Does it check that my insertion keeps the reading frame?

Yes. Insertions and deletions are constrained to whole codons, and the tool states why a proposed length is rejected instead of producing a frameshifted primer.

Can it remove a restriction site without changing the protein?

Yes. Silent scrubbing searches for synonymous codon substitutions that destroy the recognition site and leave the encoded protein unchanged.

Cloning · experimental

Site-Directed Mutagenesis

Pick a coding sequence, state the change you want, and get the mutagenesis primers for it. The tool works on the CDS features already annotated on the sequence, so a residue change is expressed in codons rather than in raw offsets, and a frameshift is caught before you order anything.

Open Site-Directed Mutagenesis Open the Site-directed mutagenesis sample

Five real substrates — EGFP, pBR322, an unannotated pUC19, a TEV-tagged vector and a linear genomic CDS: design SOE/QuikChange primers, or scrub sites silently

What it does

01Point mutation by residue or by codon, in the frame and strand of the covering CDS
02Insertion and deletion design constrained to whole codons, so a partial codon cannot silently frameshift the downstream sequence
03Primer output in overlap-extension (SOE) and QuikChange style
04Silent scrubbing, which removes an internal restriction site without changing the encoded protein
05Primer map view marking which part of each primer is template-derived and which part is a 5-prime tail
06Selectable NCBI genetic code

What it runs on

Codon handling and the mutagenesis operations run on the headless engine in packages/ports, using the bundled codon tables rather than a hardcoded table. The panel runs on @ports/enzymes, @ports/mutagenesis, @ports/oligo-structure, @ports/variant-effect.

Everything runs client-side. Files are parsed in the browser and projects are saved on this machine, so an unpublished sequence is never uploaded.

Questions

Does it check that my insertion keeps the reading frame?: Yes. Insertions and deletions are constrained to whole codons, and the tool states why a proposed length is rejected instead of producing a frameshifted primer.
Can it remove a restriction site without changing the protein?: Yes. Silent scrubbing searches for synonymous codon substitutions that destroy the recognition site and leave the encoded protein unchanged.

Also searched as

site directed mutagenesis primer design · SDM primer design · QuikChange primer design online · point mutation primer designer · mutagenesis calculator · silent mutation restriction site removal · codon substitution tool · overlap extension primer design · QuikChange alternative · NEBaseChanger alternative · design mutagenesis primers online · introduce a point mutation into a plasmid · deletion and insertion primer design