1. What is Molar Extinction Coefficient?

The molar extinction coefficient (ε) is a measure of how strongly a chemical species absorbs light at a given wavelength. For DNA, it quantifies absorption at 260 nm and is essential for nucleic acid quantification and purity assessment.

2. How Does the Calculator Work?

The calculator uses the nearest-neighbor method for single-stranded DNA:

Where:

• \( A \) — Number of adenine bases
• \( T \) — Number of thymine bases
• \( G \) — Number of guanine bases
• \( C \) — Number of cytosine bases
• 15,400 — Extinction coefficient for adenine (M⁻¹ cm⁻¹)
• 8,700 — Extinction coefficient for thymine (M⁻¹ cm⁻¹)
• 11,500 — Extinction coefficient for guanine (M⁻¹ cm⁻¹)
• 7,400 — Extinction coefficient for cytosine (M⁻¹ cm⁻¹)

Explanation: This method provides more accurate estimates than simple base counting by accounting for nearest-neighbor interactions that affect UV absorption.

3. Importance of Extinction Coefficient

Details: The extinction coefficient is crucial for determining DNA concentration from UV absorbance measurements, assessing nucleic acid purity (A260/A280 ratio), and preparing accurate solutions for molecular biology experiments.

4. Using the Calculator

Tips: Enter the number of each nucleotide base in your DNA sequence. All values must be non-negative integers. The calculator will compute the total molar extinction coefficient at 260 nm.

5. Frequently Asked Questions (FAQ)

Q1: Why use nearest-neighbor method instead of simple base counting?
A: Nearest-neighbor method accounts for base stacking interactions that affect UV absorption, providing more accurate extinction coefficients than simple additive models.

Q2: What is the typical range for DNA extinction coefficients?
A: For single-stranded DNA, extinction coefficients typically range from 50,000 to 500,000 M⁻¹ cm⁻¹ depending on length and sequence composition.

Q3: How does double-stranded DNA differ?
A: Double-stranded DNA has lower extinction coefficients due to base pairing and stacking, typically requiring different calculation methods or experimental determination.

Q4: Can I use this for RNA calculations?
A: No, RNA has different extinction coefficients. Use RNA-specific calculators that account for uracil instead of thymine.

Q5: How accurate is this calculation method?
A: The nearest-neighbor method is generally accurate within 5-10% for most sequences, but experimental validation is recommended for critical applications.