Abstract
To quantitate the gene expression, real-time RT-PCR or quantitative PCR (qPCR) is one of the most sensitive, reliable, and commonly used methods in molecular biology. The reliability and success of a real-time PCR assay depend on the optimal experiment design. Primers are the most important constituents of real-time PCR experiments such as in SYBR Green-based detection assays. Designing of an appropriate and specific primer pair is extremely crucial for correct estimation of transcript abundance of any gene in a given sample. Here, we are presenting a quick, easy, and reliable method for designing target-specific primers using Primer Express® software for real-time PCR (qPCR) experiments.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual, 3rd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
Bustin SA (2000) Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays. J Mol Endocrinol 25:169–193
Thornton B, Basu C (2010) Real-time PCR (qPCR) primer design using free online software. Biochem Mol Biol Educ 39:145–154
Ginzinger DG (2002) Gene quantification using real-time quantitative PCR: an emerging technology hits the mainstream. Exp Hematol 30:503–512
Belgrader P, Benett W, Hadley D et al (1999) PCR detection of bacteria in seven minutes. Science 284:449–450
Johnson MP, Haupt LM, Griffiths LR (2004) Locked nucleic acid (LNA) single nucleotide polymorphism (SNP) genotype analysis and validation using real-time PCR. Nucleic Acids Res 32:e55
Singh A, Giri J, Kapoor S et al (2010) Protein phosphatase complement in rice: genome-wide identification and transcriptional analysis under abiotic stress conditions and reproductive development. BMC Genomics 11:435
Singh A, Baranwal V, Shankar A et al (2012) Rice phospholipase A superfamily: organization, phylogenetic and expression analysis during abiotic stresses and development. PLoS One 7:e30947
Singh A, Pandey A, Baranwal V et al (2012) Comprehensive expression analysis of rice phospholipase D gene family during abiotic stresses and development. Plant Signal Behav 7:847–855
Singh A, Kanwar P, Pandey A et al (2013) Comprehensive genomic analysis and expression profiling of phospholipase C gene family during abiotic stresses and development in rice. PLoS One 8:e62494
Singh A, Kanwar P, Yadav AK et al (2014) Genome-wide expressional and functional analysis of calcium transport elements during abiotic stress and development in rice. FEBS J 281:894–915
Sharma R, Agarwal P, Ray S et al (2012) Expression dynamics of metabolic and regulatory components across stages of panicle and seed development in indica rice. Funct Integr Genomics 12:229–248
Trevisan S, Manoli A, Begheldo M et al (2011) Transcriptome analysis reveals coordinated spatiotemporal regulation of hemoglobin and nitrate reductase in response to nitrate in maize roots. New Phytol 192:338–352
Xu J, Sun J, Du L et al (2012) Comparative transcriptome analysis of cadmium responses in Solanum nigrum and Solanum torvum. New Phytol 196:110–124
Acknowledgement
Research work in GKP’s lab is partially supported by grants from University of Delhi, Department of Biotechnology (DBT), Department of Science and Technology (DST), and Council of Scientific and Industrial Research (CSIR), India. AS acknowledges CSIR for research fellowship.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer Science+Business Media New York
About this protocol
Cite this protocol
Singh, A., Pandey, G.K. (2015). Primer Design Using Primer Express® for SYBR Green-Based Quantitative PCR. In: Basu, C. (eds) PCR Primer Design. Methods in Molecular Biology, vol 1275. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2365-6_11
Download citation
DOI: https://doi.org/10.1007/978-1-4939-2365-6_11
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-2364-9
Online ISBN: 978-1-4939-2365-6
eBook Packages: Springer Protocols