Abstract
Recently, we cloned six new green fluorescent protein (GFP)-like fluorescent proteins from five species of Antozoa (1), including one red-emitting variant (DsRed), which is now commercially available. This project did not require expeditions and collection of animals on reefs: In all cases, the starting material was just several milligrams of tissue (e.g., a tentacle tip of a sea anemone), collected from a specimen in a private aquarium. This truly noninvasive kind of study was possible because the approach of total cDNA amplification, which is extensively applied to various tasks and biological models in our lab. This chapter outlines several year’s of experience in this helpful technique.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Matz, M. V., Fradkov, A. F., Labas, Y. A., Savitsky, A. P., Zaraisky, A. G., Markelov, M. L., and Lukyanov, S. A. (1999) Fluorescent proteins from nonbioluminescent Anthozoa species. Nat. Biotechnol. 17, 969–973.
Gonzalez, P., Zigler, J. S., Jr, Epstein, D. L., and Borras, T. (1999) Identification and isolation of differentially expressed genes from very small tissue samples.Biotechniques 26, 884–886, 888–892.
Spirin, K. S., Ljubimov, A. V., Castellon, R., Wiedoeft, O., Marano, M., Sheppard, D., Kenney, M. C., and Brown, D. J. (1999) Analysis of gene expression in human bullous keratopathy corneas containing limiting amounts of RNA. Invest. Opthalmol. Vis. Sci. 40, 3108–3115.
Wang, E., Miller, L. D., Ohnmacht, G. A., Liu, E. T., and Marincola, M. (2000) High-fidelity mRNA amplification for gene profiling. Nat. Biotechnol. 18, 457–459.
Livesey, F. J., Furukawa, T., Steffen, M. A. Church, G. M., and Cepko, C. L.(2000) Microarray analysis of the transcriptional network controlled by the pho-toreceptor homeobox gene Crx. Curr. Biol. 10, 301–310.
Chenchik, A., Diachenko, L., Moqadam, F., Tarabykin, V., Lukyanov, S., and Siebert, P. D. (1996) Full-length cDNA cloning and determination of mRNA 5′ and 3′ ends by amplification of adaptor-ligated cDNA. Biotechniques 21, 526–534.
Matz, M., Shagin, D., Bogdanova, E., Britanova, O., Lukyanov, S., Diatchenko, L., and Chenchik, A. (1999) Amplification of cDNA ends based on template-switching effect and step-out PCR. Nucl. Acids Res. 27, 1558–1560.
Diatchenko, L., Lukyanov, S., Lau, Y. F., and Siebert, P. D (1999) Suppression subtractive hybridization: a versatile method for identifying differentially expressed genes. Meth. Enzymol. 303, 349–380.
Matz, M., Usman, N., Shagin, D., Bogdanova, E., and Lukyanov, S. (1997) Ordered differential display: a simple method for systematic comparison of gene expression profiles. Nucl. Acids Res. 25, 2541–2542.
Chomczynski, P. and Sacchi, N. (1987) Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Analyt. Biochem. 162, 156–159.
Lee, Y. H., Huang, G. M., Cameron, R. A., Graham, G., Davidson, E. H., Hood, L., and Britten, R. J. (1999) EST analysis of gene expression in early cleavage-stage sea urchin embryos. Development 126, 3857–3867.
Siebert, P. D., Chenchik, A., Kellogg, D. E., Lukyanov, K. A., and Lukyanov, S. A.(1995) An improved PCR method for walking in uncloned genomic DNA. Nucl.Acids Res. 23, 1087–1088.
Lukyanov, K. A., Diachenko, L., Chenchik, A., Nanisetti, A., Siebert, P. D., Usman, N. Y., Matz, M. V., and Lukyanov, S. A. (1997) Construction of cDNA libraries from small amounts. 18 of total RNA using the suppression PCR effect.Biophys. Biochem. Res. Comm. 230, 285–288.
Schmidt, W. M. and Mueller, M. W. (1999) CapSelect: a highly sensitive method for 5′ CAP-dependent enrichment of full length cDNA in PCR-mediated analyses of mRNAs. Nucleic Acid Res. 27, e31.
Chenchik, A., Zhu, Y. Y., Diatchenko, L., Li, R., Hill, J., and Siebert, P. D. (1998) Gene Cloning and Analysis by RT-PCR (Siebert, P. and Larrick, J., eds.) BioTechniques, Natick, MA, 305–319.
Ishikawa, H. (1977) Evolution of ribosomal RNA. Comp. Biochem. Physiol. B 58, 1–7.
Lukyanov, K. A., Matz, M. V., Bogdanova, E. A., Gurskaya, N. G., and Lukyanov, S. A. (1996) Molecule by molecule PCR amplification of complex DNA mixtures for direct sequencing: an approach to in vitro cloning. Nucleic Acids Res. 24, 2194–2195.
Fradkov, A. F., Lukyanov, K. A., Matz, M. V., Diatchenko, L. B., Siebert, P. D.,and Lukyanov, S. A. (1998) Sequence-independent method for in vitro generation of nested deletions for sequencing large DNA fragments. Analyt. Biochem. 258, 138–141.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2002 Humana Press Inc.
About this protocol
Cite this protocol
Matz, M.V. (2002). Amplification of Representative cDNA Samples from Microscopic Amounts of Invertebrate Tissue to Search for New Genes. In: Hicks, B.W. (eds) Green Fluorescent Protein. Methods in Molecular Biology, vol 183. Humana Press. https://doi.org/10.1385/1-59259-280-5:003
Download citation
DOI: https://doi.org/10.1385/1-59259-280-5:003
Publisher Name: Humana Press
Print ISBN: 978-0-89603-905-6
Online ISBN: 978-1-59259-280-7
eBook Packages: Springer Protocols