# Chapter 14 - Site-Specific Recombination and Transposition ## 14.1 - Mechanisms of Site-Specific Recombination There are two major classes of genetic recombination responsible for many DNA rearrangements: 1. **Site-Specific Recombination (SSR)**: Recombination between *two defined sequence elements* 2. **Transpositional Recombination (Transposition):** Recombination between *one specific sequence* and *one non-specific DNA site*. Both of these methods move around via transposable elements (TE) and use special enzymes called recombinases. ### Site-Specific Recombination Basics - Seen in both bacteria and eukaryotes - Occurs at specific DNA sequences within the target DNA - Required for diverse DNA rearrangement in the cell (both bad and good): - Chromosomal segregation - Integration and excision of bacteriophage DNA elements (lytic vs lysogenic) - Inversion of DNA segments to control gene expression DNA segments that are moved will carry “specific short sequence elements” known as **recombination sites**. These sites contain: - *Recombinase Recognition Sequences (RRS)* which are specifically bound to by the recombinase. They come in pairs to indicate the beginning and end points and are symmetric/palindromic. - *Crossover Region/”Core”* sequence where DNA will be cleaved and rejoined. This sequence is asymmetric (aka nonpalindromic) and placed between the two RRS sites; allows the region to have a notion of polarity/directionality. The recombination sites as a whole are typically only ~20nt long and sometimes contain additional motifs or protein bind sites (i.e. for architectural proteins that may assist in bending of DNA). ### SSR Recombinases Both classes of recombinases use a nucleophilic attack by a -OH group (tyrosine or serine residue). This breaks a phosphodiester bond on DNA and forms a new covalent bond between DNA and the protein. **Tyrosine Recombinases:** breaks and rejoins one pair of DNA strands at a time. - Forms a a Holliday intermediate **Serine Recombinases:** double-stranded breaks in the DNA leading to the strands swapping to promote recombination - Enzyme cleaves off four strands prior to strand exchange - “Flat surface that is used to rotate"