1. What is Oligonucleotide Molecular Weight?

The molecular weight (MW) of an oligonucleotide is the sum of the atomic weights of all atoms in the molecule. It's essential for preparing accurate concentrations in molecular biology experiments.

2. How Does the Calculator Work?

The calculator uses the following formula:

Where:

• \( base\_masses \) - Molecular weights of individual bases (A, T, C, G, U)
• \( n \) - Number of nucleotides in the sequence
• 79.0 - Molecular weight of PO₃ (phosphate group)
• 61.0 - Molecular weight of terminal groups (5' OH and 3' H)

Explanation: The formula accounts for the backbone phosphates and terminal groups in addition to the nucleotide bases.

3. Importance of MW Calculation

Details: Accurate MW calculation is crucial for preparing solutions with precise molar concentrations, essential for PCR, sequencing, and other molecular biology techniques.

4. Using the Calculator

Tips: Enter DNA/RNA sequence in 5' to 3' direction (uppercase or lowercase). Select any modifications if applicable. The sequence should only contain A, T, C, G, or U.

5. Frequently Asked Questions (FAQ)

Q1: Does this calculator work for RNA?
A: Yes, simply use U instead of T for RNA sequences.

Q2: How are modifications handled?
A: Additional molecular weight from modifications is added to the total.

Q3: What about degenerate bases?
A: This calculator doesn't support degenerate bases (N, R, Y, etc.). Use standard bases only.

Q4: Why is the MW different from my synthesis report?
A: Different salt forms or calculation methods may cause slight variations.

Q5: Can I calculate nmol from OD260?
A: Not directly with this calculator. You would need the extinction coefficient.