Creating Oligonucleotides

Gene Designer enables two main oligonucleotide functions which can be performed in the Construct Editor

• Oligonucleotides can be created manually to match any segment of sequence within a construct in either direction.
• GeneDesigner will also automatically design oligonucleotides for sequencing a construct.

• Oligonucleotides can be created in the Workspace Pane of the Construct Editor
  • Select a portion of one or both strands of the final construct sequence at the top of the sequence display
    • The Tm of the selected sequence is automatically displayed
  • Select the “Annotate” button just above the annotation grid. You will be prompted to select a Tm annotation, an oligonucleotide or a general annotation. You can also name the annotations.
    • If the top strand of the final construct sequence is selected the oligonucleotide is created in the forward direction.
    • If the bottom strand is selected the oligonucleotide is created in the reverse direction.
    • If both strands are selected, both directions are created.

• Oligonucleotides suitable for sequencing can be created for a region of the construct selected by:
  • Selecting the icons for one or more elements within the Navigation Pane (Not yet working in beta version)
  • Highlighting a region of the sequence
    • by clicking on one end of the desired sequence and dragging to the other end of the selection
    • or by clicking on one end of the desired sequence, scrolling to the other end and clicking at the other end of the selection while holding down the shift key.
  • Select “Design Sequencing Oligos” from the “Tools” tab.
• You will then be able to choose between
  • The best oligo in the region in the forward or reverse direction
  • Single Strand Oligos for coverage of the region
  • Double Strand Oligos for coverage of the region
• You will also be asked to choose

• Approximate spacing between oligonucleotides.
• Direction desired.

• Maximum, minimum and optimal
  • Size
  • GC content
  • Tm

• Oligonucleotides can be named individually when created manually, or systematically when generating an oligonucleotide report.