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DNA, RNA & Protein

DNA and RNA Sequence Molecular-Weight Workbench

Calculate an average molecular weight from every base in one exact DNA oligonucleotide or RNA transcript and an explicitly selected terminal-chemistry model.

Biology · experimental measurements

Replace length-times-average guesses with a reproducible sequence ledger and named end correction.

Private calculations in your browser · explicit inputs and model boundaries
Example preview · Synthetic DNA oligoBase contributions to molecular weight
A939.63 g/mol
C867.54 g/mol
G1,316.84 g/mol
T1,216.8 g/mol

Bars show the contribution before the -61.96 g/mol terminal correction.

  1. 1EnterProvide the known values
  2. 2CalculateResults update automatically
  3. 3VerifyReview the details and units
Try an example

Use canonical A/C/G/T for DNA or A/C/G/U for RNA; ambiguity codes cannot produce one exact mass.

Calculation result

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Understand the relationship

The reasoning behind the result

Sequence identity changes molecular weight

MW = Σ nᵢMᵢ + terminal correction

A, C, G and T/U have different average molecular weights. Length alone cannot produce the exact value for a known sequence.

The calculator adds each retained canonical base before applying the selected terminal model.

Terminal chemistry belongs in the model

A hydroxylated synthetic DNA oligo, 5′-phosphorylated DNA and a 5′-triphosphate RNA transcript do not share one correction.

The selected model is repeated in the result so the number remains interpretable.

Average molecular weight is not monoisotopic mass

The coefficients are average molecular weights suitable for the named equation, not an exact isotopologue or mass-spectrum peak.

Counterions, hydration state and adducts can change an experimental mass representation.

Unspecified modifications prevent an exact total

Labels, linkers, caps, modified bases, conjugates and other end groups require their own chemical masses.

Ambiguity symbols are rejected because a set of possible bases does not have one sequence-specific value.

Follow the numbers

Calculate an unmodified DNA oligo mass

  1. Declare the molecule as single-stranded DNA with 5′ and 3′ hydroxyl ends.
  2. Count every A, C, G and T in ATGCGTACGTTAGC.
  3. Multiply each count by its named average nucleotide mass.
  4. Sum the four base contributions.
  5. Subtract 61.96 g/mol for the hydroxyl-end equation and report the total in Da and kDa.

The result applies only to the entered sequence and selected unmodified terminal model.

Quick guide

How to use this calculator

  1. Choose the terminal model that matches the molecule actually prepared.
  2. Enter the exact unmodified sequence with the correct DNA or RNA alphabet.
  3. Use the base ledger and end correction to reconcile the total.

Calculation method

Calculation and interpretation

Replace length-times-average guesses with a reproducible sequence ledger and named end correction.

DNA 5′/3′-OH MW = Σ nucleotide masses − 61.96 g/mol; DNA 5′-P adds 79.0 g/mol. RNA transcript MW = Σ ribonucleotide masses + 159.0 g/mol for the declared 5′ triphosphate model.

Worked example

Calculate an unmodified DNA oligo mass

The result applies only to the entered sequence and selected unmodified terminal model.

DNA 5′/3′-OH MW = Σ nucleotide masses − 61.96 g/mol; DNA 5′-P adds 79.0 g/mol. RNA transcript MW = Σ ribonucleotide masses + 159.0 g/mol for the declared 5′ triphosphate model.

Supported inputs

Precision and limits

Canonical bases required

Ambiguity symbols and nonstandard nucleotides are rejected because they do not define one exact sequence mass.

Single strand

The result describes the entered single strand; a duplex requires both strand sequences and terminal states.

Named end models only

Only DNA hydroxyl, DNA 5′ monophosphate and RNA-transcript 5′ triphosphate models are included.

No modifications or adducts

Caps, labels, linkers, conjugates, counterions, hydration and other modifications are excluded.

Numerical support

The sequence-specific sum supports up to 200,000 canonical nucleotide symbols.

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