IDT Molecular Weight Calculator
DNA/RNA Sequence Molecular Weight Calculator
Enter your sequence and any modifications to calculate the molecular weight (MW) in Daltons (Da) or grams per mole (g/mol).
Enter your DNA or RNA sequence (A, T, G, C, U). Case-insensitive.
None
Phosphate (PO4)
Phosphoramidite (no O)
Amino Modifier (C6)
Biotin
FAM Dye
Cy3 Dye
Cy5 Dye
Tide Quench-2
Dabcyl Quencher
BHQ-1
BHQ-2
BHQ-3
Select a common 5′ modification.
None
Phosphate (PO4)
Amino Modifier (C12)
Dabcyl Quencher
TET Dye
HEX Dye
Cy3 Dye (3′)
Cy5 Dye (3′)
BHQ-1 (3′)
BHQ-2 (3′)
BHQ-3 (3′)
Select a common 3′ modification.
Enter the number of internal modifications. A fixed average MW of 30 Da per modification is used.
Calculation Results
Base MW
Da
Da
5′ Mod MW
Da
Da
3′ Mod MW
Da
Da
Internal Mods MW
Da
Da
Total Bases
Formula Used: Total MW = (Sum of individual base MWs) + (5′ Modification MW) + (3′ Modification MW) + (Internal Modifications MW). The MW of bases (A, T, G, C, U) are averaged, and internal modifications add a fixed amount.
Molecular Weight vs. Sequence Length
This chart visualizes how the molecular weight increases with the length of your DNA/RNA sequence, considering a common modification scenario.
| Base | Monoisotopic Mass (Da) | Average Mass (Da) |
|---|---|---|
| Adenosine (A) | 313.2116 | 313.22 |
| Guanosine (G) | 329.2067 | 329.22 |
| Cytidine (C) | 289.1765 | 289.18 |
| Thymidine (T) | 304.1716 | 304.18 |
| Uridine (U) | 288.1500 | 288.17 |
** Values are for the nucleoside/deoxyribonucleoside and do not include the phosphate backbone linkage. These are illustrative; precise calculations depend on the exact chemical structure and state (e.g., free acid vs. salt). Our calculator uses average values for simplicity.
What is IDT Molecular Weight Calculation?
An IDT molecular weight calculator is a specialized tool used in molecular biology and biotechnology to determine the mass of a synthesized DNA or RNA oligonucleotide (like primers or probes) produced by Integrated DNA Technologies (IDT) or similar synthesis services. Molecular weight, often expressed in Daltons (Da) or grams per mole (g/mol), is a fundamental property of any molecule. For oligonucleotides, it's crucial for accurate quantification, experimental design, and quality control.
This calculation is essential for researchers who order custom synthesized nucleic acids. Knowing the precise molecular weight helps in:
- Accurate Stock Preparation: Calculating the exact volume of buffer needed to create solutions of specific molar concentrations (e.g., 10 µM).
- Reagent Stoichiometry: Ensuring correct molar ratios when mixing oligonucleotides with other reagents in reactions like PCR, qPCR, or sequencing.
- Mass Spectrometry Analysis: Verifying the identity and purity of synthesized oligonucleotides.
- Experimental Design: Estimating the mass of oligonucleotide needed for various downstream applications.
Who should use it? Biologists, biochemists, geneticists, molecular diagnostics developers, and anyone working with synthetic DNA or RNA sequences, especially when ordering from commercial synthesis providers like IDT.
Common Misconceptions:
- Oversimplification: Assuming all bases have the same weight. In reality, A, T, G, C, and U have distinct molecular weights.
- Ignoring Modifications: Neglecting the significant mass added by common 5′ or 3′ modifications (like fluorescent dyes, quenchers, or biotinylation) or internal modifications (like LNA or 2′-O-Methyl).
- Using Generic Values: Relying on online calculators that don't account for specific synthesis provider conventions or common modification masses. IDT calculators often use specific, validated values for their reagents.
Molecular Weight Formula and Mathematical Explanation
The molecular weight (MW) of a synthesized single-stranded DNA or RNA oligonucleotide is calculated by summing the contributions of its constituent parts: the individual nucleotide bases, any modifications at the 5′ end, and any modifications at the 3′ end. Internal modifications also add to the total mass.
The Core Formula:
Total MW = (Sum of MW of each base in the sequence) + (MW of 5′ Modification) + (MW of 3′ Modification) + (Total MW of Internal Modifications)
Variable Explanations:
- Sequence: The string of nucleotide bases (A, T, G, C for DNA; A, U, G, C for RNA). The length and composition of this sequence are primary determinants of the oligonucleotide's MW.
- Base MWs: Each base has a specific molecular weight based on its chemical structure (e.g., Adenine, Guanine, Cytosine, Thymine, Uracil).
- 5′ Modification MW: A specific chemical group attached to the 5′ phosphate of the terminal nucleotide. This could be a label, quencher, or chemical linker.
- 3′ Modification MW: A specific chemical group attached to the 3′ hydroxyl of the terminal nucleotide. Common examples include quenchers, labels, or specialized linkers (e.g., for solid-phase attachment).
- Internal Modifications MW: Chemical modifications incorporated within the oligonucleotide chain, replacing a standard base or occurring on the sugar-phosphate backbone. Examples include Locked Nucleic Acids (LNA), 2′-O-Methyl modifications, etc. Our calculator uses an average MW contribution per internal modification for simplicity.
Variables Table:
| Variable | Meaning | Unit | Typical Range / Values |
|---|---|---|---|
| Sequence Length | Number of nucleotides in the oligonucleotide. | Bases | 1 to 200+ |
| Base Composition | The count of each specific base (A, T/U, G, C). | Count | Varies with sequence |
| Base MW | Mass of individual deoxyribonucleotides (for DNA) or ribonucleotides (for RNA). | Da (Daltons) | Approx. 288 (U) to 329 (G) |
| 5′ Modification MW | Mass of the chemical group attached at the 5′ end. | Da | 0 (None) to 676+ (e.g., Quenchers, Dyes) |
| 3′ Modification MW | Mass of the chemical group attached at the 3′ end. | Da | 0 (None) to 372+ (e.g., Quenchers, Dyes) |
| Internal Modification MW | Mass contribution from modifications within the sequence. | Da | Approx. 30 Da per modification (calculator estimate) |
| Total MW | The final calculated mass of the oligonucleotide. | Da (g/mol) | Highly variable based on length and modifications |
Practical Examples (Real-World Use Cases)
Example 1: Standard qPCR Probe
A researcher needs to order a standard TaqMan® probe for a gene expression study. The sequence is 25 bases long, with a FAM dye at the 5′ end and a BHQ-1 quencher at the 3′ end. There are no internal modifications.
Inputs:
- Sequence:
5'-[FAM]AAAAAAAAAAAAAAAATTTTTTTTTTTTTT-[BHQ-1]-3'(25 bases total, 15 A's, 10 T's) - 5′ Modification: FAM Dye (MW ≈ 312.1979 Da)
- 3′ Modification: BHQ-1 (MW ≈ 156.1117 Da)
- Internal Modifications: 0
Calculation Steps:
- Base MW Calculation: (15 * Avg MW of A) + (10 * Avg MW of T) = (15 * 313.22) + (10 * 304.18) = 4698.3 + 3041.8 = 7740.1 Da
- 5′ Modification MW: 312.1979 Da
- 3′ Modification MW: 156.1117 Da
- Internal Modifications MW: 0 Da
- Total MW: 7740.1 + 312.1979 + 156.1117 + 0 = 8208.41 Da
Output: The calculated molecular weight is approximately 8208.41 Da. This value is critical for preparing accurate stock solutions for the qPCR experiment.
This demonstrates how the choice of fluorescent dye and quencher significantly adds to the total mass.
Example 2: siRNA with Internal Modifications
A research lab requires a 21-nucleotide siRNA duplex with 2′-O-Methyl modifications on specific internal positions to enhance stability. They have a particular sequence in mind and need to estimate the MW.
Inputs:
- Sequence:
[Example 21-mer sequence](e.g., 10 Guanines, 11 Cytosines) - 5′ Modification: None (MW = 0 Da)
- 3′ Modification: None (MW = 0 Da)
- Internal Modifications: 2 (e.g., 2′-O-Methyl on two internal bases)
Calculation Steps:
- Base MW Calculation: (10 * Avg MW of G) + (11 * Avg MW of C) = (10 * 329.22) + (11 * 289.18) = 3292.2 + 3180.98 = 6473.18 Da
- 5′ Modification MW: 0 Da
- 3′ Modification MW: 0 Da
- Internal Modifications MW: 2 * 30 Da (estimated per modification) = 60 Da
- Total MW: 6473.18 + 0 + 0 + 60 = 6533.18 Da
Output: The estimated molecular weight is approximately 6533.18 Da. This value helps in planning the synthesis order and anticipating downstream assay concentrations.
This highlights the impact of internal modifications, even if they are relatively small individually, they contribute to the overall mass, especially when present in multiple copies.
How to Use This IDT Molecular Weight Calculator
Using this calculator is straightforward. Follow these simple steps to get an accurate molecular weight for your oligonucleotide:
Step-by-Step Instructions:
- Enter Your Sequence: In the "DNA/RNA Sequence" field, type or paste the exact sequence of your oligonucleotide. Ensure you use standard IUPAC codes (A, T, G, C, U). The calculator is case-insensitive.
- Select 5′ Modification: If your oligonucleotide has a modification at the 5′ end, choose it from the dropdown list. If there is no modification, select "None". The calculator includes common modifications offered by IDT and other synthesis services.
- Select 3′ Modification: Similarly, select any modification present at the 3′ end of your sequence from the dropdown. Choose "None" if applicable.
- Specify Internal Modifications: If your sequence contains internal modifications (like LNA, 2′-O-Methyl, etc.), enter the total number of such modifications in the designated field. Our calculator applies an estimated average molecular weight contribution for each internal modification.
- Calculate: Click the "Calculate Molecular Weight" button.
How to Read the Results:
- Primary Result: The largest, most prominent number displayed is the Total Molecular Weight in Daltons (Da). This is the key figure you'll use for most calculations.
- Intermediate Values: Below the primary result, you'll find breakdowns:
- Base MW: The combined molecular weight of all the nucleotides in your sequence.
- 5′ Mod MW: The molecular weight contributed by the 5′ modification.
- 3′ Mod MW: The molecular weight contributed by the 3′ modification.
- Internal Mods MW: The total molecular weight added by internal modifications.
- Total Bases: Simply the length of your sequence.
- Formula Explanation: A brief description reiterates how the total molecular weight was computed.
Decision-Making Guidance:
The primary use of the calculated MW is to convert between molarity and mass. For example, to prepare a 10 µM (micromolar) stock solution:
Mass (mg) = Molarity (µmol/mL) × Molecular Weight (g/mol) × Volume (mL)
For instance, if your oligonucleotide has a MW of 8000 Da (g/mol) and you want to make 1 mL of a 10 µM solution:
Mass (mg) = 0.01 µmol/mL × 8000 g/mol × 1 mL = 80 mg
Always use the calculated Total MW for these conversions. The intermediate results help in understanding the contribution of each component to the final mass, which can be useful for troubleshooting or optimizing synthesis orders.
Key Factors That Affect IDT Molecular Weight Results
Several factors influence the final calculated molecular weight of an oligonucleotide. Understanding these is key to obtaining accurate results and interpreting their significance:
- Sequence Length: This is the most significant factor. Longer sequences inherently have higher molecular weights because they contain more nucleotide bases, each contributing its mass. A 50-mer will always weigh more than a 20-mer of the same base composition.
- Base Composition: While all bases contribute mass, Guanine (G) and Adenine (A) are heavier than Cytosine (C) and Thymine/Uracil (T/U). A sequence rich in Gs and As will have a higher MW than a sequence of the same length composed primarily of Cs and Ts/Us.
- 5′ and 3′ Modifications: These are critical. Attaching fluorescent dyes (like FAM, Cy3, Cy5), quenchers (like BHQ series, Dabcyl), biotin, or other labels adds substantial mass. The specific type and size of the modification directly impact the total MW. Dyes and large quenchers can add hundreds of Daltons.
- Internal Modifications: Modifications within the oligonucleotide chain, such as Locked Nucleic Acids (LNA), 2′-O-Methyl (2′-OMe), or phosphoroates, increase the molecular weight. Each type of internal modification has its own specific mass addition, and the total count multiplies this effect.
- Oligonucleotide Type (DNA vs. RNA): RNA bases (especially Uridine) have slightly different molecular weights compared to their DNA counterparts (Thymine). This difference, while small per base, can become noticeable in longer sequences.
- Chemical State and Counterions: While most calculators provide the mass of the oligonucleotide itself, the actual mass in a salt form (e.g., sodium salt) would be slightly higher due to the associated counterions. For practical purposes in molecular biology, the oligonucleotide's base MW is usually sufficient, but for precise mass spectrometry, this can be a consideration.
- Synthesis Purity and Yield: While not directly part of the MW calculation, the purity of the synthesized oligo affects the concentration of the *actual* desired molecule. A lower purity means a portion of your mass is impurities, not your target sequence. Calculators typically assume 100% purity for the target sequence.
Frequently Asked Questions (FAQ)
- What is the difference between Monoisotopic Mass and Average Mass?
- Monoisotopic mass uses the mass of the most abundant isotopes of each atom (e.g., 1H, 12C, 14N, 16O, 31P). Average mass uses the weighted average of all naturally occurring isotopes. For molecular biology calculations, average mass is commonly used and is what most calculators provide for bases.
- Does the calculator account for the phosphate backbone?
- Yes, the calculation implicitly includes the mass of the phosphodiester backbone linkages. The MW of each deoxyribonucleotide or ribonucleotide already incorporates the base, sugar, and phosphate group. The "Base MW" calculation sums these up.
- How accurate is the internal modification estimate?
- The 30 Da estimate is a simplification. Actual internal modifications have specific weights (e.g., 2′-O-Methyl adds around 14-15 Da). For precise calculations involving many specific internal modifications, consult the synthesis provider's detailed specifications or a more advanced calculator.
- Should I use Daltons (Da) or grams per mole (g/mol)?
- For practical purposes in molecular biology, Daltons (Da) and grams per mole (g/mol) are numerically equivalent when discussing molecular weight. Most researchers use Da for oligonucleotides. The key is consistency in your calculations.
- What if my modification isn't listed?
- If your specific 5′ or 3′ modification is not listed, you will need to find its molecular weight from the manufacturer's datasheet (often in Da or g/mol) and manually add it to the calculated base MW. For internal modifications, you'd need to sum their individual weights and add that total.
- Does the calculator handle DNA and RNA differently?
- Yes, the underlying base weights are different. While this calculator uses average weights that might be generalized, precise calculations would use distinct sets of weights for DNA bases (A, T, G, C) and RNA bases (A, U, G, C). This tool implicitly uses a set suitable for general oligonucleotide MW calculation.
- What is the typical molecular weight range for common primers?
- A standard 20-mer DNA primer (no modifications) typically falls in the range of 6,000 to 7,000 Da. Modifications can add significantly to this weight.
- Can this calculator be used for double-stranded DNA?
- This calculator is designed for single-stranded oligonucleotides. For double-stranded DNA, you would calculate the MW of each strand separately (using this calculator) and then sum them. However, remember that in dsDNA, the strands are held together, and the calculation often focuses on the mass of the components used rather than a simple sum.
Related Tools and Internal Resources
- Oligo Properties Calculator Calculate melting temperature (Tm), GC content, and other essential properties for your DNA/RNA sequences.
- Understanding DNA Synthesis Learn about the chemical processes behind synthesizing custom DNA oligonucleotides, including the role of modifications.
- Primer Design Best Practices A comprehensive guide to designing effective primers for PCR and qPCR, including considerations for sequence length and modifications.
- Molar Concentration Dilution Calculator Easily calculate dilutions for stock solutions when you know the molecular weight and desired molarity.
- DNA Quantification Methods Explore different techniques used to measure the concentration of DNA, including spectrophotometry and fluorometry.
- Common DNA Modifications Explained An overview of frequently used modifications in DNA synthesis, their purposes, and associated chemical properties.