Accuracy and efficiency define Bxb1 integrase as the best of fifteen candidate serine recombinases for the integration of DNA into the human genome

Xu, Zhengyao; Thomas, Louise; Davies, Ben; Chalmers, Ronald; Smith, Maggie; Brown, William

doi:10.1186/1472-6750-13-87

Table 2 Accuracy of integrase mediated site-specific recombination in human HT1080 and mouse ES cells

From: Accuracy and efficiency define Bxb1 integrase as the best of fifteen candidate serine recombinases for the integration of DNA into the human genome

Integrase	Sequence	Integrations	Deletions
BxB1	HT1080	ES
attB	TCGGCCGGCTTGTCGACGACGGCGGTCTCCGTCGTCAGGATCATCCGGGC
attP	GTCGTGGTTTGTCTGGTCAACCACCGCGGTCTCAGTGGTGTACGGTACAAACCCCGAC
attL	TCGGCCGGCTTGTCGACGACGGCGGTCTCAGTGGTGTACGGTACAAACCCCGAC	3/3
attR	GTCGTGGTTTGTCTGGTCAACCACCGCGGTCTCCGTCGTCAGGATCATCCGGGC	7/7	2/2
fC31
attB	TGCGGGTGCCAGGGCGTGCCCTTGGGCTCCCCGGGCGCGTACTCC
attP	GTGCCCCAACTGGGGTAACCTTTGAGTTCTCTCAGTTGGGGG
attL	TGCGGGTGCCAGGGCGTGCCCTTGAGTTCTCTCAGTTGGGGG	3/3
attR	TTGCCCCAACTGGGGTAACCTTTGGGCTCCCCGGGCGCGTACTCC	7/7	3/3
R4
attB	GCGCCCAAGTTGCCCATGACCATGCCGAAGCAGTGGTAGAAGGGCACCGGCAGACAC
attP	AGGCATGTTCCCCAAAGCGATACCACTTGAAGCAGTGGTACTGCTTGTGGGTACACTCTGC
attL	GCGCCCAAGTTGCCCATGACCATGCCGAAGCAGTGGTACTGCTTGTGGGTACACTCTGC	3/3
attR	AGGCATGTTCCCCAAAGCGATACCACTTGAAGCAGTGGTAGAAGGGCACCGGCAGACAC	2/9	1/2
del clone 1 DattR	AGGCATGTTCCCCAAAGCGATACCAC AAGCAGTGGTAGAAGGGCACCGGCAGACAC
del clone 2 DattR	AGGCATGTTCCCCAAAGCGATACCACTT AAGCAGTGGTAGAAGGGCACCGGCAGACAC
del clone 3 DattR	AGGCATGTTCCCCAAAGCGATACCACTTG GCAGTGGTAGAAGGGCACCGGCAGACAC
del clone 4 DattR	AGGCATGTTCCCCAAAGCGATA GCAGTGGTAGAAGGGCACCGGCAGACAC
del clone 5 DattR	AGGCATGTTCCCCAAAGCGATACCA GTGGTAGAAGGGCACCGGCAGACAC
del clone 6 DattR	AGGCATGTTCCCCAAAGCGATACCA GAAGCAGTGGTAGAAGGGCACCGGCAGACAC
del clone 7 DattR	AGGCATGTTCCCCAAAGCGATACCAC AAGCAGTGGTAGAAGGGCACCGGCAGACAC
ES del clone 1 DattR	AGGCATGTTCCCCAAAGCGATACCA AGCAGTGGTAGAAGGGCACCGGCAGACAC	1/2
intn clone 1-3 DattR	AGGCATGTTCCCCAAAGCGATA CAGTGGTAGAAGGGCACCGGCAGACAC	3/3
fBT1
attB	GTCCTTGACCAGGTTTTTGACGAAAGTGATCCAGATGATCCAGCTCCACACCCCGAACGC
attP	GGTGCTGGGTTGTTGTCTCTGGACAGTGATCCATGGGAAACTACTCAGCACCACCAATG
attL	GTCCTTGACCAGGTTTTTGACGAAAGTGATCCATGGGAAACTACTCAGCACCACCAATG	3/3
attR	GGTGCTGGGTTGTTGTCTCTGGACAGTGATCCAGATGATCCAGCTCCACACCCCGAACGC	7/7	2/2
intn clone 1DattR	GGTGCTGGGTTGTTGTCTC GATCCAGATGATCCAGCTCCACACCCCGAACGC	1/3
Wβ
attB	AAGGTAGCGTCAACGATAGGTGTAACTGTCGTGTTTGTAACGGTACTTCCAACAGCTGGCG
attP	TAGTTTTAAAGTTGGTTATTAGTTACTGTGATATTTATCACGGTACCCAATAACCAATGAA
attR	TAGTTTTAAAGTTGGTTATTAGTTACTGTGATATTTGTAACGGTACTTCCAACAGCTGGCG	7/7	2/2
SPBc
attB	AGTGCAGCATGTCATTAATATCAGTACAGATAAAGCTGTATCTCCTGTGAACACAATGGGTG	7/7	2/4
attP	AAAGTAGTAAGTATCTTAAAAAACAGATAAAGCTGTATATTAAGATACTTACTAC
attR	AAAGTAGTAAGTATCTTAAAAAACAGATAAAGCTGTATCTCCTGTGAACACAATGGGTG
ES del clone 1 DattR	AAAGTAGTAAGTATCTTAAAAAACA———AGCTGTATCTCCTGTGAACACAATGGGTG	1/4
ES del clone 2 DattR	aaaatacagcgtttttcatgtacaactatact GCTGTATCTCCTGTGAACACAATGGGTG	1/4
TP901
attB	TGATAATTGCCAACACAATTAACATCTCAATCAAGGTAAATGCTTTTTCGTTTT
attP	AATTGCGAGTTTTTATTTCGTTTATTTCAATTAAGGTAACTAAAAAACTCCTTT
attR	AATTGCGAGTTTTTATTTCGTTTATTTCAAGGTAAATGCTTTTTCGTTTT	4/5
del clone 1 DattR	AATTGCGAGTTTTTATTTCGTTTATTTC GGTAAATGCTTTTTCGTTTT	1/5

The results show the sequences of the recombinant sites detected following integrase mediate site specific recombination in human HT1080 or mouse ES cells. Underlined and in lowercase in the case of one sequence from a deletion event occurring in ES cells following expression of the SPBc integrase is the sequence of a flanking φ370.1 attP site discussed in the text.

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ISSN: 1472-6750

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