1. What is Oligo Molar Extinction Coefficient?

The oligo molar extinction coefficient (ε) is a measure of how strongly an oligonucleotide absorbs light at a specific wavelength (usually 260 nm). It is used to determine the concentration of nucleic acid solutions and is essential for various molecular biology applications.

2. How Does the Calculator Work?

The calculator uses the following formula:

Where:

• \( ε \) — Total molar extinction coefficient (M⁻¹·cm⁻¹)
• \( ε_n \) — Extinction coefficient per nucleotide (M⁻¹·cm⁻¹)
• \( n \) — Number of each nucleotide type

Standard Extinction Coefficients:

• Adenine (A): 15,400 M⁻¹·cm⁻¹
• Thymine (T): 8,800 M⁻¹·cm⁻¹
• Guanine (G): 11,500 M⁻¹·cm⁻¹
• Cytosine (C): 7,400 M⁻¹·cm⁻¹

3. Importance of Extinction Coefficient Calculation

Details: Accurate extinction coefficient calculation is crucial for determining oligonucleotide concentration, which is essential for PCR, sequencing, hybridization experiments, and other molecular biology techniques.

4. Using the Calculator

Tips: Enter the oligonucleotide sequence using only A, T, G, C characters (case insensitive). The calculator will automatically sum the extinction coefficients of all nucleotides in the sequence.

5. Frequently Asked Questions (FAQ)

Q1: Why is extinction coefficient important?
A: It allows accurate determination of oligonucleotide concentration using UV spectrophotometry, which is essential for reproducible experimental results.

Q2: What wavelength is used for measurement?
A: Nucleic acids are typically measured at 260 nm, where they exhibit maximum absorption.

Q3: How do I calculate concentration from extinction coefficient?
A: Concentration (M) = Absorbance at 260nm / Extinction coefficient × Path length (cm)

Q4: Are extinction coefficients additive?
A: Yes, for single-stranded DNA, the total extinction coefficient is the sum of individual nucleotide coefficients.

Q5: Do secondary structures affect extinction coefficient?
A: Yes, base pairing in double-stranded DNA can cause hypochromicity, reducing the observed extinction coefficient by 20-40%.