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This article is now in press in DRA Replication and Muta~en~sis, a volu~e of invited contributions to a conference held last ~ove~ber on F1arco Island,FLA. Chapter 40 Use of Predesigned Plasmids To Study Deletions: Strategies for Dealing with a Complex Problem Elias Balbinde~" Although the existence of large genetic r~- arrangements such as deletions, duplica- tlons, inversions, translocations, etc., has been known for close to 50 years, the mech- anisms that bring them about are not yet understood. Interest in their study has been increasing in recent Feat's since genetic rear- rangements in both procaryotes and curacy- • ores are at the base of important blological processes (7, 42) and also constitute a major class of dlsease-related genetic events (59, 57). The complexity of eucaryo¢ic systems has made it difficult to study genetic rear- rangements at the molecular level, iv~ost 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 oc- cur either as the result of the movdment of transposable elements (transposition; 44) or naturally from the resolution of transient .~'1~ ,~alblndee • Department of B|ochem~stry. B|ophys~cs and Generics. Univcrslty of" C.olo~do Health Sciences Center, Denver, Colorado 80262. secondary structures formed in the course of DNA metabolism (1, 17, 22, 43). We 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 Streisinge~ et el. to explain the origin,of fr~eshift mutatio~ (SD and .~ postu,ate important roles fff~direct and in- ver~ed repeats. These models are based on exte~ive sequencing of deletion mutations and propose either that deletions take place between direct termin~ repeats and can be facilitated by the presence of int~'ening inverted repeats (palindromes) (1), or they can occur at the end of palindromes ia absence of direct end repeats (22, 43). Pal- indromes are believed to stabilize mis~ign- ments resulting from slippage ~f {ra~iendy single-stmnded regions during DNA replica- .tion (1, 22, 43). Tmnsposon excision k a deletion event t~ing place between dkect repeats at the end is considerable support for these m~els (1. I1, 17, 24, 27, 37, 45, 50, 55)) and they explain most of the deletions reported to date. A certain number of deletions can be -t 40000212