Extinction Coefficient Calculator Oligo

Extinction Coefficient Formula:

\[ \varepsilon_{260} = [\Sigma \varepsilon_{bases} + \Sigma \varepsilon_{mods}] \times 0.9 \]

Extinction Coefficient at 260 nm (ε_260):

Unit Converter ▲

Unit Converter ▼

From:	To:

1. What is the Extinction Coefficient?

The extinction coefficient (ε_260) is a measure of how strongly oligonucleotides absorb light at 260 nm wavelength. It is used to quantify DNA/RNA concentration and is essential for molecular biology applications including PCR, sequencing, and hybridization studies.

2. How Does the Calculator Work?

The calculator uses the extinction coefficient formula:

\[ \varepsilon_{260} = [\Sigma \varepsilon_{bases} + \Sigma \varepsilon_{mods}] \times 0.9 \]

Where:

\( \Sigma \varepsilon_{bases} \) — Sum of extinction coefficients for all nucleotide bases
\( \Sigma \varepsilon_{mods} \) — Sum of extinction coefficients for all modifications
0.9 — Hypochromicity correction factor accounting for base stacking effects

Explanation: The formula accounts for the fact that in double-stranded DNA or structured oligonucleotides, base stacking reduces the actual absorbance compared to the sum of individual base contributions.

3. Importance of Extinction Coefficient Calculation

Details: Accurate extinction coefficient calculation is crucial for determining oligonucleotide concentration, ensuring proper experimental conditions, and achieving reproducible results in molecular biology experiments.

4. Using the Calculator

Tips: Enter the sum of base extinction coefficients and sum of modification extinction coefficients in M⁻¹ cm⁻¹. Both values must be non-negative. The calculator automatically applies the 0.9 hypochromicity correction factor.

5. Frequently Asked Questions (FAQ)

Q1: What are typical extinction coefficient values for nucleotides?
A: Typical values are approximately: A=15,400, C=7,400, G=11,500, T=8,700 M⁻¹ cm⁻¹ at 260 nm.

Q2: Why is the 0.9 correction factor used?
A: The 0.9 factor accounts for hypochromicity - the reduction in absorbance due to base stacking interactions in oligonucleotides.

Q3: How do modifications affect extinction coefficients?
A: Chemical modifications like fluorescent dyes, biotin, or other tags have their own extinction coefficients that must be added to the base sum.

Q4: When should I use this calculation?
A: Use this for oligonucleotide quantification, primer preparation, and any application requiring accurate DNA/RNA concentration determination.

Q5: Are there limitations to this equation?
A: The 0.9 factor is an approximation; actual hypochromicity may vary with sequence composition, length, and secondary structure.