BBa_K2005003
1
BBa_K2005003
LacZ-alpha, oxidation-resistant
2016-10-17T11:00:00Z
2016-10-18T08:32:04Z
Synthetic variant of Bba_I732006
LacZ alpha fragment with its coding DNA redesigned to minimize its susceptibility to oxidative DNA damage. Compared with standard LacZ, this gene is therefore more stable and less likely to evolve out of a population of cells.
===Sequence Design===
To generate this artificial DNA sequence, we employed our custom-made algorithm for modifying gene sequences to eliminate mutagenic sites. These sites were identified based on prior research on DNA oxidation, which identified poly-guanine motifs as particularly vulnerable. At these motifs, synonymous codon substitutions were made to eliminate oxidation-prone nucleotide sequences and replace them with ones with a lower mutation risk. In addition, our algorithm used heuristics to factor in the effect different codons have on gene expression to ensure that the gene not only produced the same protein but produced it at similar levels. For this sequence, our algorithm could eliminate 61% of poly-guanine motifs and an overall reduction in oxidizable guanines.
===Assembly===
This sequence was synthesized and ligated into pSB1C3. We confirmed that this construct was synthesized and integrated correctly by sequencing.
false
false
_2472_
19415
19415
9
false
To generate this artificial DNA sequence, we employed our custom-made algorithm for modifying gene sequences to eliminate mutagenic sites. These sites were identified based on prior research on DNA oxidation, which identified poly-guanine motifs as particularly vulnerable. At these motifs, synonymous codon substitutions were made to eliminate oxidation-prone nucleotide sequences and replace them with ones with a lower mutation risk. In addition, our algorithm used heuristics to factor in the effect different codons have on gene expression to ensure that the gene not only produced the same protein but produced it at similar levels. For this sequence, our algorithm could eliminate 61% of poly-guanine motifs and an overall reduction in oxidizable guanines.
false
Jarrod Shilts
BBa_K2005003_sequence
1
atgactatgattactgattctttagcagttgttttacaacgtcgtgattgggaaaatccaggtgttactcaattaaatcgtttagcagcacatccaccatttgcatcttggcgtaattctgaagaagcacgtactgatcgtccatctcaacaattacgttctttaaatggtgaatggcgttttgcatggtttccagcaccagaagcagttccagaatcttggttagaataataa
igem2sbol
1
iGEM to SBOL conversion
Conversion of the iGEM parts registry to SBOL2.1
Chris J. Myers
James Alastair McLaughlin
2017-03-06T15:00:00.000Z