Instantly calculate the molecular weight, GC content, and nucleotide composition of your RNA sequences.
Designed for biochemists, molecular biologists, and researchers requiring precise stoichiometric data.
Accepts A, C, G, U, T (converted to U). Case insensitive. Whitespace is ignored.
Please enter a valid RNA sequence containing only A, C, G, U (or T).
Synthetic RNA (5′-OH, 3′-OH)
In Vitro Transcript (5′-ppp, 3′-OH)
Select "Synthetic" for standard oligos or "Transcript" for enzymatic synthesis.
Total Molecular Weight
0.00 g/mol (Da)
Sequence Length
0
nucleotides
GC Content
0.0%
stability metric
Extinction Coeff. (Approx)
0
L/(mol·cm) at 260nm
Nucleotide Composition Analysis
Figure 1: Distribution of nucleotide bases in the provided sequence.
Composition Breakdown Table
Base
Count
Individual MW (g/mol)
Total Contribution (g/mol)
Table 1: Detailed mass contribution by nucleotide type based on input sequence.
Formula Used:MW = Σ(Count × Residue_MW) – Modification_Correction
What is a Molecular Weight Calculator RNA?
A molecular weight calculator rna is a specialized computational tool used by molecular biologists, biochemists, and geneticists to determine the precise molar mass of Ribonucleic Acid (RNA) sequences. Unlike DNA, RNA is typically single-stranded and contains Uracil (U) instead of Thymine (T), which alters the molecular weight calculations significantly compared to DNA tools.
This tool allows researchers to input a specific string of nucleotides (Adenine, Cytosine, Guanine, Uracil) and instantly obtain the total molecular weight in Daltons (Da) or grams per mole (g/mol). This metric is critical for preparing molar solutions, analyzing mass spectrometry data, and verifying the integrity of synthesized RNA oligonucleotides.
Common misconceptions include assuming RNA and DNA have identical residue weights or ignoring the 5′ and 3′ end modifications. A precise molecular weight calculator rna must account for whether the RNA is a chemical synthesis product (typically having a 5′-hydroxyl group) or an in vitro transcript (often retaining a 5′-triphosphate).
Molecular Weight Calculator RNA Formula and Math
The calculation relies on the summation of the individual molecular weights of the nucleotide residues comprising the RNA chain, plus adjustments for the ends of the molecule. The standard formula used in this molecular weight calculator rna is derived from the specific weights of ribonucleotide residues.
The General Equation:
MW = (NA × MWA) + (NC × MWC) + (NG × MWG) + (NU × MWU) + MWends
Variable Definitions
Variable
Meaning
Value (Approx)
MWA
Adenosine Residue Weight
329.21 g/mol
MWC
Cytidine Residue Weight
305.18 g/mol
MWG
Guanosine Residue Weight
345.21 g/mol
MWU
Uridine Residue Weight
306.17 g/mol
MWends
End Modification Correction
-61.96 (Synthetic) / +159.0 (Transcript)
Table 2: Standard atomic weights used for RNA residues.
Note: The "Residue Weight" assumes the nucleotide is incorporated into the chain (monophosphate form minus water). The "End Modification" adjusts for the extra atoms at the 5′ and 3′ termini.
Practical Examples
Below are real-world scenarios showing how to utilize the molecular weight calculator rna for lab preparations.
Example 1: Short siRNA (Small Interfering RNA)
Scenario: A researcher orders a synthetic siRNA strand for gene silencing experiments. The sequence is 21 nucleotides long: AUG GGC CCU UUA AAA GGG C.
Interpretation: The researcher expects a mass spec peak near 6752 Da. If the peak is significantly different, synthesis failed.
Example 2: In Vitro Transcribed RNA
Scenario: A scientist produces a short RNA aptamer using T7 RNA polymerase. The sequence is 15 nt: GGG AGA CUC GUA CUA.
Input Sequence: GGGAGACUCGUACUA
Type: Transcript (5′-ppp)
Result: Approx 4985.2 g/mol
Interpretation: The 5′-triphosphate adds significant mass compared to a synthetic oligo. The molecular weight calculator rna accounts for this +159.0 Da difference automatically.
How to Use This Molecular Weight Calculator RNA
Enter Sequence: Paste your RNA sequence into the main text area. The tool supports standard bases (A, C, G, U). If you paste DNA (with T), the calculator automatically treats T as U.
Select Modification: Choose "Synthetic" if you ordered the RNA from a vendor (standard synthesis). Choose "Transcript" if you made it enzymatically (T7/SP6 polymerase).
Review Intermediates: Check the "Sequence Length" and "GC Content" cards to verify you pasted the correct sequence.
Analyze Results: The primary blue box shows the exact Molecular Weight. Use this number for molarity calculations (Mass / MW = Moles).
Copy Data: Use the green "Copy Results" button to save the data to your lab notebook or electronic records.
Key Factors That Affect Molecular Weight Calculator RNA Results
Several biochemical and physical factors influence the final calculation in any molecular weight calculator rna.
Chemical Modifications: Standard calculators assume unmodified bases. Methylation, fluorophores (e.g., FAM, Cy5), or biotin tags add significant mass.
Counter Ions: In solution, RNA is often associated with Na+ or Mg2+ ions. This calculator provides the "Free Acid" or "Ammonium salt" equivalent weight, not the salt weight.
End Groups (5′ and 3′): As shown in the formula section, a 5′-triphosphate (common in biological transcripts) weighs ~221 Da more than a 5′-hydroxyl.
Isotopic Distribution: This tool uses average atomic weights. For high-resolution mass spectrometry, one might need monoisotopic masses.
Purification Purity: While not a calculation factor, the purity affects the measured weight vs. the calculated weight. Salt adducts can broaden mass spec peaks.
Secondary Structure: While structure (hairpins) doesn't change molecular weight, it affects how the RNA runs on a gel, often leading to discrepancies between estimated size and calculated mass.
Frequently Asked Questions (FAQ)
1. Does this molecular weight calculator rna handle DNA sequences?
It is specifically designed for RNA. However, if you input "T" (Thymine), the system interprets it as "U" (Uracil) for convenience, assuming you pasted a gene sequence intended to be transcribed.
2. What is the difference between Synthetic and Transcript mode?
Synthetic RNA usually has a hydroxyl group (-OH) at both ends. Enzymatically transcribed RNA starts with a triphosphate (-ppp) at the 5′ end. This results in a mass difference of approximately 159 Da.
3. Why is the GC content important?
GC content determines the thermal stability (melting temperature) of the RNA. Higher GC content usually implies a more stable structure with a higher melting point.
4. Can I calculate the mass of a double-stranded RNA (dsRNA)?
This calculator processes single-stranded sequences. For dsRNA (like siRNA), calculate the weight of the sense strand and antisense strand separately using this molecular weight calculator rna, then add them together.
5. What units are displayed?
The result is in Daltons (Da), which is numerically equivalent to grams per mole (g/mol).
6. Does this account for phosphorylation?
If you select "Transcript", it accounts for the 5′-triphosphate. For a simple 5′-monophosphate (common in some degradation products), you would need to adjust the calculation manually or subtract the difference between triphosphate and monophosphate weights.
7. How accurate is the calculation?
It uses standard atomic weights suitable for general laboratory preparation. For high-precision mass spectrometry, ensure you are using the specific atomic weights calibrated for your instrument.
8. Why do I get an error message?
The calculator validates inputs to ensure only valid nucleotide characters (A, C, G, U, T) are processed. Non-nucleotide characters or numbers will trigger an error.
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