Calculated Results
Results appear below the header and above the form after submission.
No calculation has been run yet. Enter your plasmid details below, then submit the form to generate molecular weight, copies, molarity, exports, and the graph.
Calculator Form
Example Data Table
| Example | Mode | Molecule | Length | GC % | Mass | Volume | Estimated MW | Copies |
|---|---|---|---|---|---|---|---|---|
| pUC19 style plasmid | Length | Double-Stranded DNA | 2686 bp | 50 | 100 ng | 50 µL | 1.7564 MDa | 3.43e10 |
| Medium cloning vector | Length | Double-Stranded DNA | 5000 bp | 52 | 250 ng | 100 µL | 3.2695 MDa | 4.60e10 |
| Large expression plasmid | Length | Double-Stranded DNA | 9200 bp | 60 | 500 ng | 200 µL | 6.0159 MDa | 5.01e10 |
Formula Used
Length mode equations
Approximate GC count:
GC count = length × (GC% / 100)
Approximate AT or AU count:
Remaining bases = length − GC count
Double-stranded DNA:
MW = (AT pairs × 653.4) + (GC pairs × 654.4) + topology correction
Single-stranded DNA:
MW = Σ(base count × residue mass) + topology correction
RNA:
MW = Σ(base count × residue mass) + topology correction
Derived outputs
Moles:
moles = mass in grams ÷ molecular weight
Copies:
copies = moles × 6.02214076 × 1023
nM concentration:
nM = (ng/µL × 1,000,000) ÷ molecular weight
Topology correction:
Linear molecules receive a small terminal mass correction. Circular molecules use zero terminal correction.
Sequence mode:
The calculator counts cleaned residues directly instead of estimating composition from GC percentage.
How to Use This Calculator
- Choose a calculation mode. Use length mode for quick estimates or sequence mode for direct residue counting.
- Select the molecule type and topology. Most plasmids are double-stranded and circular.
- Enter length and GC percentage for estimate mode, or paste the nucleic acid sequence for sequence mode.
- Enter sample mass in nanograms to calculate pmol, fmol, and estimated copy number.
- Add sample volume to obtain concentration in ng/µL and nM.
- Submit the form. The result panel above the form updates instantly on reload.
- Use the CSV button for spreadsheet export and the PDF button for a clean report.
- Review the Plotly graph to compare your plasmid against other nucleic acid lengths.
FAQs
1. Should plasmid length be entered in base pairs or nucleotides?
For double-stranded plasmids, enter base pairs. For single-stranded molecules or RNA, enter nucleotides. Sequence mode calculates length automatically from the cleaned sequence.
2. Which mode is better, length mode or sequence mode?
Sequence mode is better when you know the exact bases. Length mode is faster when you only have plasmid size and an estimated GC percentage.
3. Why does topology have only a tiny effect on mass?
Circular and linear topologies have almost identical mass. The calculator applies only a small terminal correction for linear molecules, which mainly affects theoretical precision.
4. Why does GC percentage matter?
GC percentage slightly changes the estimate because G and C are heavier than A and T or U. Sequence mode handles this directly.
5. What is the copy number output useful for?
Copy number helps with cloning plans, standards, and transformations. The calculator converts your entered mass into molecules using Avogadro’s constant and molecular weight.
6. Can I use the nM output for dilution planning?
Yes. The nM result uses entered mass and volume, so it is useful for dilution targets, reaction setup, and storage calculations.
7. What sequence characters are accepted?
The tool removes spaces and unsupported characters automatically. DNA mode keeps A, C, G, and T, while RNA mode keeps A, C, G, and U.
8. Are salts, dyes, or proteins included in the mass?
No. The estimate covers only the nucleic acid itself. Experimental salts, dyes, and bound proteins are excluded, so purified samples give the best match.