A novel approach to prepare extended DNA fibers in plants

Background: The extended DNA fiber preparation procedure is still imperfect in plants due to the existence of a hard cell wall; thus, high quality of extended DNA fibers for fluorescence in situ hybridization (FISH) analysis is often difficult to be obtained rapidly and efficiently. In this study we have developed a fast and widely effective method to prepare DNA fibers from various plant species and the fibers are suitable for fiber FISH mapping. Methods: Fresh young leaves were chopped with a sharp sterile scalpel in a Petri dish that contained ice-cold nucleus isolation buffer followed by filtration through 33-mum nylon mesh. Nuclei were obtained by centrifuging the filtrates at high speed (16,000g) for 40 s. Nucleus lysis buffer (0.5% sodium dodecylsulfate, 5 mM ethylenediaminetetraacetic acid, 100 mM Tris, pH7.0) was added to nuclei on slides, and DNA fibers were dragged and extended with a clean coverslip. Results: The key of this method is that liquid nitrogen grinding of leaves is replaced by chopping with a blade in ice-cold nucleus isolation buffer. With the liquid nitrogen method, over- or under-grinding of leaves occurs more frequently, and DNA fibers with the desired quality are not obtained easily. in contrast, it is easier to release nuclei from cells in nucleus isolation buffer by chopping, which results in fewer nuclei being destroyed. Highly extended, intact, and long DNA fibers can be generated to a great probability with this method. In addition, this method is very simple and rapid, requiring only 20 min for the entire process, and is also safe because poisonous mercaptoethanol is replaced by dithiothreitol. The results of fiber-FISH with maize genomic DNA and 45S rDNA as probes showed that DNA fiber size as long as 1.96 Mb could be measured. The successful and reliable preparation of maize, wild rice, and barley DNA fibers suitable for FISH mapping proves that this technique is a widely effective approach for obtaining extended DNA fibers in plants. Conclusions: A simple, rapid, safe, and widely effective method for getting extended DNA fibers has been developed in plants. (C) 2005 Wiley-Liss, Inc.