ARIADNE
Under development
ARIADNE is being built to read a target locus, design candidate guide RNAs, and rank the targets worth pursuing.
One target in. An ordered shortlist out.
Name the target.
A gene, a locus, a variant. ARIADNE is designed to take the target from a curated record rather than from a paste buffer, so the run can always be traced back to the file it started from.
Target
Gene model, not to scale
TTRexon 2
- Locus
- chr18:31,592,900 · GRCh38
- Source
- THREAD · THR-4TQ8-KX2M-9.v3
Illustrative data, not a real result.
Score the candidates.
ARIADNE will generate candidate guide RNAs across the site and score each one, then order them by that score. The evidence behind a candidate is meant to travel with it, so a reviewer can disagree with the order.
Candidate guides
As found
- sg-018Two near-matches elsewhere in the genome
- sg-041No near-match under three mismatches
- sg-007Sits across the variant
- sg-052Clean flank, high-confidence PAM
- sg-029Repeat-adjacent; low confidence
Illustrative data, not a real result.
Return a shortlist.
What leaves ARIADNE is designed to be a short, ordered list of candidates with the reasoning attached — a starting point for human review, not a decision.
Prioritized
3 of 5 candidates
- sg-041Best-separated off-target profile in this set
- sg-052Second choice; different cut position
- sg-007Held for review: overlaps the variant
Illustrative data, not a real result.
A guide is only as good as where it lands.
With SpCas9, a guide RNA carries a 20-base spacer. It pairs with the strand opposite the one it matches, and only next to an NGG PAM. Many near-matching sites exist elsewhere in the genome, and telling them apart from the intended site is the problem ARIADNE is being built to address.
The spacer is the same 20 bases as the protospacer, so it pairs with the opposite strand. The NGG next to it — here TGG — is the PAM, and the spacer does not pair across it.
Illustrative data, not a real result.
- Spacer
- 5′-GACCAAGUGGCAUUGCUAGA-3′
- Protospacer and PAM
- 5′-GACCAAGTGGCATTGCTAGA TGG-3′
- Target strand
- 3′-CTGGTTCACCGTAACGATCTACC-5′
Software being built to design candidate guide RNAs for a named target and rank them for human review.
Under development
ARIADNE is under development.
There is nothing to sign up for yet. If you work on genome-informed therapy design and want to talk about what ARIADNE is being built to do, write to us.