Biology and life-science lab
DNA, RNA and protein molecular weight calculator
Molecular weight of DNA, RNA and protein sequences from atomic weights, with nearest-neighbour ε260 for oligos and ε280 for proteins (Pace 1995).
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Result
- Molecular weight
- 5228.47 g/mol
- Length
- 17 nt
- ε260 (nearest-neighbour)
- 172500 M⁻¹ cm⁻¹
- GC content
- 52.9 %
- nmol per A260 unit
- 5.797
- µg per A260 unit
- 30.31
Working
- M = Σ residues + H₂O − HPO₃ (5′-OH, 3′-OH) = 5228.47 g/mol
- ε260 = Σ ε(pairs) − Σ ε(internal bases) = 172500 M⁻¹ cm⁻¹
- One A260 unit is the amount that gives A260 = 1 in 1 mL with a 1 cm path: n = 10⁶ ÷ ε nmol.
- Single strand with a 5′-OH end and 3′-OH, as the free acid (sodium or other counter-ions not included). Synthetic oligos usually have 5′-OH; in-vitro transcripts have a 5′-triphosphate.
- The nearest-neighbour ε260 applies to single strands at neutral pH and room temperature; modified bases and dyes add their own absorbance.
Method and limits
Paste a sequence and choose its type. Results update as you type; very long sequences (up to 100 000 letters) work too.
Molecular weight
M(strand) = Σ residue masses + H₂O − HPO₃ (5′-OH) or + 0 (5′-phosphate) or + 2 HPO₃ (5′-triphosphate)
Each residue is a nucleotide monophosphate minus water (dAMP − H₂O = C₁₀H₁₂N₅O₅P, 313.21 g/mol) or an amino acid minus water, weighed with the CIAAW 2024 atomic weights. This reproduces the familiar oligo formula M = 313.21 nA + 304.20 nT + 289.18 nC + 329.21 nG − 61.96 for a 5′-OH strand. Proteins add one water for the free termini; the mass is the average (not monoisotopic) mass of the unmodified chain.
Extinction coefficients
ε260 = Σ ε(nearest-neighbour pairs) − Σ ε(internal bases) 1 A260 unit = 10⁶ ÷ ε nmol
For single strands the nearest-neighbour method (Cantor, Warshaw and Shapiro 1970) sums the 16 dinucleotide values and subtracts the bases counted twice; it captures base stacking that a simple sum of bases misses.
ε280 = 5500 nTrp + 1490 nTyr + 125 n(cystine) (M⁻¹ cm⁻¹, Pace et al. 1995)
Two values are given for proteins: with every pair of cysteines joined as a cystine, and with all cysteines reduced. A280 of a 1 g/L solution = ε280 ÷ M.
Limits
- Masses are for the free acid; oligos are usually sodium salts (add about 22 g/mol per phosphate) and may carry dyes or modifications.
- Duplex DNA absorbs less than its two strands (hypochromicity), so no ε260 is given for double strands; A260 = 1 is about 50 µg/mL of dsDNA, 33 µg/mL of ssDNA and 40 µg/mL of RNA.
- Protein ε280 from sequence is typically within about 5 % of measured values for proteins with tryptophans; post-translational modifications are not included. Degenerate bases (N, R, Y) are not accepted.
Worked example
5′-ACGT-3′ (5′-OH): M = 313.21 + 289.18 + 329.21 + 304.20 − 61.96 = 1173.84 g/mol (1173.83 with these atomic weights); ε260 = ε(AC) + ε(CG) + ε(GT) − ε(C) − ε(G) = 21 200 + 18 000 + 20 000 − 7400 − 11 500 = 40 300 M⁻¹ cm⁻¹, so one A260 unit is 24.8 nmol or 29.1 µg.
References
- Cantor, Warshaw and Shapiro, Oligonucleotide interactions III: circular dichroism studies of the conformation of deoxyoligonucleotides, Biopolymers 9, 1059–1077 (1970)
- Pace, Vajdos, Fee, Grimsley and Gray, How to measure and predict the molar absorption coefficient of a protein, Protein Sci. 4, 2411–2423 (1995)
- CIAAW, Abridged standard atomic weights (2024 table, five significant figures)
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