, M., Turunen, M., and Palotie, A. (1992) N-ras gene mutations in acute myeloid leukemia: accurate detection by solid-phase minisequencing. Int. J. Cancer 50, 713–718.
Pastinen, T., Partanen, J., and Syvänen, A.-C. (1996) Multiplex, fluorescent solid-phase minisequencing for efficient screening of DNA sequence variation. Clin. Chem. 42, 1391–1397.
Bengtström, M., Jungell-Nortamo, A., and Syvänen, A.-C. (1990) Biotinylation of oligonucleotides using a water soluble biotin ester. Nucleosides Nucleotides 9, 123–127.
Wu, R., Wu, N.-H., Hanna, Z., Georges, F., and Narang, S. (1984) In Oligonucleotide synthesis: a practical approach (Gait, M. J., ed.), IRL Press, Oxford, p. 135.
Ihalainen, J., Siitari, H., Laine, S., Syvänen, A.-C, and Palotie, A. (1994) Towards automatic detection of point mutations: use of scintillating microplates in solid-phase minisequencing. BioTechniques 16, 938–943.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2000 Humana Press Inc., Totowa, NJ
About this protocol
Cite this protocol
Suomalainen, A., Syvänen, AC. (2000). Quantitative Analysis of RNA Species by Polymerase Chain Reaction and Solid-Phase Minisequencing. In: Rapley, R. (eds) The Nucleic Acid Protocols Handbook. Springer Protocols Handbooks. Humana Press, Totowa, NJ. https://doi.org/10.1385/1-59259-038-1:229
Download citation
DOI: https://doi.org/10.1385/1-59259-038-1:229
Publisher Name: Humana Press, Totowa, NJ
Print ISBN: 978-0-89603-459-4
Online ISBN: 978-1-59259-038-4
eBook Packages: Springer Book Archive