1. What is Oligonucleotide Concentration?

The oligonucleotide concentration is calculated from the absorbance at 260 nm (OD₂₆₀), the extinction coefficient, and the path length of the cuvette. This measurement is essential for molecular biology experiments involving DNA or RNA oligonucleotides.

2. How Does the Calculator Work?

The calculator uses the following equation:

Where:

• \( OD_{260} \) — Absorbance at 260 nm (dimensionless)
• \( Extinction\ Coefficient \) — Molar absorptivity (L/mol/cm)
• \( Path\ Length \) — Cuvette path length (cm)

Explanation: The equation relates the measured absorbance to concentration using Beer-Lambert law, accounting for the specific extinction coefficient of the oligonucleotide and the path length of the measurement.

3. Importance of Concentration Measurement

Details: Accurate oligonucleotide concentration is crucial for PCR, sequencing, hybridization experiments, and other molecular biology applications where precise amounts of DNA or RNA are required.

4. Using the Calculator

Tips: Enter the measured OD₂₆₀ value, the extinction coefficient (usually provided with synthesized oligos), and the path length (typically 1 cm for standard cuvettes). All values must be positive numbers.

5. Frequently Asked Questions (FAQ)

Q1: What is a typical extinction coefficient for oligos?
A: For DNA, it's typically 15,000-50,000 L/mol/cm depending on length and sequence. RNA coefficients are slightly higher.

Q2: Why use 260 nm for measurement?
A: Nucleic acids absorb maximally at 260 nm due to the aromatic rings in the nucleobases.

Q3: How should I prepare my sample for measurement?
A: Dilute in the same buffer used for blank measurement, typically TE buffer (10 mM Tris, 1 mM EDTA, pH 8.0).

Q4: What if my OD₂₆₀ is too high?
A: For accurate measurements, OD should be between 0.1-1.0. Dilute your sample if necessary.

Q5: How does temperature affect the measurement?
A: Measurements are typically done at room temperature. Higher temperatures can increase absorbance slightly.