Primers & oligos

Site-directed mutagenesis designer

Design site-directed mutagenesis primers (QuikChange overlapping or Q5 back-to-back) for a base substitution, an amino-acid codon swap, or an insertion/deletion/delins. The edit can be given as fields or, more simply, by NAME in mutation: "E52K", "p.Glu52Lys", "c.155A>G", "c.76_78del", "c.76_77insGGA", "c.76_78dup". A named mutation is checked against the template — if the reference allele it states is not what is actually at that position, the call is refused and the real base or residue is quoted back, because a coordinate belonging to a different transcript or the other strand yields perfectly well-formed primers for the wrong base. interpretedAs in the response says which reading was designed.

post/site_directed_mutagenesis

Request

  • Base URL: https://seqbench.com/api/v1
  • URL: https://seqbench.com/api/v1/site_directed_mutagenesis
  • Auth: none required

Request body

templatestring required

Nucleotide sequence (raw or FASTA; IUPAC accepted).

mutationstring

The edit by name — "E52K", "p.Glu52Lys", "Q100*", "c.155A>G", "A155G", "c.76_78del", "c.76_77insGGA", "c.76_78dup", "c.76delinsAA". Replaces the field-by-field forms below. An unprefixed "A123G" is a legal reading at BOTH levels; it is resolved by which one matches the template, and refused if both do.

editKind'nt' | 'aa' | 'delins'

Edit level. Normally omitted — it is inferred from the fields you send (newBase means nt, targetAa means aa, insert/deleteLength means delins).

style'quikchange' | 'q5'

Mutagenic primer style.

armTmTargetnumber

Target Tm (°C) for each template-binding arm.

positioninteger

1-based position to substitute (nt), or the first base of the span to replace (delins). Required for those forms — it is never assumed. For a pure insertion (deleteLength 0) it is the base the insert goes in FRONT of.

newBase'A' | 'C' | 'G' | 'T'

Replacement base (nt edit).

deleteLengthinteger

Template bases to remove, starting at position (delins edit). 0 with insert set is a pure insertion, placed immediately before position.

insertstring

Bases to put in place of the deleted span (delins edit). Omit for a pure deletion. NOTE the convention when deleteLength is 0: the insert lands immediately BEFORE position, so position 101 + insert "GGA" is the same edit as mutation: "c.100_101insGGA" — HGVS names the two flanking bases, this names the base the insert sits in front of. interpretedAs states which bases the insert ended up between.

frameStartinteger

1-based position of the first base of codon 1. Needed whenever the coding sequence does not start at base 1 of the template — a residue number means nothing without it.

residueinteger

1-based residue number to change (aa edit).

targetAastring

Target amino acid, one-letter code incl '*' (aa edit).

organism'ecoli' | 'human' | 'yeast' | 'cho' | 'pichia' | 'insect' | 'arabidopsis' | 'zebrafish'

Codon-usage table for choosing the new codon (aa edit). Latin names and common strain/cell-line names are accepted.

oligoNMnumber

Total strand concentration (nM).

naMMnumber

Monovalent cation [Na+]/[K+] (mM).

mgMMnumber

Divalent cation [Mg2+] (mM).

dntpMMnumber

Total [dNTP] (mM), chelates Mg2+.

Response

Tool ran successfully.

okunknown required
toolstring required

The tool slug that ran.

resultobject required

Tool-specific output object. Its shape depends on the tool — call GET /{tool} or see the docs for each tool's fields.

Example response

{
  "provenance": {
    "apiVersion": "1.1.0"
  }
}

Changes

No recorded changes to this operation across all 1 revision of this API.