Insertions and deletions

SA Benner, GH Gonnet, MA Cohen. Empirical and stractural models for insertions and deletions m the divergent evolution of proteins. I Mol Biol 229 1065-1082, 1993. 

Examples of a polymorphism include single nucleotide substitutions, insertions and deletions of nucleotides, and repetitive sequences. While most polymorphisms are harmless and part of normal human genetic variations, studies have established links between certain gene polymorphisms and metabolic alterations or human diseases. 

Murakami, H., Hohsaka, T. and Sisido, M. (2002) Random insertion and deletion of arbitrary number of bases for codon-based random mutation of DNAs. Nature Biotechnology, 20, 76-81. 

In some cases, in particular for lattice and polymeric systems, volume change moves may be hard to perform, but particle insertions and deletions may be relatively... 

The acceptance criteria for particle insertion and deletion moves are determined from the detailed balance condition applied to these probabilities. The final expressions are... 

All these techniques create genetic diversity by recombination and point mutations and are well developed. However, insertions and deletions (indels) are also important types of mutation which are probably underrepresented in many conventional mutagenesis strategies. Methods for incorporation of indels in predefined positions in a combinatorial manner have been developed.Although there are some published studies on their use in the directed evolution of biocatalysts,the full potential of these newer methods of gene mutation for enzyme improvement are yet to be demonstrated. 

Fujii, R., Kitaoka, M. and Hayashi, K., RAISE a simple and novel method of generating random insertion and deletion mutations. Nucleic Acids Res., 2006, 34, 30. 

Z. Zhang, and M. Gerstein, Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes. Nucleic Acids Res. 31, 5338-5348 (2003). 

The variety of AVPR2 mutations that are known to cause X-linked NDI include SNPs, insertions, and deletions (117). For example, familial NDI may result from substitutions of Serl67Thr—a residue conserved across many GPCRs—and Leu44Pro. The Hopewell mutation, a Trp71 truncation, results in NDI in the largest... 

Interesting new homology-dependent and -independent methods have been developed that are not discussed in detail here, including RDA-PCR (55), MURA 54), RETT (55), ITCHY (56), SISDC (57), SCOPE 58), SCATCHY 59), and SHIPREC 60). These and other methods have been reviewed critically by Lutz and Patrick (57). A novel method based on random insertion and deletion of arbitrary number of bases for codon-based random mutation (RID) was developed by Sisido, which introduces additional amino acids or deletes them in the WT 61). Of special note is the fact that some non-natural amino acids can also be introduced, although this process is more complicated. 

---