The oligo design tool takes as input two sequences that correspond to the two alleles to be screened (e.g., wild-type/unedited and SNP/edited versions of the genomic target sequence), with each including at least 35 bases on either side of the modification site (i.e., the site at which a researcher is seeking to engineer a single-nucleotide substitution using genome editing technology). The first nucleotide sequence input typically corresponds to the native or wild-type version of the genomic target sequence (i.e., the sequence before editing), while the second nucleotide sequence is identical to the first sequence, except that it includes a single-nucleotide substitution (i.e., the sequence after editing). Once the sequences have been input successfully, clicking the [Submit] button will initiate the oligo design process. The [Reset] button can be used to clear the inputs if needed. An example of this input is shown below:
Please note that the following conditions must be satisfied in order to use the tool successfully:
- Edited input sequences must include exactly one SNP.
- Both wild-type and edited input sequences must be the same length (e.g., if one is 512 bases, the other is also 512).
- Input sequence lengths cannot exceed 1,000 bases.
- Input sequences should consist of at least 35 bases on either side of the SNP site. For optimal probe design, we recommend including ≥50 bases on either side.
NOTE: Please be careful to avoid the inclusion of extra spaces when inputting sequences, as these will be interpreted as part of the input and will likely return an error message.