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HomeFAQsDo degenerate recognition sites need to be palindromic?
FAQ: Do degenerate recognition sites need to be palindromic?
Most restriction enzyme recognition sites are palindromic and include only specified base pairs (i.e., EcoRI recognizes GAATTC). However, some enzymes have degenerate sites, meaning that they contain one or more base pairs that are not specifically defined (i.e., BsrFI-v2 recognizes RCCGGY, where R= A or G and Y= C or T). For degenerate enzymes, any base represented by the single letter code may be present at either location in the recognition site for cleavage to occur. For example, BsrFI-v2 recognizes all of the following sequences: ACCGGC, ACCGGT, GCCGGC, GCCGGT.