I’m studying Darwin’s finches genome and I say in some articles that the researchers used restriction enzymes to cut the DNA in their double digest RAD protocol. They are using EcoRI and MseI (GAATTC and TTAA), the two enzymes similar and used in Peterson, B. K., J. N. Weber, E. H. Kay, H. S. Fisher, and H. E. Hoekstra. 2012. Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS ONE 7:e37135. (they are using EcoRI and MspI (GAATTC and CCGG).

Considering the huge list of restriction enzymes how to choose the appropriate enzyme? Is it a complete guess? The size of the genome of finches is about 1.07Gb. Do I have to take this in consideration?

The reference genome is available Zhang, G., P. Parker, B. Li, H. Li, and J. Wang. 2012. The genome of Darwin’s Finch (Geospiza fortis). GigaScience.

  • $\begingroup$ maybe R.EcoRII or FokI/Taq52I? $\endgroup$
    – Ebbinghaus
    Jan 30 '16 at 16:32
  • $\begingroup$ Why would you choose these? $\endgroup$ Jan 30 '16 at 17:02
  • 1
    $\begingroup$ R.EcoRII because of its molecular mass (45.2 kDa), it targets CCWGG, C-terminal domain of restriction endonuclease and apologies, I meant Tsp49I rather than Taq52I and this because of its relatively high pH optimum, reaching enzyme activity peak at rather "high" temperatures, its a thermostable neoschizomer $\endgroup$
    – Ebbinghaus
    Jan 30 '16 at 17:45

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