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A Simple Method for Obtaining DNA Suitable for RAPD Analysis From Azospirillum [chapter]

Raúl O. Pedraza, Juan C. Díaz Ricci
Environmental Microbiology  
Introduction The random amplified polymorphic DNA (RAPD) technique has increasingly been used in the last decade as a simple, low-cost, and time-effective technique for the analysis of genomic polymorphism among related organisms. This method proved to be particularly useful in genomic fingerprinting and phylogenetic studies of microorganisms that present taxonomic problems or a large diversity within the taxon, such as clinical and soil microorganisms (1-5). However, this technique presents
more » ... chnique presents persistent problems of reproducibility that have been attributed to a high sensitivity to subtle procedure changes and to the quality of the DNA used as template (6-8). For this reason, other techniques that are more time and budget demanding, such as restriction fragment-length polymorphism (RFLP) and amplified fragment-length polymorphism (AFLP) have been used as valid and more reliable alternatives to assess genomic diversity (9,10). Although DNA fingerprints obtained by RFLP and AFLP yield excellent results, often cost considerations make RAPD the technique of choice. Additionally, because the RAPD method is much faster and simpler than RFLP and AFLP, it is also well-suited when large numbers of specimens, or microbial isolates that require previous laborious manipulations, have to be analyzed. Thus, any procedural simplification of tedious and time-consuming steps is welcome, provided that the information quality does not decrease due to technical artifacts or loss of reproducibility; the latter is precisely the most sensitive issue of the RAPD technique, attributed mainly to DNA quality. Hence, obtaining DNA of such a quality that it can be directly used in RAPD
doi:10.1385/1-59259-765-3:151 fatcat:vbzy4poc3vhl5pziyey5vjzf3q