Accurate synthesis calculations for DNA & RNA sequences
Supported characters: A, C, G, T, U, I. Non-alphabetic characters are ignored.
Invalid characters detected.
DNA (Deoxyribonucleic Acid)
RNA (Ribonucleic Acid)
Molecular Weight
0.00
Daltons (g/mol)
Sequence Length0 bases
GC Content0%
Approx. Extinction Coeff. (260nm)0 L/(mol·cm)
Mass for 1 OD2600 µg
Base Type
Count
Molar Contribution (g/mol)
% Composition
Figure 1: Nucleotide Base Composition Distribution
Formula used: MW = Σ(Count × Residue MW) – (End Adjustments). DNA assumes 5′-OH/3′-OH unless modified. Calculated based on anhydrous molecular weights.
Understanding the Oligo Molecular Weight Calculator
In the precise world of molecular biology and genetic engineering, knowing the exact properties of your synthetic DNA or RNA is critical for experimental success. An oligo molecular weight calculator is an essential tool for researchers designing primers for PCR, sequencing probes, or synthetic gene fragments.
What is an Oligo Molecular Weight Calculator?
An oligo molecular weight calculator is a computational tool designed to determine the molar mass of an oligonucleotide sequence based on its specific nucleotide composition (A, C, G, T, or U). This value is typically expressed in Daltons (Da) or grams per mole (g/mol).
This tool is primarily used by molecular biologists, biochemists, and geneticists who need to prepare solutions of specific molarity from lyophilized DNA/RNA pellets. A common misconception is that all 20-mer primers have the same weight; however, because the four bases have different atomic structures and masses, the specific sequence significantly alters the final weight.
Oligo Molecular Weight Formula and Mathematical Explanation
The calculation of oligonucleotide molecular weight involves summing the individual weights of each nucleotide residue and adjusting for the presence or absence of terminal groups (typically phosphate or hydroxyl groups). The standard formula assumes an anhydrous state.
The term -61.96 accounts for the removal of a phosphate group and the addition of a hydrogen atom at the ends relative to the internal residue weights.
Variable Definitions
Variable
Meaning
Unit
Typical Mass
N_A
Count of Adenine
Integer
313.21 Da (DNA)
N_C
Count of Cytosine
Integer
289.18 Da (DNA)
N_G
Count of Guanine
Integer
329.21 Da (DNA)
N_T
Count of Thymine
Integer
304.20 Da (DNA)
MW
Molecular Weight
Daltons
varies
Practical Examples (Real-World Use Cases)
Example 1: Standard PCR Primer
Scenario: A researcher orders a 20-mer DNA primer with the sequence 5'-ATCGATCGATCGATCGATCG-3'.
Calculation: The calculator sums the residue weights for a perfectly balanced mix.
Result: Approx 6,176 Daltons.
Application: If the synthesis yield is 20 ODs, the researcher uses the MW to calculate exactly how many microliters of water to add to achieve a 100 µM stock solution.
Example 2: RNA Oligo for siRNA
Scenario: Designing a short interfering RNA (siRNA) sequence.
Difference: RNA nucleotides have an extra hydroxyl group on the 2′ carbon, making them heavier than their DNA counterparts (e.g., rA is ~329.2 Da vs dA ~313.2 Da).
Result: The molecular weight will be higher than a DNA sequence of identical length.
How to Use This Oligo Molecular Weight Calculator
Enter Sequence: Paste your nucleotide sequence into the text area. The calculator strips whitespace automatically.
Select Type: Choose between DNA and RNA. This adjusts the atomic weights used in the formula.
Modifications: If your oligo has a 5′ Phosphate group (common for cloning), check the box.
Review Results: Instantly view the Molecular Weight, GC Content, and Extinction Coefficient.
Use the Data: Use the "Mass for 1 OD260" to convert spectrophotometer readings into physical mass (micrograms).
Key Factors That Affect Oligo Molecular Weight Results
DNA vs. RNA Backbone: RNA has a ribose sugar (with a 2′-OH group), whereas DNA has deoxyribose. This adds 16 Daltons per base to RNA sequences relative to DNA.
5′ and 3′ Modifications: Adding fluorescent dyes (like FAM or HEX), biotin, or phosphate groups adds significant mass. For example, a 5′ Phosphate adds ~80 Da.
Counter Ions: While this calculator provides the anhydrous molecular weight, in solution, oligos exist as salts (e.g., sodium or ammonium salts). This affects the "gross weight" but not the molecular weight used for molarity calculations.
Base Composition: Purines (A, G) are heavier than Pyrimidines (C, T/U). A purine-rich sequence will be heavier than a pyrimidine-rich sequence of the same length.
Synthesis Purity: Incomplete synthesis sequences (N-1 products) reduce the average molecular weight of the bulk sample, though the theoretical weight remains calculated for the full-length product.
Chemical Hydration: Water molecules tightly bound to the DNA structure can affect measured weight in physical weighing but are excluded from theoretical calculations.
Frequently Asked Questions (FAQ)
1. Does this calculator account for salt ions?
No, this oligo molecular weight calculator provides the molecular weight of the oligonucleotide as a free acid (anhydrous). This is the standard for calculating molarity.
2. How accurate is the calculation?
The calculation is precise to the atomic weight of the constituent atoms. It uses standard IUPAC atomic weights for C, H, N, O, and P.
3. Can I calculate mixed DNA/RNA bases?
Currently, the tool applies either DNA or RNA weights to the entire sequence. For chimeric oligos, manual adjustment would be required.
4. Why is the Extinction Coefficient important?
It allows you to determine concentration from absorbance. According to the Beer-Lambert law (A = εcL), knowing ε (epsilon) lets you calculate concentration (c) from Absorbance (A).
5. How does GC content affect the oligo?
While GC content doesn't drastically skew weight compared to length, it is critical for the melting temperature (Tm) and stability of the duplex.
6. What is the difference between average and exact mass?
This calculator uses average atomic weights (appropriate for bulk chemistry). "Exact mass" usually refers to monoisotopic mass used in mass spectrometry.
7. Why do I need to know the molecular weight?
It is impossible to make a solution of a specific molarity (e.g., 100 µM) from a dry weight (e.g., micrograms) without knowing the molecular weight.
8. Does this support degenerate bases (like N or R)?
The calculator currently ignores non-standard bases (N, R, Y, etc.) or treats them as zero weight. For accurate results, use specific sequences.