Molecular Biology Calculators — Scientific Basis

Last reviewed: 2026-08-23

These calculators provide planning estimates and calculation records. They do not replace a validated laboratory SOP, a reagent manufacturer’s instructions, or assay-specific validation. Source wording below is paraphrased.

Oligo resuspension and working stocks

Formula:

resuspension volume (L) = amount (mol) / concentration (mol/L)
working stock volume = target concentration × final volume / source concentration
diluent volume = final volume − stock volume

The calculation uses full unit normalization. DNA versus RNA and the selected diluent are recorded in the result, but neither changes the molar volume equation.

Scientific source:

Oligo Resuspension and Dilution Calculators, Integrated DNA Technologies. IDT describes calculating the volume needed to resuspend a dry-shipped oligo to a selected concentration and emphasizes using the amount actually supplied.

Known limitations:

The calculator does not infer synthesis yield, purity, chemical modifications, extinction coefficient, or storage stability.
Small-volume and large-volume messages are planning warnings, not universal laboratory limits.

Tests tied to the assumption:

10 nmol at 100 µM → 100 µL
25 nmol at 50 µM → 500 µL
20 nmol at 100 µM → 200 µL
500 pmol at 10 µM → 50 µL
100 µM to 10 µM at 1 mL → 100 µL stock plus 900 µL diluent

DNA and RNA copy number

Constants and formulas:

Avogadro constant: exactly 6.02214076 × 10^23 mol^-1.
dsDNA default: MW = length × 660 g/mol per bp.
ssDNA default: MW = length × 307.97 g/mol per nt + 18.02 g/mol.
ssRNA transcript default: MW = length × 320.5 g/mol per nt + 159 g/mol, explicitly representing the documented 5′-triphosphate end correction.
moles = mass / MW.
fmol/µL = mol/µL × 10^15.
copies = moles × Avogadro constant.

The dsDNA constant is deliberately fixed at 660 g/mol per bp across code, UI, fixtures, and documentation. It is an average estimate, not an exact sequence-dependent molecular weight. Custom molecular weight is required for modified nucleic acids.

Scientific sources:

Biomath Calculators, Promega. The dsDNA conversion uses an average molecular weight of 660 pg/pmol for a nucleotide pair, equivalent to 660 g/mol per bp.
NEBioCalculator ssDNA mass-to-moles calculation, New England Biolabs. NEB documents length × 307.97 + 18.02 g/mol for unmodified ssDNA under its stated assumptions.
DNA and RNA Molecular Weights and Conversions, Thermo Fisher Scientific. Thermo Fisher documents the approximate ssRNA formula length × 320.5 + 159 g/mol and identifies the 159 g/mol terminal correction as a 5′ triphosphate.
Nucleic Acid Data, New England Biolabs. NEB also publishes a 650 Da/bp dsDNA convention, illustrating why the selected approximation must be stated rather than presented as exact.

Known limitations:

Average molecular weights do not capture sequence composition, end chemistry, modifications, counterions, or damage.
Molecular copies do not necessarily equal intact, amplifiable, infectious, or functional copies.
Sequence parsing in Pack 1 counts and validates bases; it does not claim sequence-dependent molecular weight.

Tests tied to the assumptions:

Constant-drift tests for Avogadro’s constant and all three default molecular-weight constants.
1,000 bp dsDNA at 1 ng/µL → approximately 9.124 × 10^8 copies/µL.
1,000 bp dsDNA at 1 ng/µL → approximately 1.515 fmol/µL.
3,000 bp dsDNA at 10 ng/µL → approximately 3.041 × 10^9 copies/µL.
FASTA parsing and molecule-specific DNA/RNA alphabets.
Target-copy dilution and raw-sequence URL exclusion tests.

Nucleic acid mass ↔ moles

Constants and formulas:

Avogadro constant: exactly 6.02214076 × 10^23 mol^-1.
moles = mass (g) / molecular weight (g/mol).
mass (g) = moles × molecular weight (g/mol).
molecules = moles × Avogadro constant.
molarity = moles / sample volume (L) when volume is supplied.
Length-based dsDNA, ssDNA, and ssRNA use the same shared molecular-weight source as the Copy Number calculator.
1 Da per molecule is numerically equivalent to 1 g/mol; custom molecular weight accepts Da, kDa, MDa, or g/mol.

Scientific sources:

The mole, Bureau International des Poids et Mesures. The SI defines the Avogadro constant as exactly 6.02214076 × 10^23 mol^-1.
Biomath Calculators, Promega. The dsDNA model uses the published average of 660 g/mol per base pair.
NEBioCalculator ssDNA mass-to-moles calculation, New England Biolabs. The unmodified ssDNA length model is length × 307.97 + 18.02 g/mol under its documented phosphate/hydroxyl assumptions.
DNA and RNA Molecular Weights and Conversions, Thermo Fisher Scientific. The length-based ssRNA transcript model is length × 320.5 + 159 g/mol, including the specified 5′-triphosphate correction.

Known limitations:

All length-based molecular weights are approximations and do not capture sequence composition, modifications, labels, alternate end chemistry, caps, poly(A) tails, counterions, or damage.
Sequence input validates alphabet and supplies length only; it is not used for sequence-composition molecular weight in this release.
Custom molecular weight is required for vendor-specified, sequence-specific, or modified nucleic acids.
Molecule count does not imply intact, amplifiable, infectious, or functional molecules.
The UI flags results below 1 amol or 1 fg as potentially impractical for routine handling and dsDNA above 10 Mbp as unusually large. These are transparent planning heuristics, not universal laboratory limits.

Tests tied to the assumptions:

1 µg of 1,000 bp dsDNA → 1.5151515 pmol and approximately 9.1244557 × 10^11 molecules.
50 ng of 5,000 bp dsDNA → 15.1515 fmol.
100 ng of 20 nt ssDNA with MW 6177.42 g/mol → approximately 16.188 pmol.
10 ng of a 100 nt 5′-triphosphate ssRNA transcript with MW 32209 g/mol → approximately 0.31047 pmol.
1 pmol of 1,000 bp dsDNA → 0.66 µg.
1.515151515 pmol in 10 µL → approximately 151.5151515 nM.
100 ng with a user-supplied 100 kDa molecular weight → 1 pmol.
Shared-source regression tests compare molecular weights returned to Copy Number and Mass ↔ Moles.

DNA ligation stoichiometry

Formula:

insert mass = insert:vector molar ratio × vector mass × insert length / vector length
dsDNA molecular weight = length (bp) × 660 g/mol per bp
fmol = mass (ng) × 10^6 / molecular weight (g/mol)
DNA volume = DNA mass / DNA concentration
remaining unallocated volume = reaction volume − reserved reagent volume − vector volume − insert volume

The ratio direction is always displayed as Insert : Vector. Vector and insert femtomoles use the same 660 g/mol per bp approximation as the copy-number calculator, so the displayed fmol ratio and mass-derived insert:vector ratio remain internally consistent. The calculator supplies DNA stoichiometry only and does not prescribe ligase, buffer, enzyme amount, temperature, or incubation time.

Scientific sources:

NEBioCalculator Ligation Calculator, New England Biolabs. NEB documents the insert-mass equation and displays comparison ratios of 1:1, 2:1, 3:1, 5:1, and 7:1.
DNA Ligation with T4 DNA Ligase, New England Biolabs. NEB reports both mass and molar amounts for vector and insert DNA, demonstrating molar normalization of ligation inputs.
How to Ligate Plasmid DNA, Addgene. Addgene explains that commonly used insert:vector ratios refer to molar availability rather than a simple mass ratio and recommends optimizing when needed.

Known limitations:

Stoichiometric input does not predict ligation efficiency.
Fragment ends, phosphorylation, topology, purity, damage, reaction chemistry, and transformation efficiency are outside the model.
Common ratios are starting points, not guaranteed optima.

Tests tied to the assumption:

4,000 bp vector, 1,000 bp insert, 50 ng vector, 3:1 ratio → 37.5 ng insert.
With the site-wide 660 g/mol per bp assumption, that example is approximately 18.94 fmol vector and 56.82 fmol insert.
Ratio table: 12.5, 25, 37.5, 62.5, and 87.5 ng at 1:1 through 7:1.
Vector and insert volume fixtures.
Reaction-capacity and invalid-ratio guardrail tests.