DNA and RNA: ng ↔ pmol, A260 quantification, Tm and copy number
Mass, moles, molecules and melting temperature for double-stranded DNA, single strands, RNA and synthetic oligonucleotides.
Mass ↔ moles for DNA and RNA ng ↔ pmol
Enter the length and either the mass or the amount. Molecular weight is estimated from average nucleotide masses (sodium salt).
Concentration from A₂₆₀
An A₂₆₀ of 1.00 at a 1 cm path length corresponds to 50 µg/mL dsDNA, 33 µg/mL ssDNA or oligo, and 40 µg/mL RNA.
Oligonucleotide: MW, Tm and resuspension
Paste a primer or probe sequence. Molecular weight is calculated from the actual base composition, not an average.
| Property | Value |
|---|
Plasmid / amplicon copy number qPCR standards
Convert a mass of double-stranded DNA into a molecule count, and plan a standard curve.
| Standard | Copies / reaction | Concentration |
|---|
Constants used here
| Quantity | Value | Note |
|---|---|---|
| Average MW per bp, dsDNA | 617.96 g/mol | sodium salt; + 36.04 for the two 5′-OH ends |
| Average MW per nt, ssDNA | 303.7 g/mol | − 61.96 for a 5′-OH oligo |
| Average MW per nt, RNA | 320.5 g/mol | − 61.96 for a 5′-OH transcript |
| A₂₆₀ = 1.0, dsDNA | 50 µg/mL | 1 cm path |
| A₂₆₀ = 1.0, ssDNA / oligo | 33 µg/mL | hyperchromicity of the single strand |
| A₂₆₀ = 1.0, RNA | 40 µg/mL | 1 cm path |
| 1 kb of dsDNA | 6.5 × 10⁵ g/mol | useful mental shortcut |
| 1 µg of 1 kb dsDNA | 1.52 pmol | = 9.1 × 10¹¹ molecules |
Purity ratios
- A₂₆₀/A₂₈₀ ≈ 1.8 for DNA, ≈ 2.0 for RNA. Lower means protein or phenol; higher usually means RNA contamination of a DNA prep.
- A₂₆₀/A₂₃₀ = 2.0–2.2. A low value points to guanidine, chaotropic salts, phenol or carbohydrate carryover — all common after column or Trizol preps.
- Ratios are pH- and ionic-strength-dependent. Blank against the same buffer you eluted into, not water.
Which Tm formula to trust
The nearest-neighbour thermodynamic model (SantaLucia) is the accurate one and depends on the full sequence, salt and strand concentration. The two formulas here are the classic approximations:
- Wallace rule —
Tm = 2(A+T) + 4(G+C). Only sensible below about 14 nt, and only at ~1 M salt. - GC/salt formula — reasonable for 14–70 nt oligos in standard PCR salt. Still typically ±3 °C against measured values.
For primer design, use both as a sanity check and set annealing temperatures around 3–5 °C below the lower estimate, then optimise empirically with a gradient.
Genome and vector sizes for reference
| Genome / vector | Size | Mass per haploid copy |
|---|---|---|
| pUC19 | 2 686 bp | 2.76 ag |
| Lambda phage | 48 502 bp | 49.7 ag |
| E. coli K-12 | 4.64 Mbp | 4.76 fg |
| S. cerevisiae | 12.1 Mbp | 12.4 fg |
| D. melanogaster | 180 Mbp | 185 fg |
| Human (haploid) | 3.1 Gbp | 3.18 pg |
Frequently asked questions
How do I convert ng of DNA to pmol?
pmol = ng × 1000 / (bp × 617.96) for double-stranded DNA. 100 ng of a 3000 bp fragment is 100 × 1000 / (3000 × 617.96) = 0.054 pmol = 54 fmol.
What does an A260 of 1.0 correspond to?
For a 1 cm path length: 50 µg/mL double-stranded DNA, 33 µg/mL single-stranded DNA or oligonucleotide, and 40 µg/mL RNA.
What A260/A280 ratio indicates pure nucleic acid?
About 1.8 for DNA and 2.0 for RNA. Lower values suggest protein or phenol carryover; the A260/A230 ratio should also be roughly 2.0–2.2.
How do I calculate plasmid copy number for a qPCR standard curve?
copies = (mass in g × 6.022 × 10²³) / (plasmid length in bp × 617.96 g/mol). One nanogram of a 5000 bp plasmid contains about 1.95 × 10⁸ copies.