RBS

Part:BBa_K2138001:Design

Designed by: Austin Nykiel   Group: iGEM16_UMass-Dartmouth   (2016-10-19)


RNA thermometer and RBS (39C)


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal prefix found in sequence at 1
    Illegal suffix found in sequence at 193
    Illegal EcoRI site found at 2262
    Illegal XbaI site found at 2277
    Illegal SpeI site found at 215
    Illegal PstI site found at 229
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal EcoRI site found at 1
    Illegal EcoRI site found at 2262
    Illegal NheI site found at 30
    Illegal NheI site found at 53
    Illegal SpeI site found at 194
    Illegal SpeI site found at 215
    Illegal PstI site found at 208
    Illegal PstI site found at 229
    Illegal NotI site found at 7
    Illegal NotI site found at 201
    Illegal NotI site found at 222
    Illegal NotI site found at 2268
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal EcoRI site found at 1
    Illegal EcoRI site found at 2262
    Illegal XhoI site found at 1246
    Illegal XhoI site found at 2138
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal prefix found in sequence at 1
    Illegal suffix found in sequence at 194
    Illegal EcoRI site found at 2262
    Illegal XbaI site found at 2277
    Illegal SpeI site found at 215
    Illegal PstI site found at 229
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal prefix found in sequence at 1
    Illegal EcoRI site found at 2262
    Illegal XbaI site found at 16
    Illegal XbaI site found at 2277
    Illegal SpeI site found at 194
    Illegal SpeI site found at 215
    Illegal PstI site found at 208
    Illegal PstI site found at 229
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

The primary design consideration while designing the DNA sequence was to achieve a melting temperature between thirty degrees Celsius and forty-two degrees Celsius. This was achieved by eliminating as many cytosine and guanine complementary bonds as possible leading to sequences comprised essentially of three different nucleotides.


Source

The DNA sequence is comprised of two different segments. The first segment was designed entirely de novo by utilizing Oligoanalyzer3.1 from Integrated DNA Technologies to calculate melting temperature for the complementary RNA strand. The second segment consists of the ribosome binding site which was selected based upon the Anderson ribosome binding site format for strong protein expression.

References