Oligonucleotide MW Calculator
Molecular Weights of Individual Nucleotides
| Nucleotide | Molecular Weight (g/mol) |
|---|---|
| Adenine (A) | 313.21 |
| Thymine (T) | 304.20 |
| Cytosine (C) | 289.18 |
| Guanine (G) | 329.21 |
| Uracil (U) | 306.17 |
Molecular Weights of Common Modifications
| Modification | Molecular Weight Change (g/mol) |
|---|---|
| Phosphorylation (5′ or 3′) | +79.98 |
| Methylation (CH3) | +14.03 |
| Biotin | +244.31 |
| Fluorescein | +332.31 |
| Amino Modification (NH2) | +15.03 |
Example Calculations
The molecular weight of an oligonucleotide is calculated by summing the molecular weights of the individual nucleotides and subtracting the weight of the phosphodiester bonds (18.015 g/mol) per nucleotide bond.
- Single-Stranded Oligonucleotide
For a sequence like 5′-ATCG-3′:
Molecular Weight=(313.21+304.20+289.18+329.21)−(3×18.015)\text{Molecular Weight} = (313.21 + 304.20 + 289.18 + 329.21) – (3 \times 18.015)Molecular Weight=(313.21+304.20+289.18+329.21)−(3×18.015)
=1235.80−54.045= 1235.80 – 54.045=1235.80−54.045
=1181.755 g/mol= 1181.755 \text{ g/mol}=1181.755 g/mol
- Double-Stranded Oligonucleotide
For a sequence like 5′-ATCG-3′ paired with 3′-TAGC-5′:
Molecular Weight (double-stranded)=2×1181.755=2363.51 g/mol\text{Molecular Weight (double-stranded)} = 2 \times 1181.755 = 2363.51 \text{ g/mol}Molecular Weight (double-stranded)=2×1181.755=2363.51 g/mol
Example Table for Various Sequences
| Sequence | Type | Molecular Weight (g/mol) |
|---|---|---|
| 5′-A-3′ | Single-strand | 313.21 |
| 5′-AT-3′ | Single-strand | 599.41 |
| 5′-ATC-3′ | Single-strand | 888.59 |
| 5′-ATCG-3′ | Single-strand | 1181.755 |
| 5′-ATCG-3′ / 3′-TAGC-5′ | Double-strand | 2363.51 |
Key Points to Remember
- Phosphodiester Bonds: Subtract 18.015 g/mol for each bond in the sequence (number of nucleotides – 1).
- Modifications: Add the molecular weight of any modifications to the total weight of the sequence.
- Double-stranded Calculations: Simply multiply the single-stranded molecular weight by 2 for a perfectly complementary double-stranded oligonucleotide.
This table and the example calculations provide a clear method for determining the molecular weight of various oligonucleotide sequences, taking into account both the nucleotide composition and common modifications.