Sequencing of the large (>50 kb), low-copy-number (<5 per cell) plasmids that mediate horizontal gene transfer has been hindered by the difficulty and expense of isolating DNA from individual plasmids of this class. We report here that a kit method previously devised for purification of bacterial artificial chromosomes (BACs) can be adapted for effective preparation of individual plasmids up to 220 kb from wild gram-negative and gram-positive bacteria. Individual plasmid DNA recovered from less than 10 ml of Escherichia coli, Staphylococcus, and Corynebacterium cultures was of sufficient quantity and quality for construction of highcoverage libraries, as shown by sequencing five native plasmids ranging in size from 30 kb to 94 kb. We also report recommendations for vector screening to optimize plasmid sequence assembly, preliminary annotation of novel plasmid genomes, and insights on mobile genetic element biology derived from these sequences. Adaptation of this BAC method for large plasmid isolation removes one major technical hurdle to expanding our knowledge of the natural plasmid gene pool.Recent genome sequencing and analysis has revealed extensive horizontal gene transfer among bacterial genomes (4,14). Remnants of mobile genetic elements (MGEs), such as plasmids and bacteriophages (23), are often found adjacent to horizontally transferred chromosomal regions, indicating that these elements are important mediators of gene transfer between bacterial chromosomes. The MGEs themselves also typically carry genes for virulence factors, antibiotic resistances, and novel metabolic processes that enable bacterial hosts to adapt to new environmental conditions (11,12).Despite the recognized importance of these elements, genomic analysis of MGEs has been limited. Whereas the total size of sequenced bacterial genomes is 1.3 Gb, only 61 Mb of plasmid genomes and 30 Mb of phage genomes have been sequenced previously (11). Most MGE sequences have been obtained fortuitously during sequencing of their hosts' genomes, resulting in a bias towards MGEs associated with a limited selection of organisms. Large (Ͼ50 kb), conjugative plasmids are especially poorly represented in current sequence databases, constituting only 20% of all plasmid sequences in GenBank at present. Most commercial kits for plasmid DNA preparation are designed for small, high-copy-number plasmids. The traditional methods of high-molecular-weight plasmid isolation, such as cesium chloride density gradient centrifugation (26) and pulsed-field gel electrophoresis, require equipment and expertise that are not widely available. Moreover, these and other techniques, such as Eckhardt in-well lysis (6), are time and labor intensive and thus unsuitable for a high-throughput approach.In the course of large-scale sequencing projects such as the Human Genome Project, magnetic beads were modified for purification of nucleic acids, including bacterial artificial chromosome (BAC) clones (7,15,28). The method used here, termed Solid-Phase Reversible Immobilization (SPRI)...