1. What is the Extinction Coefficient?

The extinction coefficient (EC) is a measure of how strongly a chemical species absorbs light at a given wavelength. For oligonucleotides, it's calculated as the sum of the extinction coefficients of individual bases.

2. How Does the Calculator Work?

The calculator uses the formula:

Where:

• \( EC \) — Total extinction coefficient
• \( \sum \text{(base EC)} \) — Sum of extinction coefficients of all bases in the sequence

Explanation: Each nucleotide base (A, T, G, C) has a specific extinction coefficient value that contributes to the total absorbance of the oligonucleotide.

3. Importance of Extinction Coefficient Calculation

Details: Accurate extinction coefficient calculation is crucial for determining oligonucleotide concentration using UV spectrophotometry, which is essential for various molecular biology applications.

4. Using the Calculator

Tips: Enter a valid DNA sequence containing only A, T, G, and C characters. The sequence will be converted to uppercase automatically.

5. Frequently Asked Questions (FAQ)

Q1: Why is extinction coefficient important for oligonucleotides?
A: It allows accurate concentration determination through UV absorbance measurements, which is critical for experiments requiring precise oligonucleotide quantities.

Q2: Are the extinction coefficient values constant?
A: While standard values are used, actual extinction coefficients can vary slightly depending on experimental conditions and sequence context.

Q3: Can this calculator handle modified bases?
A: This calculator uses standard A, T, G, C values. Modified bases require specific extinction coefficients that must be calculated separately.

Q4: How accurate is the nearest-neighbor method compared to this approach?
A: The nearest-neighbor method provides more accurate results as it accounts for base stacking effects, while this calculator uses a simple additive model.

Q5: What units are used for extinction coefficient?
A: Typically L/(mol·cm) or M⁻¹cm⁻¹, which represent the absorbance of a 1 M solution in a 1 cm pathlength cuvette.