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This article is now in press in DNA Replication and Muta~enesis, a volume of invited contributions to a conference held last November on Marco Island,FLA. Chapter 40 Use of Predesigned Plasmids To Study Deletions: Strategies for Den.ling with a Complex Problem Elias Balbinder Although the existence of large genetic re- arrangements such as deletions, duplica- tiorm, inversions, translocations, etc., has been known for close to 50 years, the mech- anisms thac bring them about are not yet understood. Interest in their study has been increasing in recent years since generic rear- rangements in both procaryotes and cucary- ores are at the base of important biological processes (7, 42) and also constitute a major class of disease-related genetic events (39, 57). The complexity of cucaryotic systems has made it difficult to study genetic rear- rangements at the molecular level. Most of what we know today comes from studies using procaryotic systems. These have iden- tified some of the important parameters in rearrangement formation and also brought about the realization that the mechanisms responsible for them are exceedingly com- plex. Major genetic rearrangements can 0c- cur either ,as the result of the movement of transposable elements (transposition; 44) or naturally from the resolution of transient ~1i~$ Balbindee " Dep;*rtmcnt of B[ochcmlsu'y. Biophysics sad Genetics. Un,ver*ity of Colorudo Health Sciences Center, Denver. Coloeado 80262. secondary structures formed in the course of DNA metabolism (1, 17, 22, 43). \Ve are concerned exclusively with the latter. Deletions are the most extensively stud- ied rearrangements, and most of them are explained by misalignment mutagenesis models. These are extensions of the model advanced by Streisinger et al. to explain the origin of framcshift mutations (51) and ~.~:'....,,~ .. ~ - . ,. postumte important roles .for-direct and in- verted repeats. These models are based on extensive sequencing of deletion mutations and propose either that deletions take place b~t~een direct terminal repeats and can be facilitated by the presence of inter~-cning inverted repeats (palindromes) (1), or they can occur at the end of palindromes it* the absence of direct end repeats (22. 4~). Pai- indromes are believed to stabilize misalign- meats resulting from slippage 6f transiently single-stranded regions during DNA replica- .tion (I, 22, 43). Transposon excision is a deletion event taking place between direct . --~-,, repeats at the end of a:palln, dr.o _me-(l). There , is considerable support for ~hesc models (1, II, 17, 24, 27, 37, 45, 50, 55), and they explain most of the deletions repotted to date. A certain number of deletions can be C' 378 -l 40000224