1. What is DNA Extinction Coefficient?

The DNA extinction coefficient (ε) is a measure of how strongly DNA molecules absorb light at a specific wavelength (typically 260nm). It is used to quantify DNA concentration in solution and is essential for molecular biology applications.

2. How Does the Calculator Work?

The calculator uses the IDT DNA extinction coefficient formula:

Where:

• \( \varepsilon \) — Total extinction coefficient (M⁻¹ cm⁻¹)
• \( \varepsilon_{bases} \) — Extinction coefficient per base type
• \( n_{bases} \) — Number of each base type

Standard Extinction Coefficients:

• Adenine (A): 15,400 M⁻¹ cm⁻¹
• Cytosine (C): 7,400 M⁻¹ cm⁻¹
• Guanine (G): 11,500 M⁻¹ cm⁻¹
• Thymine (T): 8,700 M⁻¹ cm⁻¹

3. Importance of Extinction Coefficient Calculation

Details: Accurate extinction coefficient calculation is crucial for determining DNA concentration, ensuring proper primer and probe concentrations in PCR, and maintaining consistency in molecular biology experiments.

4. Using the Calculator

Tips: Enter the number of each DNA base (A, C, G, T) in your sequence. All values must be non-negative integers. The calculator will sum the contributions from each base type.

5. Frequently Asked Questions (FAQ)

Q1: What wavelength is used for DNA extinction coefficient?
A: DNA extinction coefficients are typically measured at 260nm, which is the absorption maximum for nucleic acids.

Q2: How is extinction coefficient used to calculate concentration?
A: Concentration (M) = A₂₆₀ / (ε × path length), where path length is typically 1 cm.

Q3: Do extinction coefficients vary between single and double-stranded DNA?
A: Yes, double-stranded DNA has a lower extinction coefficient per base due to base stacking and hydrogen bonding effects (hyperchromic effect).

Q4: Are these values specific to IDT?
A: These are standard values used by IDT and other manufacturers, based on established spectrophotometric measurements.

Q5: Can I use this for RNA sequences?
A: No, RNA has different extinction coefficients. Use RNA-specific calculators for RNA sequences.