DNA Molecular Weight
Calculate the molecular weight of single- or double-stranded DNA sequences
Input Sequence

Paste a raw sequence or one or more FASTA sequences. Supported bases: G A T C and IUPAC degenerate codes (R Y S W K M B D H V N). Non-DNA characters are stripped automatically. Input limit: 200,000,000 characters.

💡 Quick Summary

DNA Molecular Weight accepts one or more DNA sequences and calculates their molecular weight in Daltons. Sequences can be treated as single- or double-stranded and as linear or circular molecules. Degenerate IUPAC bases (R, Y, N, etc.) produce a molecular weight range rather than a single value.

📋 How to Use
  1. Paste a raw DNA sequence or one or more FASTA sequences into the input area. Input limit is 200,000,000 characters.
  2. Choose Strand type: single-stranded or double-stranded.
  3. Choose Topology: linear or circular.
  4. Click Run. Each sequence reports its length, then its molecular weight (or weight range for degenerate sequences).
  5. Use the Copy button to copy all results to your clipboard.
  6. Click Load Example to try with three sample sequences including degenerate bases.
🧮 Formulas & Logic
Single-stranded linear MW
G×329.21 + A×313.21 + T×304.20 + C×289.18 + 17.01
Circular adjustment
Subtract 17.01 Da (one OH group removed on ligation)
Double-stranded
Forward strand MW + reverse complement strand MW
Degenerate range
Lower bound uses lightest possible base per ambiguity code; upper bound uses heaviest
📊 Result Interpretation
Sequences Processed

Number of FASTA records successfully processed.

Exact MW

Reported when all bases are unambiguous (G, A, T, C only).

MW range (X to Y Da)

Reported when the sequence contains degenerate IUPAC bases. The true MW lies within this range.

Single-stranded

Assumes a 5' monophosphate terminus. MW = sum of nucleotide residue weights + OH for the 3' end.

Circular

One OH group (17.01 Da) is subtracted per strand, representing the phosphodiester bond formed on circularisation.

🔬 Applications
  • Calculating the number of molecules (copy number) in a DNA sample of known mass
  • Estimating the mass of a PCR product or synthetic oligonucleotide
  • Checking the expected MW of a plasmid or linear construct before gel analysis
  • Determining the MW range for a degenerate primer pool or mixed sequence library
  • Teaching molecular weight calculations for nucleic acids
⚠️ Common Mistakes & Warnings
Non-DNA characters are stripped

Any character that is not a valid IUPAC DNA symbol (G A T C R Y S W K M B D H V N) is removed before calculation. U (uracil) is also stripped — for RNA use a dedicated RNA tool.

Degenerate bases produce a range

If your sequence contains ambiguity codes (e.g. N, R, Y), the tool cannot compute a single exact MW. Instead it reports the minimum and maximum possible weights based on the lightest and heaviest unambiguous substitutions.

Average vs. monoisotopic masses

The tool uses average atomic masses (the same values as the original SMS tool) rather than monoisotopic masses. Results match common molecular biology references for copy-number calculations.

❓ Frequently Asked Questions

Why does the tool use 17.01 for the OH constant?
A linear single-stranded DNA has a free 5' phosphate and a free 3' hydroxyl (OH). The formula accounts for the 3' OH by adding 17.01 Da (the weight of one water molecule minus the proton already in the phosphodiester backbone accounting). When the strand is circularised, that OH is removed as the 3' end forms a phosphodiester bond with the 5' end, so 17.01 Da is subtracted.
How is double-stranded MW calculated?
The tool calculates the MW of the forward strand and the MW of the reverse complement strand separately, then adds them together. For circular dsDNA, 17.01 Da is subtracted from each strand (2 × 17.01 total) before summing.
What IUPAC codes are supported?
The tool accepts all standard IUPAC degenerate DNA codes: R (A/G), Y (C/T), S (C/G), W (A/T), K (G/T), M (A/C), B (C/G/T), D (A/G/T), H (A/C/T), V (A/C/G), and N (any). U (uracil) is not supported.
Can I calculate copy number from this?
Yes. Copy number (molecules) = (mass in grams × Avogadro's number) ÷ MW in g/mol. For example, 1 µg of a 3,000 Da fragment ≈ (1×10⁻⁶ g × 6.022×10²³) ÷ 3000 ≈ 2×10¹⁴ molecules.
Can I process multiple sequences at once?
Yes. Paste any number of FASTA-formatted sequences. Each record is processed independently and its result is listed separately in the output.
DNA Molecular Weight — logic ported from the Sequence Manipulation Suite (Paul Stothard, University of Alberta).