BioDeviceHub

Plasmid Size Calculator

Calculate the size of a recombinant plasmid from the vector backbone, the sequence removed, the insert and any added bases, with its molecular weight.

Formula

L=Lvector−Lremoved+Linsert+LextraL = L_{\text{vector}} - L_{\text{removed}} + L_{\text{insert}} + L_{\text{extra}}
MW=L×650 g/mol per bp\mathrm{MW} = L \times 650\ \mathrm{g/mol\ per\ bp}
removed\text{removed}
the stretch cut out of the vector, for example between two restriction sites
extra\text{extra}
bases added by linkers, scars or tags

How it works

Cloning replaces part of a vector with an insert, so the new plasmid is the vector, less what was removed, plus what was added. Knowing the expected size lets you check a diagnostic digest or colony PCR, plan a ligation and calculate the amount of DNA in moles.

The molecular weight follows from the size at 650 g/mol per base pair, which can be used with the molarity and copy-number tools.

Worked example

A 2,686 bp vector with a 57 bp stretch removed and a 1,200 bp insert added.

  1. 2,686 − 57 + 1,200 + 0 = 3,829 bp.

The recombinant plasmid is 3,829 bp (3.829 kb), about 2.49 × 10⁶ g/mol.

These are the values the calculator opens with, so you can check its output against this example.

Assumptions

  • The lengths are counted consistently, for example as the top strand between cut positions.
  • Filled-in or trimmed ends are included in the numbers you enter.

Common mistakes

  • Counting the whole cloning-site region as removed when the enzymes cut only part of it.
  • Omitting a few bases of linker or scar that remain after assembly.
  • Relying on the predicted size instead of the sequence of the actual clone.

Related tools

Ligation Calculator (Vector:Insert Ratio)Insert mass for a molar ratio, or the ratio from the masses you haveOpen calculatorRestriction Digest PredictorFragment sizes for a single or multiple enzyme digestOpen calculatorDNA and RNA Molarity CalculatorConvert ng/µL to nM, pmol per µg and molecules per µLOpen calculatorDNA Copy Number CalculatorNumber of copies in a mass of plasmid, amplicon or genomeOpen calculator

Related equipment

Service documentation, failure modes and parts for the instruments this calculation is used with.