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Plasmid Molecular Weight Calculator

A plasmid is double-stranded DNA, so its average molecular weight is its length in base pairs times the mass of one base pair. On the convention used by cloning software (NEB, Promega) that is 660 g/mol per bp, giving MW = length × 660. For pUC19 at 2686 bp the molecular weight is 2686 × 660 = 1.77 × 10⁶ g/mol (1772.8 kDa). From that single number everything else in a cloning workflow follows: 0.564 pmol per µg, 1.77 µg per pmol, and 3.40 × 10¹¹ molecules per µg via Avogadro. This calculator bundles those conversions — plus mass-to-pmol and concentration-to-nM — in one place, which is what plain DNA molecular-weight tools leave out, and it points to the sequence-exact calculator when you need residue-level precision.

Plasmid molecular weight is the bridge between the mass you measure at the bench and the moles and molecules your cloning reactions actually care about. A spectrophotometer gives you ng/µL; a ligation needs a molar ratio; a transformation is reported per µg; copy number is per cell. Every one of those conversions runs through the plasmid's molecular weight. This page is part of the molecular cloning calculator set and keeps the whole chain together — length to MW to pmol/µg to molarity to molecules — instead of scattering it across separate tools.

The estimate is simple because DNA has a nearly uniform mass per base pair. Adding the average residue masses of the four nucleotides gives about 618 g/mol per bp on a free-acid basis, or about 660 g/mol per bp as the sodium salt, which is the convention the cloning tools use. Multiply by the plasmid length and you have the molecular weight. The two conventions differ by roughly 6%, so it is worth knowing which one a given protocol or tool assumes; this calculator uses 660 to match NEB and Promega and says so explicitly. For a sequence-exact mass that sums real residues rather than an average, the DNA molecular weight calculator uses the free-acid basis and is the right tool when composition matters.

Once you have the MW, the conversions are arithmetic. Moles = mass / MW, so pmol per µg = 10⁶ / MW and µg per pmol = MW / 10⁶. Molarity follows from a mass concentration: a concentration C in ng/µL is C × 10⁶ / MW in nM. And the number of molecules in a given mass comes from Avogadro's constant — molecules per µg = (10⁻⁶ g / MW) × 6.022 × 10²³. These are the numbers you feed into the ligation ratio calculator to balance insert against vector, and into the molarity calculator when a protocol specifies a molar target.

The other half of a plasmid MW question is copy number — how many plasmid molecules a cell carries. Copy number is set by the origin of replication (a high-copy pUC-type ori gives hundreds of copies per cell; a low-copy ori gives a handful) and by growth conditions, so it is a biological variable rather than a pure arithmetic one. What the MW gives you is the conversion that makes copy number computable at all: if you know the plasmid mass per cell, dividing by the single-molecule mass (MW / Avogadro) yields the copy number. This calculator provides molecules-per-µg so that step is one division away, and the guide works through a full copy-number example.

Total plasmid size in base pairs (pUC19 is 2686 bp). Preferred over a pasted sequence.

Optional. If no length is given, the bp count is taken from this sequence. For a sequence-exact mass use the DNA Molecular Weight calculator.

Recorded for context; the average mass-per-bp convention is the same for circular and linear dsDNA.

If given, converted to pmol using the plasmid MW.

If given, converted to nM and µM molarity.

Molecular weight1.773e+6 g/mol
Molecular weight1772.76 kDa
pmol per µg0.564092 pmol/µg
µg per pmol1.77276 µg/pmol
Molecules per µg3.397e+11 molecules/µg
Amount— pmol
Molarity— nM
  1. MW = length × 660 g/mol·bp = 2686 bp × 660 = 1.773e+6 g/mol (1772.76 kDa)
  2. pmol/µg = 1e6 / MW = 1e6 / 1.773e+6 = 0.564092 pmol/µg
  3. molecules/µg = (1e-6 g / 1.773e+6 g/mol) × 6.022e+23 = 3.397e+11 molecules/µg
  • Uses the ~660 g/mol·bp sodium-salt convention (NEB / Promega). The free-acid convention is ~617.9 g/mol·bp (~6% lower) — see the DNA Molecular Weight calculator for a sequence-exact mass.

How to use the plasmid molecular weight calculator

Enter the plasmid length in bp — the total size from your vector map, including the insert. pUC19 is 2686 bp; add your insert length to the backbone.

Alternatively, paste the sequence and leave the length blank; the bp count is taken from the sequence. (The MW still uses the 660/bp average — for a residue-exact mass use the DNA molecular weight calculator.)

Choose the topology. Circular is the default for an intact plasmid; linear only changes the label, since the average mass-per-bp is the same either way.

Optionally enter a mass in ng to get pmol, or a concentration in ng/µL to get nM and µM. Measure the concentration with the DNA concentration calculator first if you read it at A260.

Press Calculate. The primary card is the molecular weight in g/mol; the cards below give kDa, pmol/µg, µg/pmol, molecules/µg, and any pmol or molarity you asked for, with the derivation shown step by step.

Plasmid Molecular Weight formula

MW (g/mol) = length (bp) × 660 g/mol·bp
pmol/µg = 10⁶ / MW; µg/pmol = MW / 10⁶
pmol = mass (ng) × 10³ / MW
nM = conc (ng/µL) × 10⁶ / MW; µM = conc (ng/µL) × 10³ / MW
molecules/µg = (10⁻⁶ g / MW) × 6.02214076 × 10²³
660 g/mol·bp is the sodium-salt average used by NEB and Promega; the free-acid average is ~617.9 g/mol·bp (~6% lower). Copy number per cell = (plasmid mass per cell / MW) × Avogadro, once you know the mass per cell.

Variables and units

SymbolMeaningUnit
lengthTotal plasmid sizebp
MWMolecular weightg/mol
660Average sodium-salt mass per base pairg/mol·bp
NᴀAvogadro constantmol⁻¹
CMass concentrationng/µL

How plasmid molecular weight is calculated

  1. Get the total plasmid length in bp (backbone + insert).
  2. Multiply by 660 g/mol·bp to get the molecular weight.
  3. Convert: pmol/µg = 10⁶ / MW, and molecules/µg via Avogadro.
  4. If a mass is given, pmol = mass(ng) × 10³ / MW.
  5. If a concentration is given, nM = conc(ng/µL) × 10⁶ / MW.
  6. Carry the MW into ligation ratios, molarity targets and copy-number work.

Worked laboratory examples

Example 1 — pUC19 (2686 bp)

Given: length 2686 bp · circular

  1. MW = 2686 × 660 = 1,772,760 g/mol = 1.77 × 10⁶ g/mol (1772.8 kDa).
  2. pmol/µg = 10⁶ / 1,772,760 = 0.564 pmol/µg.
  3. molecules/µg = (10⁻⁶ / 1,772,760) × 6.022 × 10²³ = 3.40 × 10¹¹.

Result: 1.77 × 10⁶ g/mol; 0.564 pmol/µg; 3.40 × 10¹¹ molecules/µg

Example 2 — Mass to pmol

Given: a 2686 bp plasmid · 100 ng of it

  1. MW = 1.77276 × 10⁶ g/mol.
  2. pmol = 100 ng × 10³ / 1.77276 × 10⁶ = 0.0564 pmol.
  3. So 100 ng of pUC19 is about 56 fmol — the scale a ligation works at.

Result: 0.0564 pmol (56.4 fmol)

Example 3 — Concentration to molarity

Given: a 2686 bp plasmid at 50 ng/µL

  1. nM = 50 × 10⁶ / 1.77276 × 10⁶ = 28.2 nM.
  2. µM = 50 × 10³ / 1.77276 × 10⁶ = 0.0282 µM.
  3. A 50 ng/µL plasmid prep is therefore ~28 nM.

Result: 28.2 nM (0.0282 µM)

Example 4 — A larger 5000 bp construct

Given: length 5000 bp

  1. MW = 5000 × 660 = 3.3 × 10⁶ g/mol (3300 kDa).
  2. pmol/µg = 10⁶ / 3.3 × 10⁶ = 0.303 pmol/µg.
  3. A bigger plasmid has fewer pmol per µg, so the same mass delivers fewer molecules.

Result: 3.3 × 10⁶ g/mol; 0.303 pmol/µg

Want the reasoning behind the numbers? Read How to Calculate Plasmid Molecular Weight.

How to interpret the result

The molecular weight in g/mol (or Da, numerically the same) is the master number; kDa is just it divided by 1000 for readability. Everything else — pmol/µg, molarity, molecules — derives from it, so if the MW is right the rest follows.

pmol/µg and µg/pmol are the two directions you need at the bench: pmol/µg tells you how many picomoles are in a microgram of your prep, and µg/pmol tells you how much mass to weigh out for a molar target. Feed these into the ligation ratio calculator to set an insert:vector ratio by moles.

Molecules/µg is what connects a mass to a count. Divide the plasmid mass per cell by the single-molecule mass (MW / Avogadro, the reciprocal of molecules/µg scaled to grams) to get copy number per cell — a high-copy ori lands in the hundreds, a low-copy ori in the single digits.

Remember the convention. If a protocol or another tool quotes a molecular weight about 6% lower than this one, it is using the free-acid ~618/bp basis rather than 660. Neither is wrong; just be consistent within a calculation, and use the DNA molecular weight calculator when you need the sequence-exact value.

Assumptions

  • The plasmid is ordinary double-stranded DNA of average base composition.
  • The 660 g/mol·bp sodium-salt average applies; GC-rich or AT-rich plasmids deviate slightly.
  • The length entered is the full plasmid size including any insert and tags.
  • Conversions assume the mass or concentration entered refers to intact plasmid, not degraded or nicked DNA.

Limitations

  • It is an average-composition estimate, not a residue-exact mass — use the sequence-based DNA MW calculator for precision.
  • The 660 vs ~618 convention difference (~6%) means values are not directly comparable across tools that assume different bases.
  • Copy number per cell is biological (ori, strain, growth phase) and needs a mass-per-cell input this tool does not assume.
  • Modifications, labels or unusual bases are not accounted for in the average mass.

Common mistakes

  • Using the backbone size and forgetting to add the insert length.
  • Mixing the 660 and 618 conventions within one calculation and getting a 6% discrepancy.
  • Confusing g/mol with Da (numerically equal) or with kDa (divide by 1000).
  • Treating copy number as a fixed arithmetic output rather than an ori- and condition-dependent variable.
  • Entering a concentration in ng/µL where a mass in ng is expected, or vice versa.

FAQ

Why 660 g/mol per base pair and not 618?

Both are correct under different conventions. 660 g/mol·bp is the average mass of a base pair as a sodium salt, the convention NEB and Promega cloning tools use; ~618 g/mol·bp is the free-acid average from summing anhydrous nucleotide residue masses. They differ by about 6%. This calculator uses 660 to match cloning software and flags the difference so you can convert if a protocol assumes the other.

How do I get the plasmid length?

Add the backbone size from your vector map to the length of your insert. For pUC19 the backbone is 2686 bp; a 1000 bp insert makes a 3686 bp plasmid. If you have the full sequence, paste it here and the bp count is taken from it, or use the DNA molecular weight calculator for a sequence-exact mass.

How do I convert plasmid mass to pmol?

pmol = mass(ng) × 1000 / MW(g/mol). For 100 ng of a 2686 bp plasmid (MW 1.77 × 10⁶), that is 100 × 1000 / 1.77 × 10⁶ = 0.0564 pmol. The calculator does this whenever you enter a mass, and reports pmol/µg so you can scale to any amount.

What is plasmid copy number and how is it calculated?

Copy number is how many plasmid molecules a single cell carries, set mainly by the origin of replication — high-copy pUC-type origins give hundreds per cell, low-copy origins give a handful. To calculate it you need the plasmid mass per cell: copy number = (mass per cell / MW) × Avogadro. The molecules-per-µg output here is the conversion that makes that one division.

Does circular versus linear change the molecular weight?

Not on the average mass-per-bp convention — a circular and a linear molecule of the same length have the same average MW. The topology selector is recorded for context. A true sequence-exact mass differs only by the small terminal-group correction, which the DNA molecular weight calculator handles.

How is this different from the DNA molecular weight calculator?

The DNA molecular weight calculator computes a residue-exact mass from a sequence on the free-acid basis, aimed at oligos and precise work. This calculator is length-based on the 660 cloning convention and bundles the downstream conversions plasmid work needs — pmol/µg, molarity, molecules and the copy-number path — so it is the cloning-workflow tool rather than the sequence-precision tool.

Scientific Sources

External links open in a new tab and carry rel="nofollow". We cite primary references (NIST, NIH/NCBI, peer-reviewed papers) and established manufacturer technical documentation (NEB, Thermo Fisher, Promega, IDT). Calculated results are estimates; your protocol and manufacturer guidance take precedence.

Last reviewed: 2026-09 · Method version: 1.0