HpaI
GTT▾AACBlunt
HpaI is a 6 bp-recognition restriction enzyme. It runs best in rCutSmart at 37°C, and is prone to star activity under non-standard conditions.
NEB buffer activity
| Buffer | % Activity |
|---|---|
| rNEBuffer 1.1 | 0% |
| rNEBuffer 2.1 | 75% |
| rNEBuffer 3.1 | 25% |
| rCutSmartbest | 100% |
- Incubation
- 37°C
- Heat inactivation
- Not inactivable
- Star activity
- Yes
- Methylation blocked
- CpG
GTTAAC. Not heat-inactivable. NEB reports CpG blocking for some combinations of overlapping methylation. Some star propensity.
Find HpaI sites in your own sequence
Paste a sequence below and this scans it for every HpaI recognition site — the same engine behind the full Restriction Sites tool, scoped to just this one enzyme.
Enzymes with ends compatible with HpaI
HpaI leaves blunt ends. Of the other 48 enzymes in the restriction enzyme table, these 10 leave an end that can be ligated to a HpaI end:
Frequently asked questions
What does HpaI recognize?
HpaI recognizes the 6 bp sequence GTTAAC (5′→3′), cutting the top strand between position 3 and 4 within the site to leave a blunt.
What buffer should I use for HpaI?
rCutSmart gives the highest activity (incubate at 37°C).
Does HpaI have star activity?
Yes — under non-standard conditions (excess enzyme/glycerol, long incubation, low ionic strength) it can cleave at sites resembling but not matching GTTAAC.
Is HpaI blocked by DNA methylation?
Yes — blocked by CpG methylation. Use methylation-free template (e.g. a dam⁻/dcm⁻ strain) if this matters for your digest.
Can I heat-inactivate HpaI?
No — HpaI is not heat-inactivable. Use a column cleanup or phenol-chloroform extraction to stop the reaction instead.