I want to design cloning primers with NdeI and XhoI restriction sites. Does anyone know what are the best additional base-pair requirements for these restriction enzymes?
Is there a preference between the nucleotides composition of the additional base-pairs?
NEB used to have a table showing the optimal bases flanking the restriction sites for cleavage close to the end of DNA fragments. Could though be that this is specific to restriction enzymes from NEB.
The table can be found through this link: https://www.neb.com/~/media/NebUs/Files/Chart%20image/cleavage_olignucleotides_old.pdf
The additional bases for NdeI should according to the table be: GAATTCC
And for XhoI: CGG
NdeI: 3bp
XhoI: 4bp for maximum efficiency.
For requirements, read the info under the link:
https://www.neb.com/tools-and-resources/usage-guidelines/cleavage-close-to-the-end-of-dna-fragments
NEB used to have a table showing the optimal bases flanking the restriction sites for cleavage close to the end of DNA fragments. Could though be that this is specific to restriction enzymes from NEB.
The table can be found through this link: https://www.neb.com/~/media/NebUs/Files/Chart%20image/cleavage_olignucleotides_old.pdf
The additional bases for NdeI should according to the table be: GAATTCC
And for XhoI: CGG
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