Table 1.

DNA target site constructs

Protein	Structural family	Site name and site type	Sequence of duplex (target site in bold)
I-PpoI	His-Cys box homodimer	WT: wild-type cognate pseudopalindrome	5′ GGGGGAGTAACTATGACTCTCTTAAGGTAGCCAAAGGGGG 3′ 3′ CCCCCTCATTGATACTGAGAGAATTCCATCGGTTTCCCCC 5′
I-PpoI	His-Cys box homodimer	LL: left–left palindrome	5′ GGGGGTGCAGTGACTCTCTTAAGAGAGTCAGACGTGGGGG 3′ 3′ CCCCCACGTCACTGAGAGAATTCTCTCAGTCTGCACCCCC 5′
I-PpoI	His-Cys box homodimer	RR: right–right palindrome	5′ GGGGGTGCAGTGGCTACCTTAAGGTAGCCAGACGTGGGGG 3′ 3′ CCCCCACGTCACCGATGGAATTCCATCGGTCTGCACCCCC 5′
I-MsoI	LAGLIDADG homodimer	WT: wild–type cognate pseudopalindrome	5′ GGGGGGCAGAACGTCGTGAGACAGTTCGGGGGGG 3′ 3′ CCCCCCGTCTTGCAGCACTCTGTCAAGCCCCCCC 5′
I-MsoI	LAGLIDADG homodimer	LL: left–left palindrome	5′ GGGGGGCAGAACGTCGTACGACGTTCTGGGGGGG 3′ 3′ CCCCCCGTCTTGCAGCATGCTGCAAGACCCCCCC 5′
I-MsoI	LAGLIDADG homodimer	RR: right–right palindrome	5′ GGGGGGCGAACTGTCTCGAGACAGTTCGGGGGGG 3′ 3′ CCCCCCGCTTGACAGAGCTCTGTCAAGCCCCCCC 5′
I-MsoI	LAGLIDADG homodimer	MIS: miscognate pseudopalindrome	5′ GGGGGGCAGAAGGTCGTGAGACCGTTCGGGGGGG 3′ 3′ CCCCCCGTCTTCCAGCACTCTGGCAAGCCCCCCC 5′
I-AniI	LAGLIDADG monomer	WT: wild–type cognate asymmetric	5′ CCTTCCCTGAGGAGGTTTCTCTGTAAACCCTTCC 3′ 3′ GGAAGGGACTCCTCCAAAGAGACATTTGGGAAGG 5′
I-AniI	LAGLIDADG monomer	WT-OPT: selected optimal target asymmetric	5′ CCTTCCCTGAGGAGGTTACTCTGTTAACCCTTCC 3′ 3′ GGAAGGGACTCCTCCAATGAGACAATTGGGAAGG 5′
I-SspI	PD-D/E-XK tetramer	WT: wild-type cognate pseudopalindrome	5′ GGGCCTTCGGGCTCATAACCCGAAGGGACG 3′ 3′ CCCGGAAGCCCGAGTATTGGGCTTCCCTGC 5′
I-HmuI	HNH monomer	WT: wild-type cognate asymmetric	5′GGGGGGTAATGAGCCTAACGCTCAGCAATTCCCACGTAAGGGGGG3′ 3′CCCCCCATTACTCGGATTGCGAGTCGTTAAGGGTGCATTCCCCCC5′

Underlined bases indicate positions in target sites for homodimeric (I-PpoI, I-MsoI) or tetrameric (I-SspI) homing endonucleases that are not conserved between DNA half-sites (i.e. they contribute to asymmetry in otherwise palindromic targets).