Isolation of Total RNA from a Freshwater Green Alga, Zygnema cruciatum, Containing High Levels of Pigments

For the study of gene transcription, obtaining total intact RNA is very important. But it is difficult to get intact RNA from some plants. This is mainly because of high contents of polysaccharides, pigments, and other unidentified compounds in these plants (Wang et al. 2004). This causes problems by interfering in RNA experiments such as a RT-PCR, DD-RT-PCR or Northern blot analysis. Various protocols for RNA isolation have been reported for plants containing high levels of polysaccharides and pigments which overcome the above mentioned limitations (Gao et al. 2001; Tai et al. 2004; Tao et al. 2004; Wang et al. 2004; Meisel et al. 2005; Birtic and Kranner 2006; Salter and conlon 2007). However, some plant materials have not yet been studied using these modified methods. Zygnema spp. are well known freshwater conjugating green algae that form free floating mats in shallow waters (Kim et al. 2007). Zygnema spp. have been reported in every biome from tundra through boreal forest to tropical rain forest and desert chaparral. It is one of few filamentous freshwater algae that lives in the Arctic as well as the Antarctic (Hawes 1989). However, little is known regarding gene transcription and translation in this complex. Because of high pigment amounts and RNA interactive molecules, it has been impossible to isolate and purify mRNA from Zygnema using conventional methods. In this paper we describe the development of a new method of RNA isolation using DEAE-cellulose resin and compare the results with other RNA isolation methods.