Calculate the exact mass, melting temperature, and GC content of your oligonucleotide sequences.
Supported characters: A, T, C, G, N. Non-standard characters will be ignored.
Please enter a valid DNA sequence.
Single-Stranded (ssDNA)
Double-Stranded (dsDNA)
Select dsDNA to include the complementary strand mass.
None (Hydroxyl)
5′ Phosphate
Adds mass for 5′ phosphorylation if selected.
Molecular Weight
0.00 Daltons (g/mol)
Length
0 nt
GC Content
0%
Melting Temp (Tm)
0 °C
Base
Count
% Composition
Adenine (A)
0
0%
Thymine (T)
0
0%
Cytosine (C)
0
0%
Guanine (G)
0
0%
Table 1: Nucleotide composition breakdown.
Figure 1: Distribution of nucleotides in sequence.
What is a DNA Molecular Weight Calculator Online?
A dna molecular weight calculator online is a specialized bioinformatics tool designed for researchers, molecular biologists, and students. It computes the precise molecular mass of a DNA sequence based on its nucleotide composition. Whether you are designing primers for PCR, synthesizing oligonucleotides, or performing mass spectrometry analysis, knowing the exact molecular weight (MW) is critical for accurate concentration calculations and stoichiometry.
This tool goes beyond simple mass calculation. It analyzes the sequence to provide the GC content, melting temperature (Tm), and length, which are essential parameters for experimental success. Unlike generic calculators, this tool allows you to toggle between single-stranded (ssDNA) and double-stranded (dsDNA) modes and accounts for common modifications like 5′ phosphorylation.
Common misconceptions include assuming all nucleotides have the same mass or that double-stranded DNA is exactly twice the weight of single-stranded DNA. In reality, the specific sequence and the chemistry of base pairing (hydrogen bonds do not add mass, but the complementary strand has a different composition) dictate the final weight.
DNA Molecular Weight Formula and Mathematical Explanation
The calculation of DNA molecular weight relies on summing the individual weights of the deoxyribonucleotides present in the chain. The formula differs slightly depending on whether the DNA is single-stranded or double-stranded.
Single-Stranded DNA (ssDNA) Formula
For a standard oligonucleotide with a 5′ hydroxyl group and a 3′ hydroxyl group, the formula is:
A, C, G, T = The count of each base in the sequence.
The weights (e.g., 313.21 Da for dA) represent the individual deoxyribonucleotide residues.
-61.96 accounts for the removal of a phosphate group from the 5′ end and the addition of a hydrogen atom to the 3′ end to satisfy valency (often simplified as the removal of one water molecule per bond minus terminal adjustments).
Double-Stranded DNA (dsDNA) Formula
For dsDNA, the calculator computes the weight of the input strand and adds the weight of its complementary strand (A pairs with T, C pairs with G).
Scenario: A researcher designs a forward primer for a gene expression study. The sequence is 20 nucleotides long: ATCGATCGATCGATCGATCG.
Input: ATCGATCGATCGATCGATCG
Type: ssDNA (Primers are single-stranded)
Modification: None
Result: The dna molecular weight calculator online determines the MW is approximately 6,179.1 Daltons.
Interpretation: The researcher uses this value to convert the lyophilized primer (delivered in micrograms) into a specific molar concentration (e.g., 100 µM) for the stock solution.
Example 2: Double-Stranded Gene Fragment
Scenario: You have a synthetic dsDNA gene block that is 10 base pairs long: GGGGCCCCAA.
Input: GGGGCCCCAA
Type: dsDNA
Result: The calculator computes the sense strand (MW ~3090 Da) and the antisense strand (TTGGGGCCCC, MW ~3090 Da). Total MW is approximately 6,180 Da.
Interpretation: Knowing the total mass allows for precise ligation calculations when cloning this fragment into a plasmid vector.
How to Use This DNA Molecular Weight Calculator
Enter Sequence: Paste your DNA sequence into the text area. The tool accepts raw text and automatically filters out numbers or spaces.
Select Strand Type: Choose "Single-Stranded" for primers and probes, or "Double-Stranded" for plasmid inserts or genomic DNA fragments.
Apply Modifications: If your oligo was synthesized with a 5′ phosphate (common for ligation), select "5′ Phosphate" from the dropdown.
Review Results: The primary result shows the Molecular Weight in Daltons. Check the intermediate metrics for GC content and Melting Temperature (Tm).
Analyze Visuals: Use the generated table and chart to verify the base composition of your sequence.
Key Factors That Affect DNA Molecular Weight Results
When using a dna molecular weight calculator online, several factors influence the final calculation:
Sequence Length: The primary driver of weight. Each added nucleotide adds roughly 303-329 Daltons depending on the base.
Base Composition (GC Content): Guanosine is the heaviest base (329.21 Da), while Cytosine is the lightest (289.18 Da). A GC-rich sequence will have a different weight than an AT-rich sequence of the same length.
Phosphorylation State: Synthetic oligos usually lack a 5′ phosphate unless specified. Adding a phosphate group adds approximately 80 Da, which is significant for short sequences.
Counterions (Salts): While this calculator provides the molecular weight of the DNA anion, in solution, DNA is associated with cations like Na+. Some calculators include the weight of the sodium counterion, but for molarity calculations, the anion weight is standard.
Hydration: DNA is heavily hydrated in solution. However, molecular weight is calculated based on the dry mass of the molecule itself, excluding the hydration shell.
Modifications: Fluorescent tags (like FAM or HEX) or quenchers add significant mass. This calculator focuses on standard DNA, so external mass must be added for modified probes.
Frequently Asked Questions (FAQ)
What is the unit of Molecular Weight used here?
The unit is Daltons (Da), which is equivalent to grams per mole (g/mol). This is the standard unit used in chemistry and biology for molecular mass.
Does this calculator work for RNA?
No, this is specifically a dna molecular weight calculator online. RNA contains Uracil instead of Thymine and has an extra hydroxyl group on the ribose sugar, making it heavier. You would need an RNA-specific calculator.
How is Melting Temperature (Tm) calculated?
For sequences shorter than 14 bases, the Wallace rule (2°C for A/T, 4°C for G/C) is used. For longer sequences, a modified nearest-neighbor approximation is applied to estimate Tm under standard salt conditions.
Why is the dsDNA weight not exactly double the ssDNA weight?
Because the two strands are complementary, not identical. A strand rich in Adenine (heavy) will pair with a strand rich in Thymine (lighter). The calculator sums the exact weight of both specific strands.
Does the calculator handle degenerate bases (N)?
The calculator accepts 'N' but calculates the weight based on an average of the four standard bases. For precise mass spectrometry, avoid using degenerate bases.
What is the difference between 5′ Phosphate and Hydroxyl?
Standard synthetic DNA has a 5′ -OH (hydroxyl). Enzymatically cleaved DNA or DNA intended for ligation often requires a 5′ -PO4 (phosphate). The phosphate adds mass and negative charge.
Can I calculate the concentration from OD260 using this?
Yes, knowing the molecular weight allows you to convert µg (mass) to pmol (moles). The formula is: Mass (µg) / MW (µg/µmol) = Amount (µmol).
Is this tool free to use?
Yes, this dna molecular weight calculator online is completely free and runs directly in your browser without storing your sequence data.
Related Tools and Internal Resources
Molarity Calculator – Convert between mass, volume, and concentration for lab solutions.