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DNA Molecular Weight Calculator

The molecular weight of a DNA oligo is the mass of one mole of it, in g/mol (equivalently daltons). This calculator gives it two ways. With a sequence it sums the free-acid residue mass of every base — A 313.21, C 289.18, G 329.21, T 304.19 — and applies a −61.96 terminal correction for a 5′-OH strand; for a duplex it adds the mass of the reverse-complement strand separately, so a non-palindromic duplex is weighted correctly. With only a length it falls back to an average-composition estimate (~309 g/mol per nt, ~618 per bp). It also reports µg per nmol and nmol per µg so you can go straight from mass to moles without a second tool.

Every downstream calculation on a nucleic acid — how many nanomoles you have, how much to weigh out, what concentration a band represents — starts from the molecular weight. Yet most tools that give you a mass hand back a single number with no way to see where it came from, and they quietly disagree with each other because they use different conventions. This page is part of the DNA & RNA calculator set and it shows its working: the residue masses, the terminal correction and the choice of strand are all exposed so you can reproduce the number by hand.

There are two honest ways to estimate the mass of a DNA molecule and they answer different questions. The sequence method is exact for what you typed: it adds the mass each base contributes once it is incorporated into a strand and corrects for the two ends. The length method is for when all you know is the size — a 1,000 bp amplicon, a 5 kb plasmid fragment — and it multiplies the length by an average mass per base. The average is genuinely an average: a GC-rich fragment is heavier per base than an AT-rich one of the same length, so the length method carries a few percent of error that the sequence method does not.

A subtlety that trips people up is which chemical form the mass refers to. The residue masses used here are the free acid values — each deoxynucleotide monophosphate minus one water — and the −61.96 terminal correction gives an unphosphorylated 5′-OH strand, the form a standard desalted oligo arrives in. If you phosphorylate the 5′ end you add about 80 g/mol per strand. Some protocols instead quote ~330 g/mol per nucleotide and ~650 per base pair; those are the sodium-salt numbers, where each phosphate carries a counter-ion. Both conventions are defensible, but they differ by roughly 5%, so it matters which one your protocol assumes. The sequence method here is internally consistent with the ~618 Da per base pair that the free-acid residue masses imply.

Why does the mass matter beyond curiosity? Because it is the bridge between what a balance or a spectrophotometer measures (mass) and what a reaction actually cares about (moles). An oligo resuspended to 100 µM, a primer working stock, a molar concentration from an A260 reading — all of them need the molecular weight, which is why this tool pairs directly with the DNA concentration calculator and reports µg/nmol and nmol/µg right next to the mass. For the composition that drives the per-base average, see the GC content calculator.

A, C, G, T (a U is read as T). Spaces and digits are ignored. Leave blank to estimate from length instead.

Used only when the sequence box is empty — an average-composition estimate (~309 g/mol per nt, ~618 per bp).

Molecular weight5524.64 g/mol
Length18 nt
StrandednessSingle-stranded
MethodSequence
µg per nmol5.52464 µg/nmol
nmol per µg0.181007 nmol/µg
Base counts
BaseCount
A4
C5
G6
T3

How to use the dna molecular weight calculator

Paste your sequence into the DNA sequence box, 5′→3′. Only A, C, G and T are summed; a U (RNA primer) is read as T because their masses are close enough for this purpose and the tool says so when it does it. Spaces and the digit groupings some tools print are ignored.

Pick the Strandedness. Single-stranded reports the mass of the one strand you typed. Double-stranded derives the reverse complement and adds its mass too, so a non-palindromic duplex is not simply doubled — the two strands can have different compositions only in length-preserving ways, but the tool still sums each one explicitly.

Leave the sequence box empty and enter a Length instead to get the average-composition estimate. This is the right mode for a large fragment or plasmid where you know the size but not the exact bases; the result is flagged as an estimate.

Press Calculate. The primary card is the molecular weight in g/mol. The cards below give the length actually used, the base counts (sequence mode), µg per nmol, nmol per µg, and which method produced the number.

Carry the molecular weight into the DNA concentration calculator to turn an A260 reading into a molar concentration, or into the molarity calculator to work out how much to weigh or dilute for a target molarity.

DNA Molecular Weight formula

Sequence (ss): MW = Σ(n_base × M_base) − 61.96
Sequence (ds): MW = MW(sense) + MW(antisense)
Residue masses: A 313.21, C 289.18, G 329.21, T 304.19 g/mol
Length (ss): MW ≈ length × 308.95
Length (ds): MW ≈ length × 617.9
Conversions: µg/nmol = MW / 1000; nmol/µg = 1000 / MW
Each residue mass is the deoxynucleotide monophosphate minus one water (e.g. dAMP 331.22 − 18.02 = 313.21). The −61.96 terminal correction equals HPO₃ (79.98) − H₂O (18.02) and yields a 5′-OH free-acid strand. The length averages are the mean of the four residue masses (308.95) and twice that for a base pair (617.9), matching the ~618 Da/bp literature value.

Variables and units

SymbolMeaningUnit
MWMolecular weight of the strand or duplexg/mol
M_baseFree-acid residue mass of each nucleotideg/mol
n_baseCount of each base in the strand—
61.96Terminal correction for a 5′-OH free-acid strandg/mol
lengthNumber of nucleotides (ss) or base pairs (ds)nt / bp
µg/nmolMicrograms of oligo per nanomole (= MW / 1000)µg/nmol

How dna molecular weight is calculated

  1. Clean the sequence: uppercase it, drop spaces and digits, and read any U as T.
  2. Count each base (A, C, G, T). For a duplex, also derive the reverse complement and count its bases.
  3. Multiply each count by its residue mass and sum: A×313.21 + C×289.18 + G×329.21 + T×304.19.
  4. Subtract the 61.96 terminal correction once per strand. For a duplex, do this for the sense and the antisense strand and add the two results.
  5. If no sequence was given, instead multiply the length by 308.95 (ss) or 617.9 (ds) and flag the result as an average-composition estimate.
  6. Report µg/nmol = MW / 1000 and nmol/µg = 1000 / MW so the mass can be converted to moles immediately.

Worked laboratory examples

Example 1 — An 18-mer primer, single-stranded

Given: sequence 5′-GCGCATGCGCATACGTAG-3′ · base counts A 4, C 5, G 6, T 3 · strandedness ss

  1. Sum the residues: 4×313.21 + 5×289.18 + 6×329.21 + 3×304.19 = 1252.84 + 1445.90 + 1975.26 + 912.57 = 5586.57.
  2. Apply the terminal correction: 5586.57 − 61.96 = 5524.61.
  3. µg/nmol = 5524.61 / 1000 = 5.525; nmol/µg = 1000 / 5524.61 = 0.181.

Result: MW ≈ 5524.6 g/mol (5.52 µg/nmol)

Example 2 — A tiny duplex, checked by hand

Given: sequence ACGT · strandedness ds

  1. Sense strand: 313.21 + 289.18 + 329.21 + 304.19 = 1235.79, minus 61.96 = 1173.83.
  2. The reverse complement of ACGT is ACGT (a palindrome), so the antisense strand has the same mass, 1173.83.
  3. Duplex = 1173.83 + 1173.83 = 2347.66.

Result: MW(ds) ≈ 2347.7 g/mol — exactly twice the single strand

Example 3 — A 1,000 bp fragment from length only

Given: length 1000 bp · no sequence · strandedness ds

  1. Length method: 1000 × 617.9 = 617,900 g/mol.
  2. The sodium-salt convention would say 1000 × 650 = 650,000 — about 5% higher.
  3. Because the composition is unknown this is an estimate; a real 1 kb fragment lands within a few percent depending on its GC content.

Result: MW ≈ 6.18 × 10⁵ g/mol (free-acid estimate)

Example 4 — From mass to moles for a resuspension

Given: the 18-mer above, MW 5524.6 g/mol · you have 41.4 µg of dried oligo

  1. nmol/µg = 1000 / 5524.6 = 0.181 nmol per µg.
  2. Total = 41.4 µg × 0.181 = 7.5 nmol.
  3. To make a 100 µM stock: 7.5 nmol / 100 nmol·mL⁻¹ = 0.075 mL = 75 µL of water.

Result: 41.4 µg = 7.5 nmol → resuspend in 75 µL for 100 µM

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

How to interpret the result

The primary number is the mass of one mole of exactly what you described. In sequence mode it is as precise as the residue masses allow (a few hundredths of a percent); in length mode it is an average and should be read as "about this heavy". The method label on the card tells you which one you are looking at, so a downstream calculation never silently inherits an estimate it did not ask for.

µg/nmol and nmol/µg are the practical outputs. Most bench work is not "what is the mass" but "I have this many micrograms, how many nanomoles is that, and how much do I dilute to reach a molarity". Those two conversions are the whole point of knowing the molecular weight, which is why they sit beside it rather than in a separate tool.

The base counts are shown so a duplex result is auditable. If the two strands were summed independently you can see each composition; if you expected a palindrome and the counts say otherwise, the sequence you typed was not what you thought. This is the transparency the black-box converters do not give you.

When the number disagrees with a vendor tool, the usual culprit is convention, not arithmetic: free acid versus sodium salt, a 5′-OH versus a 5′-phosphate strand, or an average-composition estimate versus an exact sequence. This page states which it used so you can reconcile the two instead of guessing.

Assumptions

  • The strand is unmodified: no fluorescent labels, linkers, biotin, 5′ phosphates or backbone changes, all of which add mass.
  • The free-acid convention is used; residue masses are dNMP minus one water and the terminal correction gives a 5′-OH strand.
  • A duplex is the sequence plus its Watson-Crick reverse complement, fully base-paired with no overhangs.
  • In length mode the composition is average, so the result is an estimate rather than an exact mass.
  • A U in the input is read as T; the small mass difference (uracil lacks thymine’s methyl) is noted but not modelled.

Limitations

  • Modifications and labels are ignored — a 5′-phosphate adds ~80 g/mol per strand and a fluorophore adds several hundred.
  • The length method assumes average composition; GC-rich or AT-rich molecules deviate by a few percent.
  • The free-acid mass differs from the sodium-salt value (~650/bp) some protocols quote, by roughly 5%.
  • Single-stranded secondary structure, salts of crystallisation and residual water in a dried pellet are not modelled.

Common mistakes

  • Comparing a free-acid mass from this tool with a sodium-salt mass from a protocol and concluding one of them is wrong.
  • Using the length estimate for a short oligo, where the end correction is a large fraction of the total and the exact sequence should be used.
  • Forgetting that double-stranded means summing both strands, so a duplex is roughly twice the single-strand mass, not the same number.
  • Dividing by the wrong conversion — µg/nmol is MW/1000, not MW — and getting a resuspension volume out by a factor of a thousand.
  • Weighing out an oligo as if the dried pellet were pure anhydrous DNA; salts and water mean the actual mass of nucleic acid is lower.

FAQ

What is the average molecular weight of a DNA base pair?

About 618 daltons for the free acid (this tool uses 617.9), or roughly 650 daltons for the sodium salt that many protocols quote. Per single nucleotide that is about 309 or 330 g/mol respectively. The difference is the counter-ion on each phosphate.

Why does the calculator subtract 61.96?

That is the terminal correction for a 5′-OH strand. Summing "monophosphate minus water" for every base over-removes the ends; 61.96 = HPO₃ (79.98) − H₂O (18.02) puts back exactly the right end-group mass for an unphosphorylated oligo. A 5′-phosphorylated strand would instead add about 80 g/mol.

How do I convert micrograms of oligo to nanomoles?

Use nmol = µg × (1000 / MW). The tool reports nmol/µg directly. For the 18-mer in Example 1, 1000 / 5524.6 = 0.181 nmol per µg, so 41.4 µg is 7.5 nmol.

Does double-stranded DNA weigh exactly twice the single strand?

For a palindromic sequence yes, because both strands are identical in composition. In general the tool derives the reverse complement and sums it separately, which for a normal duplex gives very nearly twice the single-strand mass (the complement just swaps A↔T and C↔G).

Should I use the sequence or the length method?

Use the sequence method whenever you have the bases — it is exact for what you typed. Use the length method only for large fragments or plasmids where you know the size but not the sequence, and treat the result as an estimate.

Why does my number differ from a vendor calculator?

Almost always a convention difference: free acid versus sodium salt, 5′-OH versus 5′-phosphate, or an average-composition estimate versus an exact sequence. This tool states which it used, so you can line the two up rather than assume an error.

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