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's used to calculate concentration from absorbance measurements at 260 nm.

2. How Does the Calculator Work?

The calculator uses the IDT extinction coefficient formula:

Where:

• \( ε \) — Total extinction coefficient (M⁻¹ cm⁻¹)
• \( ε_{nucleotides} \) — Individual nucleotide coefficients
• \( n \) — Count of each nucleotide type
• \( corrections \) — Additional adjustments for sequence-specific effects

Nucleotide Coefficients:

• DNA: A=15400, C=7400, G=11500, T=8700 M⁻¹ cm⁻¹
• RNA: A=15400, C=7200, G=11500, U=9900 M⁻¹ cm⁻¹

3. Importance of Extinction Coefficient

Details: Accurate extinction coefficient calculation is essential for determining oligonucleotide concentration, which is critical for PCR, sequencing, and other molecular biology applications.

4. Using the Calculator

Tips: Enter the oligonucleotide sequence in uppercase letters without spaces. Select DNA or RNA type. The sequence should contain only valid nucleotide characters (A, C, G, T for DNA; A, C, G, U for RNA).

5. Frequently Asked Questions (FAQ)

Q1: What is the difference between DNA and RNA coefficients?
A: RNA nucleotides have slightly different extinction coefficients due to structural differences, particularly for cytosine and uracil/thymine.

Q2: How is concentration calculated from extinction coefficient?
A: Concentration (μM) = (A260 × dilution factor) / (ε × path length in cm)

Q3: Why use 260 nm for oligonucleotides?
A: 260 nm is the wavelength where nucleic acids have maximum absorbance due to the purine and pyrimidine bases.

Q4: Are there limitations to this calculation?
A: This method assumes nearest-neighbor effects are negligible. For highly accurate results, experimental determination may be needed.

Q5: Can I use this for modified nucleotides?
A: No, this calculator is for standard nucleotides only. Modified nucleotides require specific extinction coefficients.