AkCalculators

DNA base pairs: physical length, molecular weight, copy number and practical notes

This tool helps convert DNA base pairs into physical lengths and molecular masses, compute moles and copy numbers, and provides quick sequence statistics like GC percentage. It is designed for bench biologists, students and bioengineers who need fast, reliable conversions for cloning, PCR and quantitation.

1. Rise per base pair and assumptions

B-form double-stranded DNA (the common conformation under physiological conditions) has a rise per base pair of approximately 0.34 nm (3.4 Å) and ~10.5 bp per helical turn. These are average values — local sequence, supercoiling, and binding proteins can alter local geometry. The calculator uses 0.34 nm/bp by default but you can override it in Custom Parameters.

2. Molar mass per base pair

The average molar mass per base pair for double-stranded DNA is commonly approximated as 660 g·mol⁻¹ per bp. This average accounts for the four nucleotides plus the sugar-phosphate backbone. For single-stranded DNA or precise mass calculations (when exact sequence composition is known), compute nucleotide-level masses instead — the sequence tab provides a coarse estimate using 660 g·mol⁻¹ per bp.

3. Copy number, Avogadro and mass conversions

Given a DNA length (bp) and mass (e.g., ng), you can compute the number of molecules (copies) using:

copies = (mass (g) / molar_mass (g·mol⁻¹)) × N_A

where N_A = Avogadro's number = 6.02214076×10²³ mol⁻¹. The calculator handles unit conversions (ng, µg, mg, g) automatically.

4. Worked examples

Example 1 — plasmid length: A 3000 bp plasmid has physical length ≈ 3000 × 0.34 nm = 1020 nm = 1.02 µm — useful for visualisation or gel expectations.

Example 2 — copy number: A 5000 bp PCR product with mass 10 ng — molar mass ≈ 5000 × 660 g·mol⁻¹ = 3.30×10⁶ g·mol⁻¹. Number of moles in 10 ng = 1e-8 g / 3.30×10⁶ g·mol⁻¹ ≈ 3.03×10⁻¹⁵ mol. Copies ≈ 3.03×10⁻¹⁵ × 6.022×10²³ ≈ 1.82×10⁹ molecules.

5. Sequence-based mass & GC%

Pasting a sequence provides exact bp count and GC percentage. For more accurate mass per mole use sequence-specific nucleotide masses (A/T/G/C) if available — this tool uses the average 660 g·mol⁻¹ per bp for quick estimates.

6. Practical tips

• For molar calculations and qPCR standards, be explicit about whether your DNA is double-stranded or single-stranded; single-stranded DNA molar mass per nucleotide is lower.
• When preparing standards, account for salt and buffer mass if measuring by weight — purified DNA mass may include residual salts/contaminants.
• Use spectrophotometric (A260) or fluorometric (PicoGreen) quantitation depending on sensitivity and contaminants.

7. Precision and rounding

The calculator performs conversions in double precision internally; choose display precision for reporting. For low-copy-number work, keep more significant digits in intermediate steps to avoid rounding error.

8. Limitations

Average approximations (0.34 nm/bp, 660 g·mol⁻¹ per bp) are convenient but not exact. When analyzing oligonucleotides or exact plasmid sequences for quantitative work, use sequence-specific monoisotopic masses or the exact nucleotide composition.

9. Summary

Use this tool to quickly convert between bp and length, compute masses and copy numbers, and get fast sequence stats. Toggle custom parameters if you need different assumptions, and export CSV for lab records.