The source DNA is bases 1-2435 from the M13K07 phage, which is bounded by the HpaI and BamHI restriction sites.
The following sequence of DNA is drawn from the M13K07 phage plasmid, specifically the section between the HpaI and BamHI restriction sites. This section incorporates all or parts of seven open reading frames, many of which are overlapping in the wild-type genotype. The result is a synthetic biology-oriented genome that can be better understood and hopefully will be more easily manipulated for bioengineering purposes.
Overlaps were eliminated through direct duplication of appropriate sequences. Homologous recombination possibilities were diminished by silent mutation of the first instance of duplicated codons. About half the duplicated codons were changed in this manner.
New England Biolabs M13K07. Sequenced in 2002 by L. Panganaban
This RBS is part of the bacteriophage M13 genome, initiating translation of the gene V message (BBa_M13005). The part aligns with base pairs 827-842 in M13K07 genome. It was identified as the RBS for the gene V message by Wezenbeek et al in Gene (1980) 11: 129-148
This RBS is part of the bacteriophage M13 genome, initiating translation of the gene VII message (BBa_M13007). The part aligns with base pairs 1092-1107 in M13K07 genome. It was identified as the RBS for gene VII message by Wezenbeek et al in Gene (1980) 11: 129-148
This RBS is part of the bacteriophage M13 genome, initiating translation of the gene IX message (BBa_M13009). The part aligns with base pairs 1190-1205 in M13K07 genome. It was identified as the RBS for gene IX message by Wezenbeek et al in Gene (1980) 11: 129-148
This RBS is part of the bacteriophage M13 genome, initiating translation of the gene III message (BBa_M13003). The part aligns with base pairs 1563-1578 in M13K07 genome. It was identified as the RBS for gene III message by Wezenbeek et al in Gene (1980) 11: 129-148 New England Biolabs M13K07. Sequenced in 2002 by L. Panganaban
New England Biolabs M13K07. Sequenced in 2002 by L. Panganaban.
This part is from the bacteriophage M13 genome, bp 786-835 in M13K07. It directs transcription of M13 gene V (BBa_M13505, BBa_M13005). Its identity as a promoter was described in Gene (1980) 11:129-148 based on -10,-35 homology and fragment of genome able to bind RNAP.
This part is from the bacteriophage M13 genome, bp 1500-1547 in M13K07. It directs transcription of M13 gene III (BBa_M13503, BBa_M13003). Its identity as a promoter was described in Gene (1980) 11:129-148 based on -10,-35 homology and fragment of genome able to bind RNAP.
Second Half of M13K07 g2 -Promoter g5 -RBS g5
Starts with the HpaI unique restriction site in M13K07 genome and continues until the stop codon of gII.
Codes for the g3 ORF of M13K07 phage until the BamHI unique restriction site.
Contains the open reading frame of g5 from the M13K07 phage genome. The last few codons are silently mutated to remove the g5 RBS sequence.
Changed every other codon in the RBS sequence but maintained the same amino acid sequence.
M13K07 g7 ORF -Promoter g8 -RBS g9 -ORF g9
Contains the M13K07 g7 open reading frame with the g8 promoter, g9 RBS, and g9 ORF sequences and overlaps removed by silent mutation.
Change codons in relevant sequences so that amino acid sequence is the same
Contains the M13K07 g8 open reading frame with the g3 promoter overlap removed by silent mutation.
Contains the M13K07 g9 open reading frame with the g8 RBS, and g8 ORF sequences and overlaps removed by silent mutation.
This RBS is part of the bacteriophage M13 genome, initiating translation of the gene VIII message (BBa_M13008). The part aligns with base pairs 1285-1300 in M13K07 genome. It was identified as the RBS for gene VIII message by Wezenbeek et al in Gene (1980) 11: 129-148
Derived from trp and lac promoter sequences.
Allows for regulation of following gene with laqIq and IPTG...laqIq in same plasmid represses the promoter and IPTG proportionally depresses the promoter (Boer, et al., 1983).
Conversion of the iGEM parts registry to SBOL2.1