Molecular Biology Calculator

Formulas & sources

The formulas, references and assumptions behind the calculators.

Calculators

Quick calculations

DNA

PCR

  • PCR master mix: Per-reaction and batch volumes, custom or kit example preset.
  • Primer volume: Forward and reverse primer stock volumes per reaction.

Cloning & assembly

  • DNA ligation: Insert mass and pipetting volumes for an insert:vector molar ratio.

Reagents

Formulas

  • F01 · Stock dilution: C₁·V₁ = C₂·V₂; V_stock = C_target · V_final / C_stock; V_diluent = V_final − V_stock
  • F02 · Serial dilution: DF_i = V_total,i / V_aliquot,i; DF_total = Π DF_i; C_end = C_start / DF_total
  • F03 · Mass / molarity: n = m / MW; C = m / (MW · V); m = C · MW · V
  • F04 · Reaction and master-mix preparation: V_i = C_final,i · V_reaction / C_stock,i; V_water = V_reaction − Σ V_i; V_batch,i = N · (1 + e) · V_i
  • F07 · dsDNA mass ↔ amount: n_pmol = 1000 · m_ng / (650 · L_bp); m_ng = n_pmol · 650 · L_bp / 1000
  • F08 · dsDNA concentration ↔ molarity: C_nM = 10⁶ · C_ng/µL / (650 · L_bp); C_ng/µL = C_nM · 650 · L_bp / 10⁶
  • F09 · DNA molecule count: copies = (m_ng · 10⁻⁹ / (650 · L_bp)) · N_A; N_A = 6.02214076 × 10²³ mol⁻¹
  • F10 · DNA mass ↔ volume: m_ng = C_ng/µL · V_µL; V_µL = m_ng / C_ng/µL
  • F11 · Ligation insert mass: m_insert = r · m_vector · L_insert / L_vector; V = m / C (F10, pipetting volume)
  • F15 · PCR primer stock volume: V_primer = C_primer,final · V_reaction / C_primer,stock
  • F16 · PCR master mix with template: Component scaling and water by F04; Kit values only from named, versioned presets
  • F20 · Basic DNA sequence statistics: length = A + C + G + T; GC % = 100 · (G + C) / length; reverse complement: reverse, A↔T, C↔G
  • P01 · Direct working dilution: C_source · V_source = C_working · V_prepared; DF = C_source / C_working = V_prepared / V_source; V_diluent = V_prepared − V_source
  • P02 · Stock + diluent notation: a + b = a parts stock + b parts diluent; DF = (a + b) / a; 1 + 9 = 1:10; 10 + 190 = 1:20
  • P03 · Target transfer from selected source: V_transfer = target_amount / C_source(planned); target_amount = C_stock · V_theoretical(stock) (locked)
  • P04 · Prepared concentration after setpoint rounding: C_working,planned = C_source · V_stock,planned / (V_stock,planned + V_diluent,planned); achieved DF = (V_stock + V_diluent) / V_stock (not the requested DF if rounded)
  • P05 · Planned delivery and deviation: amount_planned = C_working,planned · V_setpoint; deviation % = 100 · (amount_planned / amount_target − 1); planned ratio = (m_i,planned / L_i) / (m_v,planned / L_v)
  • P06 · Reaction balance: V_water = V_reaction − Σ V_non-water (negative ⇒ infeasible, never clamped); DNA-only: remaining = capacity − Σ V_DNA
  • P07 · Working-solution demand and batch: demand = n_transfers · V_setpoint · (1 + excess) + dead volume; batch_i = N · (1 + e) · V_i (per-well composition unchanged)
  • P08 · Instrument setpoint quantization: setpoint_nL = round(V · 1000 / increment_nL) · increment_nL (nearest | down | up); settable ⇔ range_min ≤ setpoint ≤ range_max; increment ≠ accuracy
  • P09 · Nominal practical batch and remainder: V_batch,nom = Σ setting_j · aspirations_j (integer nL); ΔV = V_batch,nom − V_batch,theoretical; V_remainder,nom = V_batch,nom − N · V_dispense,nom (< 0 ⇒ blocked; no dead-volume model)
  • P10 · Nominal final concentration from planned settings: in mix: C_final,nom = C_source · (V_i,batch,nom / V_batch,nom) · V_dispense,nom / V_reaction,nom; per well: C_final,nom = C_source · V_i,nom / V_reaction,nom; V_reaction,nom = V_dispense,nom + Σ V_per-well,nom (nominal settings, not measured)

Sources