1. What is Nucleic Acid Molecular Weight?

The molecular weight (MW) of a nucleic acid is the sum of the atomic weights of all atoms in the molecule. For oligonucleotides, it's calculated by summing the molecular weights of individual nucleotides and accounting for the loss of water during phosphodiester bond formation.

2. How Does the Calculator Work?

The calculator uses the following formula:

Where:

• \( base\_masses \) — Molecular weights of individual nucleotides (A, T/U, C, G)
• \( n \) — Number of bases in the sequence
• \( phosphate \) — Mass of phosphate group (79.0 g/mol)
• \( water \) — Mass of water molecule (18.015 g/mol)

Explanation: The equation accounts for the loss of water molecules during phosphodiester bond formation between nucleotides.

3. Importance of MW Calculation

Details: Accurate MW calculation is essential for:

• Determining oligonucleotide concentration
• Calculating molar ratios for experiments
• Designing primers and probes
• Mass spectrometry analysis

4. Using the Calculator

Tips:

• Enter sequence in 5' to 3' direction
• Only standard bases (A, T, U, C, G) are considered
• Case insensitive (a/t/c/g or A/T/C/G both work)
• Non-base characters are automatically removed

5. Frequently Asked Questions (FAQ)

Q1: What's the difference between DNA and RNA MW?
A: RNA nucleotides have an extra hydroxyl group at the 2' position, making them slightly heavier than DNA nucleotides.

Q2: How are modified bases handled?
A: This calculator only handles standard bases. For modified bases, specialized calculators are needed.

Q3: Why is the MW important for PCR?
A: Knowing the MW helps calculate the correct amount of primer to use in reactions.

Q4: Does this include 5' phosphate or 3' OH groups?
A: The calculation assumes standard 5' phosphate and 3' hydroxyl termini.

Q5: How accurate is this calculation?
A: It provides theoretical MW based on average isotopic composition. For exact mass, consider isotopic distribution.