Base and Prime Editing: Changing DNA Without a Planned Double-Strand Break · seed 1 · A4, ink-friendly. The answer key prints on its own page for grown-ups.
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Editing without a planned double-strand break

Science · Genetics & Evolution · ages 22-24
Name ______________________   Date ____________

  1. A CBE window spans positions 6 to 9. The target C is at position 6 and another C is at position 8. Why is a bystander edit possible?

    • Only the intended C can be reached inside this editing window.
    • Both C bases lie within positions where the editor can act.
    • Every C across the chromosome lies inside this editing window.

  2. A conventional cytosine deaminase base editor acts on a C in its window. What is the intended conversion on that strand?

    • C to T
    • C to A
    • C to G

  3. In prime editing, reverse transcriptase copies an editing template carried on the extended guide RNA into DNA.

    Circle one:   True   False

  4. An ABE window contains a target A and an unwanted neighbouring A. A second guide meets the required motif and keeps only the target A in its window. Which plan best reduces this bystander risk?

    • Keep the current guide and assume the neighbouring A cannot change.
    • Use a nuclease cut without a donor and assume it specifies the A to G change.
    • Test the second guide, whose window excludes the neighbouring A.

  5. You need C to A on the stated strand. Which tool can specify that substitution, if a workable target design is available?

    • A conventional cytosine editor using its C to T conversion.
    • A conventional adenine editor using its A to G conversion.
    • A prime editor with a template specifying C to A.

  6. A single-base replacement is requested at one locus. Which observation is an off-target DNA edit?

    • An unintended neighbouring C change at the intended locus.
    • A base changes at a different, unintended genomic site.
    • An unintended insertion at the intended nuclease-cut locus.

  7. A nuclease cut alone, with no donor or edit-writing machinery, reliably specifies a requested single-letter replacement.

    Circle one:   True   False

  8. Endpoint sequencing detects only the original base after a base-editing experiment. Which conclusion is justified from this endpoint alone?

    • No intended edit was detected; its absence has several possible causes.
    • The intended edit never formed, so repair had no role in this experiment.
    • The edit formed and repair erased it; this endpoint proves that sequence of events.
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Answer key

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Editing without a planned double-strand break W1-mt_roM4eWoWVn-s1

  1. Both C bases lie within positions where the editor can act. · Both C bases are inside the stated window. The editor may convert the neighbouring C as well as the target C.
  2. C to T · A conventional CBE aims for C to T on the edited strand. This is its intended conversion, not a guarantee of successful editing.
  3. True · The extended guide RNA carries the template. Reverse transcriptase copies it into an edited DNA segment.
  4. Test the second guide, whose window excludes the neighbouring A. · The supplied second guide is feasible and excludes the neighbouring A from its window. That reduces this bystander opportunity; the result still needs testing.
  5. A prime editor with a template specifying C to A. · C to A is outside the conventional CBE and ABE menus. A prime-editing template can specify it, although efficiency must be tested.
  6. A base changes at a different, unintended genomic site. · The change at another genomic site is off-target. The neighbouring C change and insertion are unintended here, but occur at the intended locus. An indel could be wanted in another experiment.
  7. False · A cut alone does not encode a replacement letter. Repair can restore the sequence or produce varied changes. Donor-assisted precise editing is a different design.
  8. No intended edit was detected; its absence has several possible causes. · The endpoint cannot distinguish failed delivery, low editing activity, repair reversal or an edited fraction below the detection limit.
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