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:/ This article is no;v in press in DNA Replication and bluta~enesis, a volume of invited contributions to a conference held last November on ~larco Island,FLA. Chapter 40 Use of Predesigned Plasmids To Study Deletions: Strategies for Den.ling with a Complex Problem ~ilias Balbinde.r Although the existence of large genetic re- arrangements such as deletions, duplica- tions, inversions, translocations, etc., has been known for close to 50 years, the mech- anisms that bring them about are noc yet understood. Interest in their study has been increasing in recent years since genetic rear- rangements in both procaryotes and euca~y- ores are at the base of important biological processes (7, 42) and also constitute a major class of disease-related genetic events (59, 57). The complexity of eucaryodc 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. ~[ajor genetic rearrangements can oc- cur e/the: as the result of the movement of transposable elements (transposition; 44) or naturally from d~e resolution of transient ~Ifas Balbindet" * Department t~f BiochemlstO'. Biophysics a,d Genetics. Um~.erslty o~" Colorado Hen|oh 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 mutageaesis models. These are extensions of the model advanced by Strelsinger et al. to explain the origin of frameshift mutations (5 ~) and Eo ~ ~.'$i.. ".,., " " ' postumte important roles fo~.~irecr and in- verted repeats. These models ate based on extensive sequencing of deletion mutations and propose either that deletions take place between direct terminal repeats and can be facilitated by the presence of in.-ervening inverted repeats (palindromes) (~), or they can occur at the end of palindromes in the absence of direct end repeats (22, 43). Pal- indromes are believed to stabilize mlsalign- ments resulting from slippage o'f transiently single-stranded regions during DNA replica- .don (1, "2-2, 43). Transposon excision is a deletion event taking place betwe~:n direct • --~" • ;" ".-:- ....... ~.. repeats at the end of a-pahndrom~l). There is considerable support for these models (1, ll, I7, 2-t, 27, 37, 45, 50, 55), and they .~,~,~l .l ~,,~, explain most o~" the deletions reported ~o ', date. ~ certain number of deletions can be L~ 3 ..... " 378 40000204