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- DNA Migration in Agarose and Polyacrylamide Gels
- Amino Acids Abbreviations
- Codons and Assigned Amino Acids
- Genome Comparisons
- Common Conversions of Nucleic Acids
- DNA/Protein Conversions
- Concentrations of Acids and Bases
- Common Conversions of Oligonucleotides
- Melting Temperature of Duplex DNA and Oligonucleotides
- Physical Constants of the Nucleoside Triphosphates and Related Compounds
- SI Unit Prefixes
- Temperature Dependence of the pH for Commonly Used Buffers
- Temperature Dependence of the pH of 50 mM Tris-HCl Solutions
- Physical Properties of Some Common Radioisotopes
- Decay Factors for Calculating the Amount of Radioactivity
- Commonly Used Media
- Commonly Used Stock Solutions
- Commonly Used Buffers
- Commonly Used Abbreviations
DNA Migration in Agarose and Polyacrylamide Gels
Recommended Gel Percentages for Separation of Linear DNA
| Agarose gel, % |
Range of separation, bp |
Polyacrylamide gel, % |
Range of separation, bp |
|---|---|---|---|
| 0.5 | 1,000-30,000 | 3.5 | 100-1,000 |
| 0.7 | 800-12,000 | 5.0 | 80-500 |
| 1.0 | 500-10,000 | 8.0 | 60-400 |
| 1.2 | 400-7,000 | 12.0 | 40-200 |
| 1.4 | 200-4,000 | 20.0 | 5-100 |
| 2.0 | 50-2,000 |
Migration Rates of the Marker Dyes through Polyacrylamide Gels (1)
| Polyacrylamide gel, % |
Bromophenol blue* |
Xylene cyanol FF* |
|---|---|---|
| Non-denaturing gels | ||
| 3.5 | 100 bp | 460 bp |
| 5.0 | 65 bp | 260 bp |
| 8.0 | 45 bp | 160 bp |
| 12.0 | 20 bp | 70 bp |
| 15.0 | 15 bp | 60 bp |
| 20.0 | 12 bp | 45 bp |
| Denaturing gels | ||
| 5.0 | 35 bases | 130 bases |
| 6.0 | 29 bases | 106 bases |
| 8.0 | 26 bases | 76 bases |
| 10.0 | 12 bases | 55 bases |
| 20.0 | 8 bases | 28 bases |
DNA Size Migration with Sample Loading Dyes
| Agarose concentration, % | Xylene cyanol FF | Bromophenol blue | Orange G |
|---|---|---|---|
| 0.7-1.7 | ~4000bp | ~300bp | ~50bp |
| 2.5-3.0 | ~800bp | ~100bp | ~30bp |
- Sambrook, J., et al., Molecular Cloning. A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., 12.89, 5.42, 2001.
Amino Acids Abbreviations
| Amino acid | 3 letter abbreviations | 1 letter abbreviations | MW, Daltons |
|---|---|---|---|
| Alanine | Ala | A | 89.1 |
| Arginine | Arg | R | 174.2 |
| Asparagine | Asn | N | 132.1 |
| Aspartic Acid | Asp | D | 133.1 |
| Asparagine or Aspartic Acid |
Asx | B | - |
| Cysteine | Cys | C | 121.2 |
| Glutamic Acid | Glu | E | 147.1 |
| Glutamine | Gln | Q | 146.1 |
| Glutamine or Glutamic Acid |
Glx | Z | – |
| Glycine | Gly | G | 75.1 |
| Histidine | His | H | 155.2 |
| Isoleucine | Ile | I | 131.2 |
| Leucine | Leu | L | 131.2 |
| Lysine | Lys | K | 146.2 |
| Methionine | Met | M | 149.2 |
| Phenylalanine | Phe | F | 165.2 |
| Proline | Pro | P | 115.1 |
| Serine | Ser | S | 105.1 |
| Threonine | Thr | T | 119.1 |
| Tryptophan | Trp | W | 204.2 |
| Tyrosine | Tyr | Y | 181.2 |
| Valine | Val | V | 117.1 |
Codons and Assigned Amino Acids
| First (5') | Second | Third (3') | |||
| U | C | A | G | ||
| U | Phe Phe Leu Leu |
Ser Ser Ser Ser |
Tyr Tyr Ter* Ter* |
Cys Cys Ter* Trp |
U C A G |
| C | Leu Leu Leu Leu |
Pro Pro Pro Pro |
His His Gln Gln |
Arg Arg Arg Arg |
U C A G |
| A | Ile Ile Ile fMet |
Thr Thr Thr Thr |
Asn Asn Lys Lys |
Ser Ser Arg Arg |
U C A G |
| G | Val Val Val Val** |
Ala Ala Ala Ala |
Asp Asp Glu Glu |
Gly Gly Gly Gly |
U C A G |
** Codes for fMet if in the initiator position
Genome Comparisons
| Virus | Length, nt | Approx. MW, Da |
|---|---|---|
| Bacteriophage PhiX174 | 5,380 | 3.5 x 106 |
| Bacteriophage Lambda | 48,502 | 3.1 x 107 |
| Human Immunodeficiency Virus 1 | 9,181 | 3.1 x 106 |
| Rous Sarcoma Virus | 9,392 | 3.2 x 106 |
| SARS Coronavirus | 29,751 | 1.0 x 107 |
| Simian Virus 40 (SV 40) | 5,224 | 3.4 x 106 |
| Vaccinia Virus | 191,737 | 1.2 x 108 |
| Variolla (Small pox) Virus | 185,578 | 1.2 x 108 |
| Archaebacteria | Length of DNA, nt | Approx. MW, Da |
| Halobacterium sp. NRC-1 | 2.01 x 106 | 1.31 x 109 |
| Methanosarcina acetivorans C2A | 5.75 x 106 | 3.74 x 109 |
| Methanococcus jannaschii DSM2661 | 1.66 x 106 | 1.08 x 109 |
| Methanosarcina mazei Go1 | 4.10 x 106 | 2.66 x 109 |
| Methanobacterium thermoautotrophicum delta H | 1.75 x 106 | 1.14 x 109 |
| Pyrococcus horikoshii OT3 | 1.74 x 106 | 1.13 x 109 |
| Pyrococcus abysii GE5 | 1.76 x 106 | 1.14 x 109 |
| Pyrococcus furiosus DSM3638 | 1.91 x 106 | 1.24 x 109 |
| Sulfolobus solfataricus P2 | 2.99 x 106 | 1.94 x 109 |
| Thermoplasma acidophilum | 1.56 x 106 | 1.01 x 109 |
| Bacteria | Length of DNA, nt | Approx. MW, Da |
| Agrobacterium tumefaciens C58-Cereon | 4.91 x 106 | 3.19 x 109 |
| Aquifex aeolicus VF5 | 1.55 x 106 | 1.00 x 109 |
| Bacillus subtilis 168 | 4.20 x 106 | 2.73 x 109 |
| Bacillus halodurans | 4.20 x 106 | 2.73 x 109 |
| Bordetella pertussis Tohama I NCTC-13251 | 4.07 x 106 | 2.65 x 109 |
| Chlamydophila pneumoniae CWL029 | 1.23 x 106 | 8.00 x 108 |
| Deinococcus radiodurans R1 | 3.28 x 106 | 2.13 x 109 |
| Escherichia coli K12 | 4.64 x 106 | 3.02 x 109 |
| Escherichia coli 0157:H7 EDL933 | 4.10 x 106 | 2.66 x 109 |
| Haemophilus influenzae KW20 | 1.83 x 106 | 1.19 x 109 |
| Helicobacter pylori 26695 | 1.66 x 106 | 1.08 x 109 |
| Lactococcus lactis IL1403 | 2.36 x 106 | 1.53 x 109 |
| Mycobacterium leprae TN | 3.27 x 106 | 2.12 x 109 |
| Mycobacterium tuberculosis H37Rv | 4.45 x 106 | 2.89 x 109 |
| Mycoplasma genitalium G037 | 5.80 x 105 | 3.77 x 108 |
| Mycoplasma pneumoniae M129 | 8.16 x 105 | 5.30 x 108 |
| Neisseria meningitidis Z2491 | 2.18 x 106 | 1.42 x 109 |
| Salmonella typhimurium LT2 SGSC1412 | 4.86 x 106 | 3.16 x 109 |
| Staphylococcus aureus MW2 | 2.82 x 106 | 1.83 x 109 |
| Streptomyces coelicolor A3(2) | 8.67 x 106 | 5.64 x 109 |
| Streptococcus pneumoniae R6 | 2.04 x 106 | 1.33 x 109 |
| Streptococcus pyogenes SF370 (M1) | 1.85 x 106 | 1.20 x 109 |
| Pseudomonas aeruginosa | 6.26 x 106 | 4.07 x 109 |
| Vibrio cholerae N16961 | 4.00 x 106 | 2.60 x 109 |
| Eukaryotes | Length of DNA, nt | Approx. MW, Da |
| Anopheles gambiae PEST (malaria mosquito) | 2.78 x 108 | 1.80 x 1011 |
| Arabidopsis thaliana (flowering plant) | 1.15 x 108 | 7.47 x 1010 |
| Caenorhabditis briggsae (soil-dwelling nematode) | 1.04 x 108 | 6.76 x 1010 |
| Caenorhabditis elegans (round worm) | 1.21 x 107 | 7.86 x 109 |
| Ciona intestinalis (ascidian tadpole) | 1.16 x 108 | 7.54 x 1010 |
| Drosophila melanogaster (fruit fly) | 1.37 x 108 | 8.90 x 1010 |
| Guillardia theta (chromophyte algae) | 5.51 x 105 | 3.58 x 108 |
| Homo sapiens (human) | 3,15 x 109 | 2.07 x 1012 |
| Mus musculus (mouse) | ~3,00 x 109 | ~1.95 x 1012 |
| Neurospora crassa OR74A (filamentous fungus) | 4.30 x 107 | 2.80 x 1010 |
| Saccharomyces cerevisiae S288C (budding yeast) | 1.21 x 107 | 7.86 x 109 |
| Schizosaccharomyces pombe (fission yeast) | 1.40 x 107 | 9.10 x 109 |
| Plasmodium falciparum 3D7 (human malaria parasite) | 2.29 x 107 | 1.49 x 1010 |
| Oryza sativa japonica (rice) | 4.20 x 108 | 2.73 x 1011 |
GOLD Genomes OnLine Database
Common Conversions of Nucleic Acids
Molar Conversions
| Phage/Plasmin DNA | bp | Quantity | |
|---|---|---|---|
| µg | pmol | ||
| DNA | 1000 | 1 | 1.52 |
| 0.66 | 1 | ||
| pUC18/19 DNA | 2686 | 1 | 0.57 |
| 1.77 | 1 | ||
| pBR322 DNA | 4361 | 1 | 0.35 |
| 2.88 | 1 | ||
| SV40 DNA | 5243 | 1 | 0.29 |
| 3.46 | 1 | ||
| phiX174 DNA | 5386 | 1 | 0.28 |
| 3.54 | 1 | ||
| M13mp18/19 DNA | 7250 | 1 | 0.21 |
| 4.78 | 1 | ||
| lambda phage DNA | 48502 | 1 | 0.03 |
| 32.01 | 11 | ||
Spectrophotometric Conversions
| NA | A260 | µg/ml | mM (in nucleotides) |
| dsDNA | 1 | 50 | 0.15 |
| ssDNA | 1 | 33 | 0.1 |
| ssRNA | 1 | 40 | 0.12 |
| dsDNA | 6.7 | 335 | 1 |
| ssDNA | 10.0 | 330 | 1 |
| ssRNA | 8.3 | 332 | 1 |
| The average MW of a deoxyribonucleotide base = 333 Da The average MW of a ribonucleotide base = 340 Da The average MW of a deoxyribonucleotide base pair = 650 Da |
|||
Estimation of Ends (3' or 5') Concentration
| Circular DNA pmol ends = pmol DNA x number of cuts x 2 |
|
| Linear DNA pmol ends = pmol DNA x (number of cuts x 2 + 2) |
|
| Phage/Plasmid DNA | pmol (1 µg) |
|---|---|
| 1000 bp DNA | 3.04 |
| linear pUC18/19 DNA | 1.14 |
| linear pBR322 DNA | 0.7 |
| linear SV40 DNA | 0.58 |
| linear phiX174 DNA | 0.56 |
| linear M13mp18/19 DNA | 0.42 |
| lambda phage DNA | 0.06 |
- Sambrook, J. et al., Molecular Cloning. A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., 2001.
DNA/Protein Conversions
| 1 kb of DNA = 333 amino acids approx. is 3.7 x 104 Da 10 kDa protein approx. is 270 bp DNA 30 kDa protein approx. is 810 bp DNA 50 kDa protein approx. is 1.32 kb DNA 100 kDa protein approx. is 2.7 kb DNA |
Concentrations of Acids and Bases
| Substance | Formula | MW | Moles/liter* | Grams/liter | % by weight | Specific gravity | ml/liter to prepare 1 M solution |
|---|---|---|---|---|---|---|---|
| Acetic acid, glacial | CH3COOH | 60.05 | 17.4 | 1045 | 99.5 | 1.05 | 57.5 |
| Acetic acid | CH3COOH | 60.05 | 6.27 | 376 | 36 | 1.045 | 159.5 |
| Formic acid | HCOOH | 46.02 | 23.4 | 1080 | 90 | 1.20 | 42.7 |
| Hydrochloric acid | HCl | 36.5 | 11.6 | 424 | 36 | 1.18 | 86.2 |
| Nitric acid | HNO3 | 63.02 | 15.99 | 1008 | 71 | 1.42 | 62.5 |
| Perchloric acid | HClO4 | 100.5 | 11.65 | 1172 | 70 | 1.67 | 85.8 |
| Phosphoric acid | H3PO4 | 97.9 | 14.8 | 1445 | 85 | 1.70 | 67.7 |
| Sulfuric acid | H2SO4 | 98.1 | 18.0 | 1766 | 96 | 1.84 | 55.6 |
| Ammonium hydroxide | NH4OH | 35.0 | 14.8 | 251 | 28 | 0.898 | 67.6 |
| Potassium hydroxide | KOH | 56.1 | 13.5 | 757 | 50 | 1.52 | 74.1 |
| Sodium hydroxide | NaOH | 40.0 | 19.1 | 763 | 50 | 1.53 | 52.4 |
Common Conversions of Oligonucleotides
| Molecular Weight MW = 333 x N Concentration of Oligonucleotides C (µM or pmol/µl) = A260 / (0.01 x N) C (ng/ml) = (A260 x MW) / (0.01 x N) MW – molecular weight, Da A260 – absorbance at 260 nm N – number of bases |
Melting Temperature of Duplex DNA and Oligonucleotides
For Duplex Oligonucleotide shorter than 25 bp, "The Wallace Rule" (1)
Tm (in °C) = 2(A+T) + 4(C+G), where
(A+T) – the sum of the A and T residues in the oligonucleotide,
(C+G) – the sum of G and C residues in the oligonucleotide.
Presence of m5C in oligonucleotide increases melting temperature of duplex. Presence of m4C or m6A decreases melting temperature (2).
For Duplex DNA, <100 bp long (3)
Tm (in °C) = 81.5°C+16.6(log10[Na+])+0.41(%[G+C])-675/n-1.0m, where
n – number of bases in the oligonucleotide,
m – the percentage of base-pair mismatches.
References
- Wallace, R.B., et al., Hybridization of synthetic oligodeoxyribonucleotides to phiX174 DNA: the effect of single base pair mismatch, Nucleic Acids Res., 6, 3543-3557, 1979.
- Butkus, V., et al., Synthesis and physical characterization of DNA fragments containing N4-methylcytosine and 5-methylcytosine, Nucleic Acids Res., 20, 8467-8478, 1987.
- Sambrook, J., et al., Molecular Cloning. A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., 10.2-10.4, 2001.
Physical Constants of the Nucleoside Triphosphates and Related Compounds
| Compound | MW, Da (acid form) | lambdamax*, nm |
epsilon**, M-1 x cm-1 |
|---|---|---|---|
| ATP | 507 | 259 | 15400 |
| CTP | 483 | 271 | 9000 |
| GTP | 523 | 253 | 13700 |
| UTP | 484 | 262 | 10000 |
| dATP | 491 | 259 | 15200 |
| dCTP | 467 | 271 | 9300 |
| dGTP | 507 | 253 | 13700 |
| dTTP | 482 | 267 | 9600 |
| ddATP | 475 | 261 | 15200 |
| ddCTP | 451 | 271 | 13100 |
| ddGTP | 491 | 253 | 13600 |
| ddTTP | 466 | 267 | 9600 |
| dm6ATP | 507 | 265 | 15400 |
| dm4CTP | 481 | 274 | 13600 |
| dm5CTP | 481 | 279 | 8770 |
| Aminoallyl-dUTP | 523 | 240 290 |
11900 7800 |
| Biotin-11-dUTP | 862 | 240 286 |
10700 7100 |
| NAD | 664 | 260 | 18000 |
| NADH | 665 | 338*** | 6200 |
| NADP | 743 | 260 | 18000 |
| NADPH | 745 | 260 | 18000 |
** molar absorption coefficient (absorbance at lambdamax for 1 M solution at pH 7.0)
*** determined at pH 10.0
| Conversion Formula |
|---|
| C = A / epsilon x 103, where C – mM concentration of compounds A – observed absorbance at lambdamax (nm) epsilon – molar absorption coefficient (M-1 x cm-1) |
SI Unit Prefixes
| Prefix | Symbol | Multiple |
|---|---|---|
| exa | E | 1018 |
| peta | P | 1015 |
| tera | T | 1012 |
| giga | G | 109 |
| mega | M | 106 |
| kilo | k | 103 |
| hecto* | h | 102 |
| deka* | da | 101 |
| deci* | d | 10-1 |
| centi | c | 10-2 |
| milli | m | 10-3 |
| micro | µ | 10-6 |
| nano | n | 10-9 |
| pico | p | 10-12 |
| femto | f | 10-15 |
| atto | a | 10-18 |
Temperature Dependence of the pH for Commonly Used Buffers
| Buffer System | Chemical name | pKa/20°C | [Delta]pKa/10°C |
|---|---|---|---|
| MES | 4-morpholineethanesulfonic acid | 6.15 | -0.110 |
| ADA | [(carbamoylmethyl)imino]diacetic acid | 6.60 | -0.110 |
| PIPES | 1,4-piperazinediethanesulfonic acid | 6.80 | -0.085 |
| ACES | 2-[(2-amino-2-oxoethyl)amino]ethanesulfonic acid | 6.90 | -0.200 |
| BES | 2-[bis(2-hydroxyethyl)amino]ethanesulfonic acid | 7.15 | -0.160 |
| MOPS | 4-morpholinepropanesulfonic acid | 7.20 | -0.013 |
| TES | 2-{[2-hydroxy-1,1-bis(hydroxymethyl)ethyl]amino}-1-propanesulfonic acid | 7.50 | -0.200 |
| HEPES | 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid | 7.55 | -0.140 |
| TRICINE | N-[2-hydroxy-1,1-bis(hydroxymethyl)ethyl]glycine | 8.15 | -0.210 |
| TRIS | 2-amino-2-hydroxymethylpropane-1,3-diol | 8.30 | -0.310 |
| BICINE | N,N-bis(2-hydroxyethyl)glycine | 8.35 | -0.180 |
| GLYCYLGLYCINE | 2-(2-aminoacetyl)aminoacetic acid | 8.40 | -0.280 |
- Good, N.E., Hydrogen ion buffers for biological research, Biochemistry 5, 467-477, 1966.
Temperature Dependence of the pH of 50 mM Tris-HCl Solutions
| 4°C | 25°C | 37°C |
|---|---|---|
| 8.1 | 7.5 | 7.2 |
| 8.2 | 7.6 | 7.3 |
| 8.3 | 7.7 | 7.4 |
| 8.4 | 7.8 | 7.5 |
| 8.5 | 7.9 | 7.6 |
| 8.6 | 8.0 | 7.7 |
| 8.7 | 8.1 | 7.8 |
| 8.8 | 8.2 | 7.9 |
| 8.9 | 8.3 | 8.0 |
| 9.0 | 8.4 | 8.1 |
| 9.1 | 8.5 | 8.2 |
| 9.2 | 8.6 | 8.3 |
| 9.3 | 8.7 | 8.4 |
| 9.4 | 8.8 | 8.5 |
Physical Properties of Some Common Radioisotopes
| Radioisotope | Half-life | Specific activity, MBq/mmol |
|---|---|---|
| 32P | 14.3 days | 102-107 |
| 33P | 25.4 days | 102-107 |
| 35S | 87.4 days | 10-107 |
| 131I | 8.06 days | 103-105 |
| 125I | 60 days | 103-107 |
| 14C | 5730 years | 10-103 |
| 3H | 12.43 years | 103-106 |
Summary of Useful Conversion
| 1 Becquerel (Bq) = 1 disintegration per second = 2.7x10-11 Curies (Ci) 1 Ci = 3.7x1010 Bq = 37 GBq = 2.22x1012 disintegrations per minute (dpm) 1 mCi = 37 MBq = 2.22x109 dpm 1 µCi = 37 kBq = 2.22x106 dpm 1 GBq = 27 mCi 1 MBq = 27 µCi 1 kBq = 27 nCi |
Decay Factors for Calculating the Amount of Radioactivity
32P, (half-life – 14.3 days)
| Days/Hours | 0 | 12 | 24 | 36 | 48 | 60 | 72 | 84 |
|---|---|---|---|---|---|---|---|---|
| 0 | 1.000 | 0.976 | 0.953 | 0.930 | 0.908 | 0.886 | 0.865 | 0.844 |
| 4 | 0.824 | 0.804 | 0.785 | 0.766 | 0.748 | 0.730 | 0.712 | 0.695 |
| 8 | 0.679 | 0.662 | 0.646 | 0.631 | 0.616 | 0.601 | 0.587 | 0.573 |
| 12 | 0.559 | 0.546 | 0.533 | 0.520 | 0.507 | 0.495 | 0.483 | 0.472 |
| 16 | 0.460 | 0.449 | 0.439 | 0.428 | 0.418 | 0.408 | 0.398 | 0.389 |
| 20 | 0.379 | 0.370 | 0.361 | 0.353 | 0.344 | 0.336 | 0.328 | 0.320 |
| 24 | 0.312 | 0.305 | 0.398 | 0.291 | 0.284 | 0.277 | 0.270 | 0.264 |
| 28 | 0.257 | 0.251 | 0.245 | 0.239 | 0.234 | 0.228 | 0.223 | 0.217 |
| 32 | 0.212 | 0.207 | 0.202 | 0.197 | 0.192 | 0.188 | 0.183 | 0.179 |
| 36 | 0.175 | 0.170 | 0.166 | 0.162 | 0.159 | 0.155 | 0.151 | 0.147 |
| 40 | 0.144 | 0.140 | 0.137 | 0.134 | 0.131 | 0.127 | 0.124 | 0.121 |
| 44 | 0.119 | 0.116 | 0.113 | 0.110 | 0.108 | 0.105 | 0.102 | 0.100 |
| 48 | 0.098 | 0.095 | 0.093 | 0.091 | 0.089 | 0.086 | 0.084 | 0.082 |
| 52 | 0.080 | 0.078 | 0.077 | 0.075 | 0.073 | 0.071 | 0.070 | 0.068 |
| Weeks/Days | 0 | 1 | 2 | 3 | 4 | 5 | 6 |
|---|---|---|---|---|---|---|---|
| 0 | 1.000 | 0.992 | 0.984 | 0.976 | 0.969 | 0.961 | 0.954 |
| 1 | 0.946 | 0.939 | 0.931 | 0.924 | 0.916 | 0.909 | 0.902 |
| 2 | 0.895 | 0.888 | 0.881 | 0.874 | 0.867 | 0.860 | 0.853 |
| 3 | 0.847 | 0.840 | 0.833 | 0.827 | 0.820 | 0.814 | 0.807 |
| 4 | 0.801 | 0.795 | 0.788 | 0.782 | 0.776 | 0.770 | 0.764 |
| 5 | 0.758 | 0.752 | 0.746 | 0.740 | 0.734 | 0.728 | 0.722 |
| 6 | 0.717 | 0.711 | 0.705 | 0.700 | 0.694 | 0.689 | 0.683 |
| 7 | 0.678 | 0.673 | 0.667 | 0.662 | 0.657 | 0.652 | 0.646 |
| 8 | 0.641 | 0.636 | 0.631 | 0.626 | 0.621 | 0.616 | 0.612 |
| 9 | 0.607 | 0.602 | 0.597 | 0.592 | 0.588 | 0.583 | 0.579 |
| 10 | 0.574 | 0.569 | 0.565 | 0.560 | 0.556 | 0.552 | 0.547 |
| 11 | 0.543 | 0.539 | 0.534 | 0.530 | 0.526 | 0.522 | 0.518 |
| 12 | 0.514 | 0.510 | 0.506 | 0.502 | 0.498 | 0.494 | 0.490 |
| Days/Days | 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 |
|---|---|---|---|---|---|---|---|---|---|---|
| 0 | 1.000 | 0.973 | 0.947 | 0.921 | 0.897 | 0.872 | 0.849 | 0.826 | 0.804 | 0.782 |
| 10 | 0.761 | 0.741 | 0.721 | 0.701 | 0.683 | 0.664 | 0.646 | 0.629 | 0.612 | 0.595 |
| 20 | 0.579 | 0.564 | 0.549 | 0.534 | 0.520 | 0.506 | 0.492 | 0.479 | 0.466 | 0.453 |
| 30 | 0.441 | 0.429 | 0.418 | 0.406 | 0.395 | 0.385 | 0.374 | 0.364 | 0.355 | 0.345 |
| 40 | 0.336 | 0.327 | 0.318 | 0.309 | 0.301 | 0.293 | 0.285 | 0.277 | 0.270 | 0.263 |
| 50 | 0.256 | 0.249 | 0.242 | 0.236 | 0.229 | 0.223 | 0.217 | 0.211 | 0.205 | 0.200 |
| 60 | 0.195 | 0.189 | 0.184 | 0.179 | 0.174 | 0.170 | 0.165 | 0.161 | 0.156 | 0.152 |
| 70 | 0.148 | 0.144 | 0.140 | 0.136 | 0.133 | 0.129 | 0.126 | 0.122 | 0.119 | 0.116 |
| 80 | 0.113 | 0.110 | 0.107 | 0.104 | 0.101 | 0.098 | 0.096 | 0.093 | 0.091 | 0.088 |
| 90 | 0.086 | 0.084 | 0.081 | 0.079 | 0.077 | 0.075 | 0.073 | 0.071 | 0.069 | 0.067 |
| 100 | 0.065 | 0.064 | 0.062 | 0.060 | 0.059 | 0.057 | 0.055 | 0.054 | 0.053 | 0.051 |
| 110 | 0.050 | 0.048 | 0.047 | 0.046 | 0.045 | 0.043 | 0.042 | 0.041 | 0.040 | 0.039 |
| 120 | 0.038 | 0.037 | 0.036 | 0.035 | 0.034 | 0.033 | 0.032 | 0.031 | 0.030 | 0.030 |
- Ausubel, F.M., et al., Current Protocols in Molecular Biology, 4, John Wiley & Sons, Inc., Brooklyn, New York, A.1E.1-A.1F.11, 1996-2004.
Commonly Used Media
| LB Medium | Per liter | Final 1X Concentration |
|---|---|---|
| Tryptone | 10 g | 1.0% (w/v) |
| Yeast extract | 5 g | 0.5% (w/v) |
| NaCl | 10 g | 1.0% (w/v) |
| H2O | to 1 liter | |
| Adjust pH to 7.0 | ||
| Low Salt LB Medium | Per liter | Final 1X Concentration |
| Tryptone | 10 g | 1.0% (w/v) |
| Yeast extract | 5 g | 0.5% (w/v) |
| NaCl | 5 g | 0.5% (w/v) |
| H2O | to 1 liter | |
| Adjust pH to 7.0 | ||
| Terrific Broth Medium | Per liter | Final 1X Concentration |
| Tryptone | 12 g | 1.2% (w/v) |
| Yeast extract | 24 g | 2.4% (w/v) |
| Glycerol | 4 ml | 0.4% (v/v) |
| Add H2O | to 900 ml | |
| Autoclave, cool to 60°C or less before adding 100 ml of filter sterilized 10X TB phosphate (0.17 M KH2PO4, 0.72 M K2HPO4) | ||
| SOB Medium | Per liter | Final 1X Concentration |
| Tryptone | 20 g | 2.0% (w/v) |
| Yeast extract | 5 g | 0.5% (w/v) |
| NaCl | 0.5 g | 0.05% (w/v) |
| 250 mM KCl | 10 ml | 2.5 mM |
| H2O | to 900 ml | |
| Adjust pH to 7.0 and add H2O to 990 ml | ||
| Autoclave, cool to room temperature and add 10 ml of sterile solution of 1 M MgCl2 before use | 10 mM | |
| SOC Medium | ||
| SOB Medium (1 liter) with the addition of 20 ml filter sterilized 1 M glucose | ||
| M9 Minimal Medium | Per liter | Final 1X Concentration |
| 5X M9 salts | 200 ml | |
| Sterile H2O | to 1 liter | |
| 1 M MgSO4 | 1 ml | 1 mM |
| 20% glucose | 10 ml | 0.2% (v/v) |
| 1 M CaCl2 | 0.1 ml | 0.1 mM |
| 5X M9 Salts | Per liter | Final 1X Concentration |
| Na2HPO4x7H2O | 64 g | 47.8 mM |
| KH2PO4 | 15 g | 22 mM |
| NaCl | 2.5 g | 8.6 mM |
| NH4 | 5 g | 18.7 mM |
| Additives | Per liter | Final 1X Concentration |
| Antibiotics (if requered) | ||
| Ampicillin | 50 µg/ml | |
| Chloramphenicol | 20 µg/ml | |
| Kanamycin | 30 µg/ml | |
| Tetracycline | 12 µg/ml | |
| Galactosides (if requered) | ||
| X-Gal | 20 µg/ml | |
| IPTG | 0.1 mM | |
| Media containing agar or agarose | ||
| Agar (for plates) | 15 g | 1.5% (w/v) |
| Agar (for top agar) | 7 g | 0.7% (w/v) |
| Agarose (for plates) | 15 g | 1.5% (w/v) |
| Agarose (for top agarose) | 7 g | 0.7% (w/v) |
- Atlas, R.M., Handbook of Microbiological Media, second edition, Ed. Parks, L.C., CRC Press, N.Y., 1997.
- Sambrook, J., et al., Molecular Cloning: A Laboratory Manual, second edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, A1.2-A2.12, 2001.
Commonly Used Stock Solutions
| 10 M Ammonium Acetate | ||
|---|---|---|
| Ammonium acetate | 385.4 g | |
| H2O | to 500 ml | |
| 1 M CaCl2 | ||
| CaCl2x6H2O | 219.1 g | |
| H2O | to 1 liter | |
| 100X Denhardt Solution | Final concentration | |
| Ficoll 400 | 10 g | 0.02% (w/v) |
| Polyvinylpyrrolidone | 10 g | 0.02% (w/v) |
| Bovine serum albumin | 10 g | 0.02% (w/v) |
| H2O | to 500 ml | |
| Filter sterilize and store at -20°C in 25 ml aliquots | ||
| 0.5 M EDTA (ethylenediamine tetraacetic acid) (pH 8.0) | ||
| Na2EDTAx2H2O | 186.1% g | |
| H2O | to 700 ml | |
| Adjust pH to 8.0 with 10 M NaOH (~50 ml) | ||
| H2O | to 1 liter | |
| 10 mg/ml Ethidium Bromide | ||
| Ethidium bromide | 0.2 g | |
| H2O | to 20 ml | |
| Mix well and store at 4°C in dark | ||
| CAUTION: Ethidium bromide is a mutagen and must be handled carefully | ||
| 1 M KCl | ||
| KCl | 74.6 g | |
| H2O | to 1 liter | |
| 1 M MgCl2 | ||
| MgCl2x6H2O | 20.3 g | |
| H2O | to 100 ml | |
| 1 M MgSO4 | ||
| MgSO4x7H2O | 24.6 g | |
| H2O | to 100 ml | |
| 5 M NaCl | ||
| NaCl | 292.2 g | |
| H2O | to 1 liter | |
| 10 M NaOH | ||
| NaOH | 400.0 g | |
| H2O | to 1 liter | |
| 1 M Tris-HCl [tris(hydroxymethyl)aminomethane] | ||
| Tris base | 121.1 g | |
| H2O | to 800 ml | |
| Adjust to desired pH with concentrated HCl | ||
| Mix and add H2O to 1 liter | ||
| 3 M Sodium Acetate (pH 5.2 and 7.0) (2) | ||
| Sodium acetate x 3H2O | 408.1 g | |
| H2O | to 800 ml | |
| Adjust the pH to 5.2 with glacial acetic acid or adjust the pH to 7.0 with dilute acetic acid | ||
| H2O | to 1 liter | |
- Atlas, R.M., Handbook of Microbiological Media, second edition, Ed. Parks, L.C., CRC Press, N.Y., 1997.
- Sambrook, J., et al., Molecular Cloning: A Laboratory Manual, second edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, A1.2-A2.12, 2001.
Commonly Used Buffers
| 10X Stock Phosphate-buffered Saline (PBS) | Per liter | Final 1X Concentration |
|---|---|---|
| NaCl | 80.0 g | 137 mM |
| KCl | 2.0 g | 2.7 mM |
| Na2HPO4 | 14.4 g | 100 mM |
| KH2PO4 | 2.7 g | 2 mM |
| H2O | to 800 ml | |
| HCl | to pH 7.4 | |
| H2O | to 1 liter | |
| 20X SSC | Per liter | Final 1X Concentration |
| NaCl | 175.3 g | 150 mM |
| Na3citrate x H2O | 88.2 g | 15 mM |
| H2O | to 800 ml | |
| Adjust pH to 7.0 with 1 M HCl | ||
| H2O | to 1 liter | |
| 20X SSPE | Per liter | Final 1X Concentration |
| NaCl | 175.3 g | 150 mM |
| NaH2PO4xH2O | 27.6 g | 10 mM |
| Na2EDTA | 7.4 g | 1 mM |
| H2O | to 800 ml | |
| Adjust pH to 7.4 with 10 M NaOH | ||
| H2O | to 1 liter | |
| 5X Tris-glycine Electrophoresis Buffer | Per liter | Final 1X Concentration |
| Tris base | 15.1 g | 25 mM |
| Glycine | 72.0 g | 192 mM |
| H2O | to 1 liter | |
| The pH of diluted solution is pH 8.3 | ||
| 5X Tris-glycine-SDS Electrophoresis Buffer | Per liter | Final 1X Concentration |
| Tris base | 15.1 g | 25 mM |
| Glycine | 72.0 g | 192 mM |
| SDS | 5.0 g | 0.1% (w/v) |
| H2O | to 1 liter | |
| The pH of diluted solution is pH 8.3 | ||
| 5X Tris-tricine-SDS Electrophoresis Buffer | Per liter | Final 1X Concentration |
| Tris base | 60.6 g | 0.1 M |
| Tricine | 89.6 g | 0.1 M |
| SDS | 5.0 g | 0.1% (w/v) |
| H2O | to 1 liter | |
| The pH of diluted solution is pH 8.3 | ||
| 50X TAE (Tris-acetate-EDTA) Electrophoresis Buffer | Per liter | Final 1X Concentration |
| Tris base | 242.0 g | 40 mM |
| Glacial acetic acid | 57.1 ml | 20 mM |
| 0.5 M EDTA (pH 8.0) | 100 ml | 1 mM |
| H2O | to 1 liter | |
| The pH of diluted solution is ~8.5 | ||
| 10X TBE (Tris-borate-EDTA) Electrophoresis Buffer | Per liter | Final 1X Concentration |
| Tris base | 108.0 g | 0.89 mM |
| Boric acid | 55.0 g | 0.89 mM |
| 0.5 M EDTA (pH 8.0) | 40 ml | 2 mM |
| H2O | to 1 liter | |
| 10X TPE (Tris-phosphate-EDTA) Electrophoresis Buffer | Per liter | Final 1X Concentration |
| Tris base | 108.0 g | 0.89 mM |
| Phosphoric acid (85%) | 15.5 ml | 27 mM |
| 0.5 M EDTA (pH 8.0) | 40 ml | 2 mM |
| H2O | to 1 liter | |
| TE (Tris-EDTA) Buffer, pH 7.4, 7.6 or 8.0 | Per liter | Final 1X Concentration |
| 1 M Tris, pH 7.4, 7.6, 8.0 | 10.0 ml | 10 mM |
| 0.5 M EDTA (pH 8.0) | 2.0 ml | 1 mM |
| H2O | to 1 liter | |
- Atlas, R.M., Handbook of Microbiological Media, second edition, Ed. Parks, L.C., CRC Press, N.Y., 1997.
- Sambrook, J., et al., Molecular Cloning: A Laboratory Manual, second edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, A1.2-A2.12, 2001.
Commonly Used Abbreviations
| A | adenine or adenosine; one-letter code for alanine |
| A260 | absorbance at 260 nm |
| ACES | N-(2-acetamido)-2-aminoethanesulfonic acid |
| Ad-2 | adenovirus-2 |
| ADA | N-(2-acetamido)-2-iminodiacetic acid |
| ADP | adenosine 5'-diphosphate |
| AMP | adenosine monophosphate |
| AMV |
Avian Myeloblastosis Virus |
| AP | alkaline phosphatase |
| APS |
ammonium persulfate |
| aRNA |
antisense RNA |
| ATP | adenosine 5'-triphosphate |
| BCIP | 5-bromo-4-chloro-3-indolyl phosphate |
| BES | N,N-bis(2-hydroxyethyl)-2-aminoethanesulfonic acid |
| BGG |
bovine gamma globulin |
| BICINE | N,N-bis(2-hydroxyethyl)glycine |
| Bio-dNTP | biotin-deoxynucleoside triphosphate |
| BME |
2-mercaptoethanol |
| bp | base pair |
| Bq | Becquerel |
| BSA | bovine serum albumin |
| B/W | blue/white cloning |
| C | cytosine or cytidine; one-letter code for cysteine |
| CA | casamino-acids |
| CAPS |
N-cyclohexyl-3-aminopropanesulfonic acid |
| cDNA | complementary deoxyribonucleic acid |
| CEU |
cohesive end ligation unit |
| Ci | Curie |
| CIAP | calf intestinal alkaline phosphatase |
| CMP |
cytidine monophosphate |
| cpm | counts per minute |
| CTP | cytidine 5'-triphosphate |
| Da | Dalton |
| DAB | 3,3'-diaminobenzidine tetrahydrochloride |
| dAMP | deoxyadenosine monophosphate |
| dATP | deoxyadenosine triphosphate |
| dCTP | deoxycytidine triphosphate |
| ddATP | dideoxyadenosine triphosphate |
| ddCTP | dideoxycytidine triphosphate |
| ddGTP | dideoxyguanosine triphosphate |
| ddNTP | dideoxythymidine triphosphate |
| ddTTP |
dideoxythymidine triphosphate |
| DE-81 | Whatman® diethylaminoethyl cellulose paper |
| DEPC | diethyl pyrocarbonate |
| DIG | digoxigenin |
| dITP |
deoxyinosine triphosphate |
| dGTP | deoxyguanosine triphosphate |
| DMSO | dimethyl sulfoxide |
| DNA | deoxyribonucleic acid |
| DNase | deoxyribonuclease |
| dNMP |
deoxyribonucleoside monophosphate |
| dNTP | deoxynucleoside triphosphate |
| dpm | disintegrations per minute |
| ds | double-stranded |
| DTE | dithioerythritol |
| DTT | dithiothreitol |
| dTTP | deoxythymidine triphosphate |
| dUTP | deoxyuridine triphosphate |
| EDTA | ethylenediaminetetraacetic acid |
| EGTA |
ethylene glycol tetraacetic acid |
| ELISA | enzyme-liked immunosorbent assay |
| EMBL | European Molecular Biology Laboratory |
| EMSA |
electrophoretic mobility shift assay |
| ENDO | endodeoxyribonuclease assay |
| endo |
endonuclease |
| exo | exonuclease |
| EXO | 5' and 3'- exodeoxyribonuclease assay |
| FOA (5-FOA) | 5-fluoroorotic acid |
| G | guanine or guanosine; one-letter code for glycine |
| Gal | D-galactose |
| GMP |
guanosine monophosphate |
| GMPD |
glycosylase mediated polymorphism detection |
| GUS | beta-D-glucuronidase |
| GTP |
guanosine 5’-triphosphate |
| GQ |
genetic quality |
| HC | high concentration |
| HEPES | N-(2-hydroxyethyl)piperazine-N'-(2-ethanesulfonic acid) |
| HRP | horseradish peroxidase |
| HPLC | high-performance liquid chromatography |
| IEF | isoelectric focussing |
| IPTG | isopropyl-beta-D-thiogalactopyranoside |
| kb | kilobase |
| kDa | kiloDalton |
| LAMP |
loop-mediated isothermal amplification |
| LB | Luria Bertani media |
| LC | low concentration |
| LE |
low electroendosmosis |
| LM |
low melting point |
| LO | labeled oligonucleotide |
| MCS | multiple cloning site |
| MES | 2-(N-morpholino)ethanesulfonic acid |
| MDA |
multiple displacement amplification |
| M-MuLV | Moloney Murine Leukemia Virus |
| MOPS | 3-(N-morpholino)propanesulfonic acid |
| mRNA | messenger ribonucleic acid |
| MW | molecular weight |
| NAD | nicotinamide adenine dinucleotide |
| NADH | nicotinamide adenine dinucleotide, reduced form |
| NADP | nicotinamide adenine dinucleotide phosphate |
| NADPH | nicotinamide adenine dinucleotide phosphate, reduced form |
| NBT | nitro blue tetrazolium |
| NDP |
nucleoside diphosphate |
| NMP |
ribonucleoside monophosphate |
| NR | not recommended |
| NP-40 | Nonidet P-40 (detergent) |
| nt | nucleotide |
| NTC |
no-template control |
| NTP | nucleoside triphosphate |
| oligo(A) | oligoadenylic acid |
| oligo(dT) | oligodeoxythymidylic acid |
| OMP | orotidine monophosphate |
| OPD | 1,2-phenylenediamine; ortho-phenylenediamine |
| Pi | inorganic phosphate |
| PAAG |
polyacrylamide gel |
| PAGE | polyacrylamide-gel electrophoresis |
| PBS | phosphate-buffered saline |
| PCR | polymerase chain reaction |
| PEI | polyethylenimine |
| PEG | polyethylene glycol |
| PIPES | piperazine-N,N'-bis(2-ethanesulfonic acid) |
| PNK | polynucleotide kinase |
| pNPP | 4-nitrophenyl phosphate; para-nitrophenyl phosphate |
| poly(A) | polyadenylic acid |
| poly(A)+ | polyadenylated (mRNA) |
| poly(dA-dT) | poly (deoxyadenylic acid - deoxythymidylic acid) |
| poly(dT) | polydeoxythymidylic acid |
| PPi |
inorganic pyrophosphate |
| PVDF |
polyvinylidene fl uoride |
| QCA | quality control assay |
| qPCR |
quantitative polymerase chain reaction |
| RACE |
Rapid Amplification of cDNA Ends |
| RCA |
rolling circle amplification |
| RDA |
random displacement amplification |
| RE | restriction enzyme |
| RNA | ribonucleic acid |
| RNase | ribonuclease |
| R-M | restriction-modification |
| rRNA | ribosomal ribonucleic acid |
| RT | reverse transcriptase |
| RT-PCR |
reverse transcription polymerase chain reaction |
| SAM | S-adenosylmethionine |
| SAP |
shrimp alkaline phosphatase |
| SDS | sodium dodecyl sulfate |
| siRNA |
small interfering ribonucleic acid |
| SNP |
single nucleotide polymorphism |
| ss | single-stranded |
| SSC | sodium chloride/sodium citrate (buffer) |
| SSCP |
single-strand conformation polymorphism |
| SSPE | sodium chloride/sodium phosphate/EDTA (buffer) |
| STR |
short tandem repeat |
| T | thymine or thymidine; one-letter code for threonine |
| TAE | Tris/acetate/EDTA (buffer) |
| TBE | Tris/borate/EDTA (buffer) |
| TdT | terminal deoxynucleotidyl transferase |
| TE | Tris/EDTA (buffer) |
| TEMED | N,N,N',N'-tetramethylethylenediamine |
| TES | N-tris(hydroxymethyl)methyl-2-aminoethanesulfonic acid |
| TLC | thin layer chromatography |
| Tm | melting temperature |
| TMB | 3,3', 5,5'-tetramethylbenzidine |
| TRICINE | N-tris(hydroxymethyl)methylglycine |
| Tris | tris(hydroxymethyl)aminomethane |
| tRNA | transfer ribonucleic acid |
| TPE | Tris/phosphate/EDTA (buffer) |
| TX-100 | triton X-100 |
| T4 |
T4 polynucleotide kinase |
| U | uracil or uridine |
| u | unit |
| UDG |
uracil-DNA glycosylase |
| UMP |
uracil monophosphate |
| UTP | uridine 5'-triphosphate |
| UV | ultraviolet |
| v/v | volume/volume |
| WGA |
whole genome amplification |
| w/v | weight/volume |
| X-Gal | 5-bromo-4-chloro-3-indolyl-beta-D-galactopyranoside |
| X-Gluc | 5-bromo-4-chloro-3-indolyl-beta-D-glucuronic acid |
