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Appendix Tables:

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

* The approximate sizes of DNA fragments with which the indicated marker dye comigrates.

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

Reference

  1. 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

*  Translation termination codon 
** Codes for fMet if in the initiator position 

Genome Comparisons

Virus

Length, nt Approx. MW, Da
Bacteriophage PhiX174 5,380 3.5 x 10E6
Bacteriophage Lambda 48,502 3.1 x 10E7
Human Immunodeficiency Virus 1 9,181 3.1 x 10E6
Rous Sarcoma Virus 9,392 3.2 x 10E6
SARS Coronavirus 29,751 1.0 x 10E7
Simian Virus 40 (SV 40) 5,224 3.4 x 10E6
Vaccinia Virus 191,737 1.2 x 10E8
Variolla (Small pox) Virus 185,578 1.2 x 10E8

Archaebacteria

  Length of DNA, bp Approx. MW, Da
Halobacterium sp. NRC-1 2.01 x 10E6 1.31 x 10E9
Methanosarcina acetivorans C2A 5.75 x 10E6 3.74 x 10E9
Methanococcus jannaschii DSM2661 1.66 x 10E6 1.08 x 10E9
Methanosarcina mazei Go1  4.10 x 10E6 2.66 x 10E9
Methanobacterium thermoautotrophicum delta H 1.75 x 10E6 1.14 x 10E9
Pyrococcus horikoshii OT3 1.74 x 10E6 1.13 x 10E9
Pyrococcus abysii GE5 1.76 x 10E6 1.14 x 10E9
Pyrococcus furiosus DSM3638 1.91 x 10E6 1.24 x 10E9
Sulfolobus solfataricus P2 2.99 x 10E6 1.94 x 10E9
Thermoplasma acidophilum 1.56 x 10E6 1.01 x 10E9

Bacteria

 Length of DNA, bp Approx. MW, Da
Agrobacterium tumefaciens C58-Cereon 4.91 x 10E6 3.19 x 10E9
Aquifex aeolicus VF5 1.55 x 10E6 1.00 x 10E9
Bacillus subtilis 168 4.20 x 10E6 2.73 x 10E9
Bacillus halodurans 4.20 x 10E6 2.73 x 10E9
Bordetella pertussis Tohama I NCTC-13251 4.07 x 10E6 2.65 x 10E9
Chlamydophila pneumoniae CWL029 1.23 x 10E6 8.00 x 10E8
Deinococcus radiodurans R1 3.28 x 10E6 2.13 x 10E9
Escherichia coli K12 4.64 x 10E6 3.02 x 10E9
Escherichia coli 0157:H7 EDL933 4.10 x 10E6 2.66 x 10E9
Haemophilus influenzae KW20 1.83 x 10E6 1.19 x 10E9
Helicobacter pylori 26695 1.66 x 10E6 1.08 x 10E9
Lactococcus lactis IL1403 2.36 x 10E6 1.53 x 10E9
Mycobacterium leprae TN 3.27 x 10E6 2.12 x 10E9
Mycobacterium tuberculosis H37Rv 4.45 x 10E6 2.89 x 10E9
Mycoplasma genitalium G037 5.80 x 10E5 3.77 x 10E8
Mycoplasma pneumoniae M129 8.16 x 10E5 5.30 x 10E8
Neisseria meningitidis Z2491 2.18 x 10E6 1.42 x 10E9
Salmonella typhimurium LT2 SGSC1412 4.86 x 10E6 3.16 x 10E9
Staphylococcus aureus MW2 2.82 x 10E6 1.83 x 10E9
Streptomyces coelicolor A3(2) 8.67 x 10E6 5.64 x 10E9
Streptococcus pneumoniae R6 2.04 x 10E6 1.33 x 10E9
Streptococcus pyogenes SF370 (M1) 1.85 x 10E6 1.20 x 10E9
Pseudomonas aeruginosa 6.26 x 10E6 4.07 x 10E9
Vibrio cholerae N16961 4.00 x 10E6 2.60 x 10E9

Eukaryotes

 Length of DNA, bp Approx. MW, Da
Anopheles gambiae PEST (malaria mosquito) 2.78 x 10E8 1.80 x 10E11
Arabidopsis thaliana (flowering plant) 1.15 x 10E8 7.47 x 10E10
Caenorhabditis briggsae (soil-dwelling nematode) 1.04 x 10E8 6.76 x 10E10
Caenorhabditis elegans (round worm) 1.21 x 10E7 7.86 x 10E9
Ciona intestinalis (ascidian tadpole) 1.16 x 10E8  7.54 x 10E10
Drosophila melanogaster (fruit fly) 1.37 x 10E8  8.90 x 10E10
Guillardia theta (chromophyte algae) 5.51 x 10E5 3.58 x 10E8
Homo sapiens (human) 3,15 x 10E9 2.07 x 10E12
Mus musculus (mouse) ~3,00 x 10E9 ~1.95 x 10E12
Neurospora crassa OR74A (filamentous fungus) 4.30 x 10E7  2.80 x 10E10
Saccharomyces cerevisiae S288C (budding yeast) 1.21 x 10E7 7.86 x 10E9
Schizosaccharomyces pombe (fission yeast) 1.40 x 10E7 9.10 x 10E9
Plasmodium falciparum 3D7 (human malaria parasite) 2.29 x 10E7 1.49 x 10E10
Oryza sativa japonica (rice)  4.20 x 10E8 2.73 x 10E11

Reference

  1. GOLD™ Genomes OnLine Database, www.wit.integratedgenomics.com

Common Conversions of Nucleic Acids

Molar Conversions
1 µg of 1000 bp DNA = 1.52 pmol 
1 µg of pUC18/19 DNA (2686 bp) = 0.57 pmol 
1 µg of pBR322 DNA (4361 bp) = 0.35 pmol 
1 µg of SV40 DNA (5243 bp) = 0.29 pmol 
1 µg of PhiX174 DNA (5386 bp) = 0.28 pmol 
1 µg of M13mp18/19 DNA (7250 bp) = 0.21 pmol 
1 µg of lambda phage DNA (48502 bp) = 0.03 pmol 

1 pmol of 1000 bp DNA = 0.66 µg 
1 pmol of pUC18/19 DNA (2686 bp) = 1.77 µg 
1 pmol of pBR322 DNA (4361 bp) = 2.88 µg 
1 pmol of SV40 DNA (5243 bp) = 3.46 µg 
1 pmol of PhiX174 DNA (5386 bp) = 3.54 µg 
1 pmol of M13mp18/19 DNA (7250 bp) = 4.78 µg 
1 pmol of lambda phage DNA (48502 bp) = 32.01 µg 

Spectrophotometric Conversions
1 A260 of dsDNA = 50 µg/ml = 0.15 mM (in nucleotides) 
1 A260 of ssDNA = 33 µg/ml = 0.1 mM (in nucleotides) 
1 A260 of ssRNA = 40 µg/ml = 0.12 mM (in nucleotides)

1 mM (in nucleotides) of dsDNA = 6.7 A260 units 
1 mM (in nucleotides) of ssDNA = 10.0 A260 units 
1 mM (in nucleotides) of ssRNA = 8.3 A260 units 

The average MW of a deoxyribonucleotide base = 333 Daltons 
The average MW of a ribonucleotide base = 340 Daltons 

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) 

1 µg of 1000 bp DNA = 3.04 pmol ends 
1 µg of linear pUC18/19 DNA = 1.14 pmol ends 
1 µg of linear pBR322 DNA = 0.7 pmol ends 
1 µg of linear SV40 DNA = 0.58 pmol ends 
1 µg of linear PhiX174 DNA = 0.56 pmol ends 
1 µg of linear M13mp18/19 DNA = 0.42 pmol ends 
1 µg of lambda phage DNA = 0.06 pmol ends

Reference

  1. 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 10E4 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 260nm 
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

  1. 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.
  2. Butkus, V., et al., Synthesis and physical characterization of DNA fragments containing N4-methylcytosine and 5-methylcytosine, Nucleic Acids Res., 20, 8467-8478, 1987.
  3. 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 e**, 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

   * determined at pH 7.0
  ** molar absorption coefficient (absorbance at lambdamax for 1 M solution at pH 7.0)
 *** determined at pH 10.0

Conversion Formula
C = A / e x 10E3, where

C - mM concentration of compounds 
A - observed absorbance at lambdamax  (nm)
e - molar absorption coefficient (M-1 x cm-1)

SI Unit Prefixes

Prefix Symbol  Multiple 
exa  (E) 10E18 
peta  (P) 10E15 
tera  (T) 10E12 
giga  (G) 10E9 
mega  (M) 10E6 
kilo  (k) 10E3 
hecto*  (h) 10E2 
deka*  (da) 10E1   
deci*  (d) 10E-1
centi  (c) 10E-2
milli  (m) 10E-3
micro  (µ) 10E-6
nano  (n) 10E-9
pico  (p) 10E-12
femto  (f) 10E-15
atto  (a) 10E-18

* Generally to be avoided

Temperature Dependence of the pH for Commonly Used Buffers

Buffer System pKa/20°C [Delta]pKa/10°C
MES 6.15 -0.110
ADA 6.60 -0.110
PIPES 6.80 -0.085
ACES 6.90 -0.200
BES 7.15 -0.160
MOPS 7.20 -0.013
TES 7.50 -0.200
HEPES 7.55 -0.140
TRICINE 8.15 -0.210
TRIS 8.30 -0.310
BICINE 8.35 -0.180
GLYCYLGLYCINE 8.40 -0.280

Reference

  1. 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 10E2-10E7
33P 25.4 days 10E2-10E7
35S 87.4 days 10-10E7
131I 8.06 days 10E3-10E5
125I 60 days 10E3-10E7
14C 5730 years 10-10E3
3H 12.43 years 10E3-10E6

Summary of Useful Conversion

1 Becquerel (Bq) = 1 disintegration per second = 2.7x10E-11 Curies (Ci)

1 Ci = 3.7x10E10 Bq = 37 GBq = 2.22x10E12 disintegrations per minute (dpm)
1 mCi = 37 MBq = 2.22x10E9 dpm
1 µCi = 37 kBq = 2.22x10E6 dpm
1 GBq = 27 mCi 
1 MBq = 27 µCi 
1 kBq = 27 nCi

Decay Factors for Calculating the Amount of Radioactivity

125I, (half-life - 60.0 days)
125I, (half-life - 60.0 days)

32P, (half-life - 14.3 days)
32P, (half-life - 14.3 days)

131I, (half-life - 8.04 days)
131I, (half-life - 8.04 days)

35S, (half-life - 87.4 days)
35S, (half-life - 87.4 days)

33P, (half-life - 25.4 days)
33P, (half-life - 25.4 days)

Reference

  1. 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, Stock Solutions and Buffers

Growth Media (1) Stock Solutions Buffers (2)

per liter:

final 1X concentration:

per liter:

final 1X concentration:
LB Medium 10 M Ammonium Acetate 10X Stock Phosphate-buffered Saline (PBS)
Tryptone 
Yeast extract
NaCl
H2O
 

10g
5g
10g
to 1 liter

 1.0% (w/v)
0.5% (w/v)
1.0% (w/v)


 		 Ammonium acetate
H2O		 385.4g
 to 500 ml		 NaCl
KCl
Na2HPO4
KH2PO4
H2O

80g
2g
14.4g
 2.4g
to 800 ml

 137 mM
2.7 mM
100 mM
2 mM
1 M CaCl2
Adjust pH to 7.0 CaCl2x2H2O 
H2O		 147g
 to 1 liter		 Adjust pH 7.4 with HCl
H2O

to 1 liter

  
Low Salt LB Medium 100X Denhardt Solution 20X SSC
Tryptone
Yeast extract
NaCl
H2O
 

10g
5g
5g
to 1 liter

 1.0% (w/v)
0.5% (w/v)
0.5% (w/v)		 Ficoll 400
Polyvinylpyrrolidone
Bovine serum albumin
H2O		 10g
10g
10g
to 500 ml		 NaCl
Na3citratexH2O
H2O

175.3g
88.2g
 to 800 ml

 150 mM
15 mM
Adjust pH to 7.0 with 1 M HCl
Adjust pH to 7.0 Filter sterilize and store at -20°C in 25 ml aliquots. H2O

to 1 liter

  
Terrific Broth Medium 0.5 M EDTA (ethylenediamine tetraacetic acid) (pH 8.0) 20X SSPE
Tryptone
Yeast extract
Glycerol 
Add H2O

12g
24g
4 ml
to 900 ml

 1.2% (w/v)
2.4% (w/v)
0.4% (w/v)		 Na2EDTAx2H2O
H2O		 186.1g
to 700 ml		 NaCl
NaH2PO4xH2O
Na2EDTA
H2O

175.3g
27.6g
7.4g
 to 800 ml

 150 mM
10 mM
10 mM
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). Adjust pH to 8.0 with 10 M NaOH (~50 ml) Adjust pH to 7.4 with 10 M NaOH
H2O to 1 liter H2O

to 1 liter

  
SOB Medium 10 mg/ml Ethidium Bromide 5X Tris-glycine Electrophoresis Buffer
Tryptone 
Yeast extract 
NaCl
250 mM KCl
H2O

20g
5g
0.5g
10 ml
to 900 ml

 2.0% (w/v)
0.5% (w/v)
0.05% (w/v)
2.5 mM		 Ethidium bromide
H2O		 0.2g
to 20 ml		 Tris base
Glycine
H2O

15.1g
72.0g
to 1 liter

 25 mM
192 mM
Adjust pH to 7.0 and add H2O to 990 ml. Mix well and store at 4°C in dark.
CAUTION: Ethidium bromide is a mutagen and must be handled carefully.		 The pH of diluted solution is 8.3.
Autoclave, cool to room temperature and add 10 ml of sterile solution of 1M MgCl2 before use.

10 mM
SOC Medium 1 M Dithiothreitol (DTT) 5X Tris-glycine-SDS Electrophoresis Buffer
SOB Medium (1 liter) with the addition of 20 ml filter sterilized 1M glucose. DTT 
H2O		 15.45g
to 100 ml		 Tris base
Glycine
SDS
H2O

15.1g
72.0g
5.0g
to 1 liter

 25 mM
192 mM
0.1% (w/v)
Store at -20°C
The pH of diluted solution is 8.3.
M9 Minimal Medium 1 M KCl 5X Tris-tricine-SDS Electrophoresis Buffer
5X M9 salts
Sterile H2O
1M MgSO4
20% glucose
1M CaCl2

200 ml
to 1 liter
2 ml
20 ml
0.1 ml

  
 
1 mM
2.0% (w/v)
0.1 mM		 KCl
H2O		 74.6g
to 1 liter		 Tris base
Tricine
SDS
H2O

121.1g
179.2g
10.0g
to 1 liter

 0.1M
0.1M
0.1% (w/v)
1 M MgCl2
MgCl2x6H2O
H2O		 20.3g
to 100 ml		 The pH of diluted solution is 8.3.
5X M9 Salts 1 M MgSO4 50X TAE (Tris-acetate-EDTA) Electrophoresis Buffer
Na2HPO4x7H2O
KH2PO4
NaCl
NH4Cl

64g
15g
2.5g
5g

 47.8 mM
22 mM
8.6 mM
18.7 mM		 MgSO4x7H2O
H2O		 24.6g
to 100 ml		 Tris base
Glacial acetic acid
0.5M EDTA (pH 8.0)
H2O

242g
57.1 ml
100 ml
 
to 1 liter

 40 mM
20 mM
1 mM
5 M NaCl
NaCl
H2O		 292g
to 1 liter		 The pH of diluted solution is ~8.5.
Additives:
Antibiotics (if required)		 10 M NaOH 10X TBE (Tris-borate-EDTA) Electrophoresis Buffer
Ampicillin
Chloramphenicol
Kanamycin
Tetracycline		 to 50 µg/ml
to 20 µg/ml
to 30 µg/ml
to 12 µg/ml		 NaOH
H2O		 400g
to 1 liter		 Tris base
Boric acid
0.5M EDTA(pH 8.0)
H2O

108g
55g
40 ml
 
to 1 liter

 90 mM
90 mM
1 mM
Additives:
Galactosides (if required)		 1 M Tris-HCl [tris(hydroxymethyl)aminomethane] 10X TPE (Tris-phosphate-EDTA) Electrophoresis Buffer
X-Gal
IPTG 		 to 20 µg/ml
to 0.1 mM		 Tris base
H2O		 121g
to 800 ml		 Tris base
Phosphoric acid (85%)
0.5M EDTA(pH 8.0)
H2O

108g
15.5 ml
 
40 ml
 
to 1 liter

90 mM
23 mM
 
1 mM
Adjust to desired pH with concentrated HCl.
Mix and add H2O to 1 liter
Additives:
Media containing agar or agarose		 3 M Sodium Acetate (pH 5.2 and 7.0) (2) TE (Tris-EDTA) Buffer, pH 7.4, 7.6 or 8.0
Agar (for plates)
Agar
(for top agar)
Agarose
(for plates)
Agarose (for top agarose)

15g
7g
 
15g
 
7g

 1.5% (w/v)
0.7% (w/v)
 
1.5% (w/v)
 
0.7% (w/v)
 		 Sodium acetate. 3H2O
H2O		 408.1g
to 800 ml		 1 M Tris, pH 7.4, 7.6, 8.0
0.5M EDTA(pH 8.0)
H2O

10 ml
 
2 ml
 
to 1 liter

 

10 mM
1 mM
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

References

  1. Atlas, R.M., Handbook of Microbiological Media, second edition, Ed. Parks, L.C., CRC Press, N.Y., 1997.
  2. 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, B, C, D, E, F, G, H, I, K, L, M, N, O, P, Q, R, S, T, U, V, W, X

A adenine or adenosine; one-letter code for alanine MCS  multiple cloning site
A260 absorbance at 260nm MES 2-(N-morpholino)ethanesulfonic acid
ACES N-(2-acetamido)-2-aminoethanesulfonic acid M-MuLV Moloney Murine Leukemia Virus
Ad-2 adenovirus-2 MOPS 3-(N-morpholino)propanesulfonic acid
ADA N-(2-acetamido)-2-iminodiacetic acid mRNA messenger ribonucleic acid
ADP adenosine 5'-diphosphate MSPU mini power supply unit
AEC 3-amino-9-ethylcarbazole MW molecular weight
AMP adenosine monophosphate NAD nicotinamide adenine dinucleotide
AP alkaline phosphatase NADH nicotinamide adenine dinucleotide, reduced form
ATP adenosine 5'-triphosphate NADP nicotinamide adenine dinucleotide phosphate
BAP bacterial alkaline phosphatase NADPH nicotinamide adenine dinucleotide phosphate, reduced form
BCIP 5-bromo-4-chloro-3-indolyl phosphate NBT nitro blue tetrazolium
BES N,N-bis(2-hydroxyethyl)-2-aminoethanesulfonic acid nd  not determined
BICINE N,N-bis(2-hydroxyethyl)glycine NR  not recommended
Bio-dNTP biotin-deoxynucleoside triphosphate NP-40  Nonidet P-40 (detergent)
bp base pair nt nucleotide
Bq Becquerel NTP nucleoside triphosphate
BSA bovine serum albumin oligo(A) oligoadenylic acid
B/W blue/white cloning oligo(dT) oligodeoxythymidylic acid
C cytosine or cytidine; one-letter code for cysteine OMP  orotidine monophosphate
CA casamino-acids OPD  1,2-phenylenediamine; ortho-phenylenediamine
cDNA complementary deoxyribonucleic acid Pi inorganic phosphate
Ci Curie PAGE polyacrylamide-gel electrophoresis
CIAP calf intestinal alkaline phosphatase PBS phosphate-buffered saline
cpm counts per minute PCR polymerase chain reaction
CTP cytidine 5'-triphosphate PEI polyethylenimine
Da Dalton PEG polyethylene glycol
DAB 3,3'-diaminobenzidine tetrahydrochloride PIPES piperazine-N,N'-bis(2-ethanesulfonic acid)
dAMP deoxyadenosine monophosphate PNK polynucleotide kinase
dATP deoxyadenosine triphosphate pNPP 4-nitrophenyl phosphate; para-nitrophenyl phosphate
dCTP deoxycytidine triphosphate poly(A) polyadenylic acid
ddATP dideoxyadenosine triphosphate poly(A)+ polyadenylated (mRNA)
ddCTP dideoxycytidine triphosphate poly(dA-dT)   poly (deoxyadenylic acid - deoxythymidylic acid)
ddGTP dideoxyguanosine triphosphate poly(dT) polydeoxythymidylic acid
ddNTP dideoxythymidine triphosphate PSU power supply unit
DE-81 Whatman® diethylaminoethyl cellulose paper QCA quality control assay
DEPC diethyl pyrocarbonate RE restriction enzyme
DIG digoxigenin RNA ribonucleic acid
dGTP deoxyguanosine triphosphate RNase ribonuclease
DMSO dimethyl sulfoxide R-M restriction-modification
DNA deoxyribonucleic acid rRNA ribosomal ribonucleic acid
DNase deoxyribonuclease RT reverse transcriptase
dNTP deoxynucleoside triphosphate SAM S-adenosylmethionine
dpm disintegrations per minute SDS sodium dodecyl sulfate
ds double-stranded ss single-stranded
DTE dithioerythritol SSC sodium chloride/sodium citrate (buffer)
DTT dithiothreitol SSPE sodium chloride/sodium phosphate/EDTA (buffer)
dTTP deoxythymidine triphosphate T thymine or thymidine; one-letter code for threonine
dUTP deoxyuridine triphosphate TAE Tris/acetate/EDTA (buffer)
EDTA ethylenediaminetetraacetic acid Taq Thermus aquaticus
ELISA enzyme-liked immunosorbent assay TBE Tris/borate/EDTA (buffer)
EMBL European Molecular Biology Laboratory TdT terminal deoxynucleotidyl transferase
ENDO endodeoxyribonuclease assay TE Tris/EDTA (buffer)
exo exonuclease TEMED N,N,N',N'-tetramethylethylenediamine
EXO 5' and 3'- exodeoxyribonuclease assay TES N-tris(hydroxymethyl)methyl-2-aminoethanesulfonic acid
FOA (5-FOA) 5-fluoroorotic acid TLC thin layer chromatography
G guanine or guanosine; one-letter code for glycine Tm melting temperature
Gal D-galactose TMB 3,3', 5,5'-tetramethylbenzidine
GUS beta-D-glucuronidase TRICINE N-tris(hydroxymethyl)methylglycine
HC high concentration Tris tris(hydroxymethyl)aminomethane
HEPES N-(2-hydroxyethyl)piperazine-N'-(2-ethanesulfonic acid) tRNA transfer ribonucleic acid
HRP horseradish peroxidase TPE Tris/phosphate/EDTA (buffer)
HPLC high-performance liquid chromatography TX-100 triton X-100
IEF isoelectric focussing U uracil or uridine
IPTG isopropyl-beta-D-thiogalactopyranoside u unit
kb kilobase UTP uridine 5'-triphosphate
kDa kiloDalton UV ultraviolet
LB Luria Bertani media v/v volume/volume
LC low concentration w/v  weight/volume
LO labeled oligonucleotide X-Gal 5-bromo-4-chloro-3-indolyl-beta-D-galactopyranoside
X-Gluc 5-bromo-4-chloro-3-indolyl-beta-D-glucuronic acid
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Updated kovo 12, 2008 09:17