Source: https://guthlabs.ai/docs/instruments/dna-rna-protein-molecular-weight-calculator/mechanism/

instrument mechanism / verified-clean

# DNA/RNA/Protein Molecular Weight Calculator mechanism

The inspectable method record for DNA/RNA/Protein Molecular Weight Calculator, kept separate from implementation and qualification.

Status: **VERIFIED_CLEAN**Lifecycle: **verified-clean**

## Model scope

The honest label is directionally appropriate, but it should explicitly state the selected mass mode, terminal chemistry, nucleic-acid residue convention, and that extinction coefficient and pI are unavailable or convention-dependent until their algorithms and reference tables are specified. The four molecular-weight vectors are computable from their supplied reference_data; they do not validate the unspecified extinction-coefficient or pI outputs.

- The molecular-weight formula is incomplete for nucleic acids: terminal adjustments depend on 5-prime and 3-prime chemistry, including hydroxyl, phosphate, cap, cyclic, and duplex states; 'strand type' alone does not specify these constraints.

- The specification permits monoisotopic or average masses but does not define a required mass mode input or default, so the same sequence can legitimately produce different outputs.

- The extinction-coefficient output has no formula, wavelength, strand-concentration convention, or extinction-coefficient table. Nucleic-acid coefficients may use base-sum or nearest-neighbor methods and differ for single-stranded versus duplex molecules.

- The protein pI output has no algorithm or pKa table. A pI calculation requires explicit ionizable-group pKa values, terminal-group assumptions, treatment of cysteine/tyrosine/histidine, and a numerical root-finding convention.

- The nucleic-acid residue-mass convention is ambiguous: tabulated nucleotide-monophosphate/polymer residue masses are not interchangeable with free nucleoside or free nucleotide masses. The terminal correction must be explicitly tied to the selected convention.

## Units and conventions

- Molecular weight is reported in daltons (Da); its numerical value is equal to g/mol for a molecular species, but the displayed unit must not be silently changed.

- The protein average-mass vectors use IUPAC standard atomic-weight conventions and residue masses, followed by one H2O terminal adjustment for an unmodified peptide with free amino and carboxyl termini.

- The protein monoisotopic vector uses neutral-light-isotope residue masses and monoisotopic H2O, followed by one H2O terminal adjustment.

- The DNA vector uses the widely tabulated deoxynucleotide polymer-residue convention and one H2O terminal adjustment, as explicitly shown in that vector; this is not a free-nucleoside calculation.

- No counterions, adducts, salts, isotopic labels, post-translational modifications, nucleotide modifications, or terminal phosphorylation are included.

## Inspectable vector

One of 4 source-bound review vectors:

````
{
  "inputs": {
    "sequence": "A",
    "sequence_type": "protein",
    "mass_mode": "average",
    "termini": "free_NH2_and_COOH"
  },
  "expected_outputs": {
    "MW_Da": 89.09408
  },
  "reference_data": {
    "residue_masses_Da": {
      "A": {
        "value": 71.0788,
        "source_convention": "IUPAC standard atomic weights; widely tabulated standard amino-acid residue value"
      }
    },
    "terminal_adjustment_H2O_Da": {
      "value": 18.01528,
      "source_convention": "IUPAC/CODATA widely tabulated average molecular mass of water"
    },
    "known_entry": "Free alanine average molecular weight = 89.09408 Da under residue-plus-H2O convention",
    "source_convention": "Widely tabulated standard biochemical amino-acid molecular-weight convention"
  },
  "working": "A residue = 71.0788 Da. Add the terminal water adjustment: 71.0788 + 18.01528 = 89.09408 Da. This lands exactly on the widely tabulated average molecular weight of alanine under this convention."
}
````

## Failure boundary

**BREAK_CLAIMED** · SELF_FLAGGED

The specification does not define validation behavior for a zero-length sequence or unknown residues, so a direct lookup implementation can return a chemically misleading water-only result or propagate an undefined mass. It also does not state a default for monoisotopic versus average masses or an explicit DNA-versus-RNA default, allowing materially different outputs.

## Other records

[01**Overview**](<https://guthlabs.ai/docs/instruments/dna-rna-protein-molecular-weight-calculator/>)[03**Implementation**](<https://guthlabs.ai/docs/instruments/dna-rna-protein-molecular-weight-calculator/implementation/>)[04**Qualification**](<https://guthlabs.ai/docs/instruments/dna-rna-protein-molecular-weight-calculator/qualification/>)

## Sources and evidence

These pointers bind the page to evidence. They do not grant authority or collapse verification into deployment.

- `VERIFIED_LEDGER.json`

- `evidence-tranche7/tranche7-results.json`

- `BOUNDARY_HAZARD_CATALOG.json`