What this does

A vrRNA recognises DNA with a noncontiguous code: it pairs with 2 bases, skips exactly 1, and repeats. All of the specificity sits in the NN dinucleotides of a repeating 5-nt scaffold — everything else is fixed backbone that must not be touched.

So designing a guide means copying every third-base-skipped dinucleotide out of your target, verbatim — no complement, no reversal — and dropping each one into its own unit. Paste a target below and this tool does that, then checks it against the published rules.

There is no PAM and either DNA strand works. The mechanism is transcriptional repression, not cutting. Full rules and the scaffold tables →

Target
 
Both strands silenced GFP in the published work, and there is no PAM — so this is a free choice.

Appears in every export.
Only used to report where the skipped bases fall. Natural targets put them on the wobble base — an observation, not a rule.
Reprogrammed guides repressed best at promoter-proximal positions.
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No design yet

Paste a target and press Design, or load one of the four published worked examples to see exactly what the tool produces.

Designed vrRNA
What is actually read

The vrRNA contacts the highlighted dinucleotides and never touches the dimmed bases between them. Changing a dimmed base does not affect targeting; inserting or deleting one shifts every downstream unit out of register.

Unit by unit

Each target triplet feeds one 5-nt unit. Hover a unit to highlight it everywhere on this page.

Where it sits

The chosen window in its surrounding sequence, read on the strand you selected.

Per-unit table
Batch design

Paste several targets — one per line, or as a multi-record FASTA. Each is designed independently at window 0 of the strand you choose. Records that are the wrong length are listed with the reason rather than skipped silently.