{
 "about": {
  "generatedBy": "pipeline/plasmid-map/reference.py",
  "scriptSha256": "0d7026c8338f04ccc78bc8d477a61d211787e4473326d4c28ed9ba62924875ff",
  "recordedOn": "2026-10-06",
  "oracle": "Biopython 1.88",
  "oracleLicence": "Biopython Licence Agreement or BSD-3-Clause",
  "text": "Bench numbers for a plasmid by exact arithmetic (Python fractions): the molecular weight of the double-stranded circular plasmid from its own sequence (residue formulas from PubChem's dNMPs less water, CIAAW 2021 atomic weights, no end groups), pmol from ng, copies per µL with the exact Avogadro constant, and the ligation insert mass; one case shows the 650 Da per bp approximation beside the exact figure.",
  "atomicWeights": {
   "H": "1.0080",
   "C": "12.011",
   "N": "14.007",
   "O": "15.999",
   "P": "30.974"
  },
  "avogadro": "6.02214076e23 (exact, SI 2019)"
 },
 "cases": [
  {
   "id": "A01",
   "label": "pUC19, 1 µg",
   "kind": "pmol",
   "input": {
    "plasmid": "L09137.2",
    "lengthBp": 2686,
    "ng": 1000
   },
   "expected": {
    "value": 0.6025208835093896,
    "exact": "0.602520884",
    "unit": "pmol"
   },
   "working": "pmol = ng x 1000 / MW = 1000 x 1000 / 1659693.5100"
  },
  {
   "id": "A02",
   "label": "pBR322, 500 ng",
   "kind": "pmol",
   "input": {
    "plasmid": "J01749.1",
    "lengthBp": 4361,
    "ng": 500
   },
   "expected": {
    "value": 0.18554121286562347,
    "exact": "0.185541213",
    "unit": "pmol"
   },
   "working": "pmol = ng x 1000 / MW = 500 x 1000 / 2694819.0770"
  },
  {
   "id": "A03",
   "label": "pUC19 at 10 ng/µL",
   "kind": "copies-per-ul",
   "input": {
    "plasmid": "L09137.2",
    "ngPerUl": 10
   },
   "expected": {
    "value": 3628465571.333107,
    "exact": "3628465571.333107159",
    "unit": "copies/µL"
   },
   "working": "copies/µL = ng/µL x 1e-9 g/ng x N_A / MW = 10 x 1e-9 x 6.02214076e23 / 1659693.5100"
  },
  {
   "id": "A04",
   "label": "pBR322 at 1 ng/µL",
   "kind": "copies-per-ul",
   "input": {
    "plasmid": "J01749.1",
    "ngPerUl": 1
   },
   "expected": {
    "value": 223471060.13158152,
    "exact": "223471060.131581516",
    "unit": "copies/µL"
   },
   "working": "copies/µL = ng/µL x 1e-9 g/ng x N_A / MW = 1 x 1e-9 x 6.02214076e23 / 2694819.0770"
  },
  {
   "id": "A05",
   "label": "50 ng pUC19, 720 bp insert, 3:1",
   "kind": "ligation-insert-ng",
   "input": {
    "vectorNg": 50,
    "vectorBp": 2686,
    "insertBp": 720,
    "ratio": 3
   },
   "expected": {
    "value": 40.20848845867461,
    "exact": "40.208488459",
    "unit": "ng"
   },
   "working": "insert ng = vector ng x (insert bp / vector bp) x ratio = 50 x (720 / 2686) x 3"
  },
  {
   "id": "A06",
   "label": "100 ng pUC19, 720 bp insert, 1:1",
   "kind": "ligation-insert-ng",
   "input": {
    "vectorNg": 100,
    "vectorBp": 2686,
    "insertBp": 720,
    "ratio": 1
   },
   "expected": {
    "value": 26.805658972449738,
    "exact": "26.805658972",
    "unit": "ng"
   },
   "working": "insert ng = vector ng x (insert bp / vector bp) x ratio = 100 x (720 / 2686) x 1"
  },
  {
   "id": "A07",
   "label": "50 ng pBR322, 1,000 bp insert, 5:1",
   "kind": "ligation-insert-ng",
   "input": {
    "vectorNg": 50,
    "vectorBp": 4361,
    "insertBp": 1000,
    "ratio": 5
   },
   "expected": {
    "value": 57.32630130703967,
    "exact": "57.326301307",
    "unit": "ng"
   },
   "working": "insert ng = vector ng x (insert bp / vector bp) x ratio = 50 x (1000 / 4361) x 5"
  },
  {
   "id": "A08",
   "label": "pUC19, 1 µg, the 650 Da per bp approximation",
   "kind": "pmol-approximate",
   "input": {
    "lengthBp": 2686,
    "ng": 1000,
    "daltonsPerBp": 650
   },
   "expected": {
    "value": 0.5727704908643106,
    "exact": "0.572770491",
    "unit": "pmol"
   },
   "working": "pmol = 1000 x 1000 / (2686 x 650)"
  },
  {
   "id": "A09",
   "label": "ng of pUC19 for 1e10 copies",
   "kind": "ng-for-copies",
   "input": {
    "plasmid": "L09137.2",
    "copies": 10000000000
   },
   "expected": {
    "value": 27.559859128898875,
    "exact": "27.559859129",
    "unit": "ng"
   },
   "working": "ng = copies x MW / N_A x 1e9 = 1e10 x 1659693.5100 / 6.02214076e23 x 1e9"
  },
  {
   "id": "A10",
   "label": "MW of pUC19, double-stranded and circular",
   "kind": "mw",
   "input": {
    "plasmid": "L09137.2",
    "counts": {
     "A": 667,
     "C": 675,
     "G": 685,
     "T": 659
    }
   },
   "expected": {
    "value": 1659693.51,
    "exact": "1659693.510000000",
    "unit": "g/mol"
   },
   "working": "sum over both strands of the residue masses (dNMP less water), no end groups (circular), CIAAW 2021"
  },
  {
   "id": "A11",
   "label": "MW of pBR322, double-stranded and circular",
   "kind": "mw",
   "input": {
    "plasmid": "J01749.1",
    "counts": {
     "A": 983,
     "C": 1210,
     "G": 1134,
     "T": 1034
    }
   },
   "expected": {
    "value": 2694819.077,
    "exact": "2694819.077000000",
    "unit": "g/mol"
   },
   "working": "sum over both strands of the residue masses (dNMP less water), no end groups (circular), CIAAW 2021"
  }
 ]
}