Variation between observed and true Terminal Restriction Fragment length is dependent on true TRF length and purine content

Terminal Restriction Fragment (TRF) pattern analysis has become a widely used and informative tool for Studying microbial communities. Variation between sequence-determined or true TRY length and observed TRF length (TRF drift) has been previously reported and can significantly affect identification of bacterial species using TRF lengths predicted from sequence databases. In this study TRF drift was determined for 21 bacterial species using an ABI 310 Genetic Analyzer. TRF drift was positively correlated with true TRF length and negatively correlated with TRF purine content. This implies that subtle differences in molecular weight, whether from purine content or dye label, can significantly affect the observed TRF length. (C) 2003 Elsevier Science B.V All rights reserved.