Calculate Molecular Weight from Nucleotide Sequence
Use this focused tool to calculate molecular weight from nucleotide sequence with base-level accuracy. Enter your DNA or RNA string, choose chemistry options, and see instant molar mass, GC balance, and strand-specific assumptions.
Calculate Molecular Weight from Nucleotide Sequence Calculator
Only letters A, C, G, T (DNA) or U (RNA). Spaces will be removed automatically.
DNA
RNA
DNA uses T and typical base masses; RNA uses U and adjusted base masses.
Yes, include terminal phosphate
No, omit terminal phosphate
Adds 79.0 g/mol if selected.
Use 0 for neutral; enter average bound Na+ per linkage (e.g., 0.5). Each adds 22.99 g/mol.
Blue bars: base counts; Green bars: base percentages
Chart: Composition dynamics update as you calculate molecular weight from nucleotide sequence.
Base Contribution Table
Base
Count
Percentage
Mass per Base (g/mol)
What is calculate molecular weight from nucleotide sequence?
Calculate molecular weight from nucleotide sequence refers to the precise determination of the molar mass of a DNA or RNA strand based on its exact base composition. Scientists, financial planners for biotech budgets, and lab managers use calculate molecular weight from nucleotide sequence to forecast reagent spend, shipping costs for oligos, and downstream assay yields. A common misconception is that calculate molecular weight from nucleotide sequence is a generic mass estimate; in reality, calculate molecular weight from nucleotide sequence depends on base-specific chemistry, terminal groups, and counter ions.
Researchers use calculate molecular weight from nucleotide sequence to set accurate molarity for PCR, qPCR, sequencing library prep, and antisense dosing models. Another misconception is that calculate molecular weight from nucleotide sequence ignores hydration; correct practice subtracts water loss per phosphodiester bond, making calculate molecular weight from nucleotide sequence a rigorous stoichiometric value.
calculate molecular weight from nucleotide sequence Formula and Mathematical Explanation
The core approach to calculate molecular weight from nucleotide sequence begins with summing each nucleotide's monoisotopic mass. To calculate molecular weight from nucleotide sequence, subtract water (18.015 g/mol) for each phosphodiester linkage, then add terminal phosphate if present, and include counter ion adjustments. This keeps calculate molecular weight from nucleotide sequence aligned with laboratory reality.
Step-by-step to calculate molecular weight from nucleotide sequence:
Clean the strand and count A, C, G, T/U.
Multiply each count by its nucleotide mass (DNA: A 313.21, C 289.18, G 329.21, T 304.20; RNA replaces T with U 306.17).
Sum masses, then subtract (n – 1) × 18.015 to account for water loss in phosphodiester bonds when you calculate molecular weight from nucleotide sequence.
Add 79.0 g/mol if a 5′ phosphate is retained.
Add 22.99 g/mol × average bound Na+ × (n – 1) to reflect counter ions in calculate molecular weight from nucleotide sequence.
Every variable in calculate molecular weight from nucleotide sequence must be clear.
Variables for calculate molecular weight from nucleotide sequence
Variable
Meaning
Unit
Typical Range
n
Total nucleotides in calculate molecular weight from nucleotide sequence
count
10–5000
A,C,G,T/U
Base counts used to calculate molecular weight from nucleotide sequence
count
0–n
Mbase
Monoisotopic mass per base
g/mol
289–329
H2O
Water loss per bond in calculate molecular weight from nucleotide sequence
g/mol
18.015
Pterm
Terminal phosphate if retained
g/mol
0 or 79.0
Naadj
Counter ion addition per linkage in calculate molecular weight from nucleotide sequence
g/mol
0–50
Practical Examples (Real-World Use Cases)
Example 1: PCR Primer Budgeting
A lab needs a 22-mer DNA primer: ACTGACTGACTGACTGACTGAC. When they calculate molecular weight from nucleotide sequence, base masses sum to about 6765 g/mol. Subtracting 21 × 18.015 yields 6387.7 g/mol. Adding no phosphate keeps the result near 6387.7 g/mol. This calculate molecular weight from nucleotide sequence value sets accurate nmol-to-mass ordering and ensures procurement budgets align with oligo pricing.
Example 2: RNA Therapeutic Strand
An RNA guide of 100 nt with 0.5 Na+ per linkage includes U instead of T. After you calculate molecular weight from nucleotide sequence, suppose base sum is 31250 g/mol. Subtracting 99 × 18.015 gives 29467.5 g/mol. Counter ion adds 99 × 0.5 × 22.99 = 1135.5 g/mol, so calculate molecular weight from nucleotide sequence outputs ~30603 g/mol. This allows dosing finance teams to model vial fill costs and aligns with GC balance budgets.
How to Use This calculate molecular weight from nucleotide sequence Calculator
Paste or type your strand in the Nucleotide Sequence field; it will auto-clean for calculate molecular weight from nucleotide sequence.
Select DNA or RNA to use the right base masses for calculate molecular weight from nucleotide sequence.
Choose whether to include a 5′ phosphate before you calculate molecular weight from nucleotide sequence.
Enter counter ion loading if relevant; the chart updates as you calculate molecular weight from nucleotide sequence.
Review the primary result and intermediate values to interpret calculate molecular weight from nucleotide sequence for ordering, dilution, and costing.
When you calculate molecular weight from nucleotide sequence here, the highlighted result shows strand mass, while intermediate panels display length, GC content, and average mass. Use the Copy Results button to share calculate molecular weight from nucleotide sequence outputs in protocols or finance sheets.
Key Factors That Affect calculate molecular weight from nucleotide sequence Results
Multiple factors shift the accuracy of calculate molecular weight from nucleotide sequence:
Base composition: G and C are heavier, so GC-rich strands raise calculate molecular weight from nucleotide sequence.
Strand length: Longer oligos accumulate more linkages and water-loss terms, altering calculate molecular weight from nucleotide sequence.
Terminal chemistry: Retaining phosphate or modifications changes calculate molecular weight from nucleotide sequence instantly.
Counter ions: Sodium or ammonium binding adds mass; include this when you calculate molecular weight from nucleotide sequence.
Secondary structure: While not mass-changing, it affects drying efficiency, impacting practical use of calculate molecular weight from nucleotide sequence.
Purification level: Truncations or salts alter the final number; accurate calculate molecular weight from nucleotide sequence assumes pure full-length product.
Hydration state: Lyophilized vs. hydrated oligos influence handling; the chemical math in calculate molecular weight from nucleotide sequence removes bound water per linkage.
Financially, these factors guide cost modeling, as calculate molecular weight from nucleotide sequence drives nmol-to-mass conversions, shipping weight forecasts, and reagent purchase timing tied to throughput planning.
Frequently Asked Questions (FAQ)
Does calculate molecular weight from nucleotide sequence handle mixed DNA/RNA? No, select the strand type; mixed chimeras need manual base mass entries, but you can approximate by splitting and summing.
How do modified bases affect calculate molecular weight from nucleotide sequence? Add the modification mass to the base term before you calculate molecular weight from nucleotide sequence.
Do I subtract water for single nucleotides? For monomers, n=1 so no phosphodiester, and calculate molecular weight from nucleotide sequence equals the single base mass.
Should I include 3′ phosphate? This calculator applies a 5′ phosphate option; for a 3′ phosphate, add 79.0 g/mol to the result after you calculate molecular weight from nucleotide sequence.
What if my sequence has N or R ambiguity? Replace with a specific base choice to calculate molecular weight from nucleotide sequence accurately.
Why is GC content important? Higher GC increases mass and thermal stability; calculate molecular weight from nucleotide sequence captures the mass change while you plan budgets.
Can I use lowercase letters? Input is case-insensitive; it will normalize when you calculate molecular weight from nucleotide sequence.
How precise is the result? It uses monoisotopic masses and hydration correction, giving lab-grade calculate molecular weight from nucleotide sequence values suitable for ordering and finance models.
Related Tools and Internal Resources
Oligo cost model – budget linkage using calculate molecular weight from nucleotide sequence outputs.
Dilution planner – convert calculate molecular weight from nucleotide sequence into working stocks.
GC calculator – align GC trends with calculate molecular weight from nucleotide sequence.
Tm estimator – pair melting data with calculate molecular weight from nucleotide sequence.
Sequencing prep guide – order quantities based on calculate molecular weight from nucleotide sequence.
Molarity converter – translate calculate molecular weight from nucleotide sequence into molar dosing.
var defaultSequence="ATGCGTACGTTAGC";
var baseMassDNA={A:313.21,C:289.18,G:329.21,T:304.2};
var baseMassRNA={A:313.21,C:289.18,G:329.21,U:306.17};
function cleanSequence(seq,type){var cleaned=seq.toUpperCase().replace(/[^ACGTU]/g,"");if(type==="DNA"){cleaned=cleaned.replace(/U/g,"T");}else{cleaned=cleaned.replace(/T/g,"U");}return cleaned;}
function countBases(seq){var counts={A:0,C:0,G:0,T:0,U:0};var i=0;for(i=0;i<seq.length;i++){var b=seq.charAt(i);if(counts.hasOwnProperty(b)){counts[b]++;}}return counts;}
function validateInputs(seq,type,salt){var valid=true;var seqErr="";var typeErr="";var saltErr="";if(seq.length===0){seqErr="Sequence cannot be empty." ;valid=false;}if(type!=="DNA"&&type!=="RNA"){typeErr="Choose DNA or RNA." ;valid=false;}if(isNaN(salt)||salt===""||salt===null){saltErr="Counter ion value must be a number.";valid=false;}else{var s=parseFloat(salt);if(s5){saltErr="Use a realistic range (0 to 5).";valid=false;}}document.getElementById("sequenceError").innerHTML=seqErr;document.getElementById("typeError").innerHTML=typeErr;document.getElementById("saltError").innerHTML=saltErr;return valid;}
function calcMass(seq,type,phos,salt){var counts=countBases(seq);var masses=type==="DNA"?baseMassDNA:baseMassRNA;var total=0;var bases=["A","C","G","T","U"];var i=0;for(i=0;i1?(n-1)*18.015:0;total-=linkLoss;if(phos==="yes"){total+=79.0;}var counterAdj=0;if(n>1){counterAdj=(n-1)*parseFloat(salt)*22.99;total+=counterAdj;}return{mw:total,length:n,gc:((counts.G+counts.C)/Math.max(1,n))*100,avg:n>0?total/n:0,counter:counterAdj,counts:counts};
}
function updateTable(counts,type){var table=document.getElementById("baseTable");table.innerHTML="";var bases=type==="DNA"?["A","C","G","T"]:["A","C","G","U"];var total=0;var i=0;for(i=0;i<bases.length;i++){total+=counts[bases[i]];}for(i=0;i0?((counts[b]/total)*100):0;var mass=type==="DNA"?baseMassDNA[b]:baseMassRNA[b];var row=document.createElement("tr");var c1=document.createElement("td");c1.appendChild(document.createTextNode(b));var c2=document.createElement("td");c2.appendChild(document.createTextNode(counts[b]));var c3=document.createElement("td");c3.appendChild(document.createTextNode(perc.toFixed(2)+"%"));var c4=document.createElement("td");c4.appendChild(document.createTextNode(mass.toFixed(2)));row.appendChild(c1);row.appendChild(c2);row.appendChild(c3);row.appendChild(c4);table.appendChild(row);}
}
function drawChart(counts,type){var canvas=document.getElementById("mwChart");var ctx=canvas.getContext("2d");ctx.clearRect(0,0,canvas.width,canvas.height);var bases=type==="DNA"?["A","C","G","T"]:["A","C","G","U"];var total=0;var i=0;for(i=0;i<bases.length;i++){total+=counts[bases[i]];}var maxCount=0;for(i=0;imaxCount){maxCount=counts[bases[i]];}}if(maxCount===0){maxCount=1;}var barWidth=50;var gap=40;var offset=60;ctx.fillStyle="#eef4ff";ctx.fillRect(0,0,canvas.width,canvas.height);for(i=0;i0?((counts[bases[i]]/total)*100):0;var percHeight=(perc/100)*180;ctx.fillStyle="#004a99″;ctx.fillRect(x,260-countHeight,barWidth,countHeight);ctx.fillStyle="#28a745″;ctx.fillRect(x+barWidth+6,260-percHeight,barWidth,percHeight);ctx.fillStyle="#12263f";ctx.fillText(bases[i],x+barWidth/2,285);ctx.fillText(counts[bases[i]],x+8,245-countHeight);ctx.fillText(perc.toFixed(1)+"%",x+barWidth+10,245-percHeight);}
ctx.fillStyle="#12263f";ctx.fillText("Counts vs Percentages",offset,20);}
function calculateMW(){var seqRaw=document.getElementById("sequenceInput").value;var type=document.getElementById("typeSelect").value;var phos=document.getElementById("phosphateSelect").value;var salt=document.getElementById("saltInput").value;if(!validateInputs(seqRaw,type,salt)){document.getElementById("mainResult").innerHTML="Molecular Weight: 0 g/mol";return;}var cleaned=cleanSequence(seqRaw,type);document.getElementById("sequenceInput").value=cleaned;var res=calcMass(cleaned,type,phos,salt);document.getElementById("mainResult").innerHTML="Molecular Weight: "+res.mw.toFixed(2)+" g/mol";document.getElementById("lengthResult").innerHTML="Total nucleotides: "+res.length;document.getElementById("gcResult").innerHTML="GC content: "+res.gc.toFixed(2)+"%";document.getElementById("avgMassResult").innerHTML="Average mass per nucleotide: "+res.avg.toFixed(2)+" g/mol";document.getElementById("saltAdjResult").innerHTML="Counter ion adjustment: "+res.counter.toFixed(2)+" g/mol";document.getElementById("formulaText").innerHTML="Formula: molecular weight = Σ(base masses) – (n – 1) × 18.015 + terminal phosphate + "+res.counter.toFixed(2)+" g/mol counter ion adjustment";updateTable(res.counts,type);drawChart(res.counts,type);}
function resetForm(){document.getElementById("sequenceInput").value=defaultSequence;document.getElementById("typeSelect").value="DNA";document.getElementById("phosphateSelect").value="no";document.getElementById("saltInput").value="0″;document.getElementById("sequenceError").innerHTML="";document.getElementById("typeError").innerHTML="";document.getElementById("saltError").innerHTML="";calculateMW();}
function copyResults(){var main=document.getElementById("mainResult").innerText;var length=document.getElementById("lengthResult").innerText;var gc=document.getElementById("gcResult").innerText;var avg=document.getElementById("avgMassResult").innerText;var salt=document.getElementById("saltAdjResult").innerText;var formula=document.getElementById("formulaText").innerText;var text=main+"\n"+length+"\n"+gc+"\n"+avg+"\n"+salt+"\n"+formula+"\nAssumptions: sequence cleaned, hydration correction applied, terminal selection="+document.getElementById("phosphateSelect").value+", counter ion="+document.getElementById("saltInput").value;var dummy=document.createElement("textarea");dummy.value=text;document.body.appendChild(dummy);dummy.select();try{document.execCommand("copy");}catch(e){}document.body.removeChild(dummy);}
document.getElementById("sequenceInput").oninput=calculateMW;
document.getElementById("typeSelect").onchange=calculateMW;
document.getElementById("phosphateSelect").onchange=calculateMW;
document.getElementById("saltInput").oninput=calculateMW;