BBa_K2005003

BBa_K2005003 Version 1

Component

Source: http://parts.igem.org/Part:BBa_K2005003

Generated By: https://synbiohub.org/public/igem/igem2sbol/1

Created by: Jarrod Shilts

Date created: 2016-10-17 11:00:00

Date modified: 2016-10-18 08:32:04

LacZ-alpha, oxidation-resistant

Details

• Types: DnaRegion
• Roles: Reporter; engineered_region
• Sequences: BBa_K2005003_sequence (Version 1)

Description

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.

Notes

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.

Source

Synthetic variant of Bba_I732006

Other Properties

• igem#status: Planning
• synbiohub#ownedBy: user/james
• synbiohub#ownedBy: user/myers
• synbiohub#topLevel: BBa_K2005003/1

Member of these Collections

• iGEM Parts Registry