1. What is Extinction Coefficient?

The extinction coefficient (ε) is a measure of how strongly a chemical species absorbs light at a particular wavelength. For oligonucleotides, it quantifies DNA/RNA concentration and purity.

2. How Does the Calculator Work?

The calculator uses the extinction coefficient formula:

Where:

• \( ε \) — Total extinction coefficient (M⁻¹ cm⁻¹)
• \( ε_{nucleotide} \) — Individual nucleotide coefficient
• \( length \) — Number of bases in sequence
• \( corrections \) — Additional correction factors

Explanation: The equation sums individual nucleotide contributions and applies corrections for accurate molar concentration calculations.

3. Importance of Extinction Coefficient

Details: Accurate extinction coefficient calculation is essential for determining oligonucleotide concentration, assessing purity, and ensuring proper experimental conditions in molecular biology applications.

4. Using the Calculator

Tips: Enter the oligonucleotide sequence (A, T, G, C, U), sequence length in bases, and any correction factors. The calculator will compute the total extinction coefficient.

5. Frequently Asked Questions (FAQ)

Q1: What are typical extinction coefficient values?
A: Values range from 50,000 to 500,000 M⁻¹ cm⁻¹ depending on sequence length and composition.

Q2: Why are correction factors needed?
A: Corrections account for sequence-specific effects, secondary structure, and experimental conditions that affect absorbance.

Q3: How is extinction coefficient used in practice?
A: Used with Beer-Lambert law (A = εcl) to calculate concentration from absorbance measurements.

Q4: Do different nucleotides have different coefficients?
A: Yes, each nucleotide has characteristic extinction coefficients at 260nm: A≈15,400, T≈8,800, G≈11,500, C≈7,400 M⁻¹ cm⁻¹.

Q5: Can this calculator handle modified nucleotides?
A: Standard calculator uses common nucleotides. Modified nucleotides require custom coefficient inputs as correction factors.