1. What is Oligonucleotide Extinction Coefficient?

The extinction coefficient (ε) of an oligonucleotide is a measure of how strongly it absorbs light at a specific wavelength (typically 260nm). It's used to quantify oligonucleotides in solution by UV spectrophotometry.

2. How Does the Calculator Work?

The calculator uses the nearest-neighbor method:

Where:

• \( \epsilon \) — Total extinction coefficient (L/mol·cm)
• \( \epsilon_{nuc} \) — Extinction coefficient per nucleotide (L/mol·cm per nuc)

Standard values at 260nm:

• A: 15,400 L/mol·cm
• C: 7,400 L/mol·cm
• G: 11,500 L/mol·cm
• T: 8,700 L/mol·cm
• U: 9,900 L/mol·cm

3. Importance of Extinction Coefficient

Details: The extinction coefficient is essential for determining oligonucleotide concentration, purity assessment, and quantitative applications in molecular biology.

4. Using the Calculator

Tips: Enter the DNA or RNA sequence (5' to 3'). The calculator sums the individual nucleotide extinction coefficients. Only standard bases (A,C,G,T/U) are accepted.

5. Frequently Asked Questions (FAQ)

Q1: Why is extinction coefficient important?
A: It allows calculation of oligonucleotide concentration using Beer-Lambert law (A = εcl).

Q2: Does this account for nearest-neighbor effects?
A: This calculator uses simple additive method. For more precision, nearest-neighbor method should be used.

Q3: How does RNA differ from DNA?
A: RNA uses U instead of T, with slightly different extinction coefficient (9,900 vs 8,700 L/mol·cm).

Q4: What about modified bases?
A: Modified bases require special consideration as they may have different extinction coefficients.

Q5: How accurate is this calculation?
A: The additive method is generally within 5-10% of measured values for typical sequences.