General Reference

• 1 mg = 10-3 g
  1 ug = 10-6 g
  1 ng = 10-9 g
  1 pg = 10-12 g

• 1 kb of double stranded DNA = 660 kD
  1 kb of single stranded DNA = 330 kD
  1 kb of single stranded RNA = 340 kD

• Average MW of a deoxynucleotide base = 324.5 Daltons
  Average MW of a deoxynucleotide base pair = 649 Daltons

• 1 ug/ml of DNA = 3.08 uM phosphate
  1 ug/ml of 1 kb of DNA = 3.08 nM 5' ends
  1 mol of pBR322 = 2.83 x10+6 g.
  1 pmol of linear pBR322, 5' ends = 1.4 ug
  1 A260 unit of duplex DNA = 50 ug
  1 A260 unit of single-stranded DNA = 37 ug
  1 A260 unit of single-stranded RNA = 50 ug

• 1 kb of DNA = 333 amino acids of coding capacity
  = 37,000 daltons
• Densities (50% GC):

RF I (supercoiled) ds DNA	1.709 g/ml
RF II (nicked) ds DNA	1.54 g/ml
ss DNA	1.726 g/ml
ss RNA	1.90 g/ml
protein	1.33 g/ml

• DNA melting point :
• For duplex DNA >50 bp:
  
  Tm = 81.5deg. C +16.6 log (M of NaCl) + 0.41(% GC)
  - [500/bp of shortest chain in duplex]
  - [0.65(% formamide)]
  
  For duplex DNA <50 bp:
  
  Add 2deg. C for each A or T
  Add 4deg. C for each G or C
• Picomoles of ends :

• pmol ends per ug linear DNA = 3030/number of bases

• Migration of marker dyes in native polyacrylamide non-denaturing gels

• Migration of marker dyes in polyacrylamide denaturing gels

• Relative positions of different DNA forms on Tris-acetate agarose gels

The exact distance between bands is influenced by percentage of agarose, time of electrophoresis, concentration of Ethidium bromide, degree of supercoiling and the size and complexity of the DNA.

Alanine                          Ala     A Arginine                         Arg     R Asparagine                       Asn     N Aspartic acid             Asp     D Asparagine or Aspartic acid      Asx     B Cysteine                         Cys     C Glutamine                        Gln     Q Glutamic acid                    Glu     E Glutamine or Glutamic acid       Glx     Z Glycine                         Gly     G Histidine                        His     H Isoleucine                       Ile     I Leucine                   Leu     L Lysine                    Lys     K Methionine                       Met     M Phenylalanine                    Phe     F Proline                   Pro     P Serine                    Ser     S Threonine    Thr     T Tryptophan                       Trp     W Tyrosine                         Tyr     Y Valine                    Val     V 
 

Assay buffers (see enzyme vendors catalogs for additional information)

 10x Low salt buffer
    10x Core buffer  
   100mM Tris-HCl, pH 7.6  500mM NaCl    100mM MgCl2    500mM Tris-HCl, pH 7.6     10mM DTT    100mM MgCl2  10x Medium salt buffer
   10x Hind buffer  
   500mM NaCl    600mM NaCl    100mM Tris-HCl, pH 7.6  100mM Tris-HCl, pH 7.6    100mM MgCl2     70mM MgCl2     10mM DTT   10x High salt buffer
   10x Sma I buffer
 (1)      1.0M NaCl    200mM KCl    500mM Tris-HCl, pH 7.6  100mM Tris-HCl, pH 7.6    100mM MgCl2    100mM MgCl2     10mM DTT    10mM DTT 

• The following enzymes CAN be heat inactivated by incubation at 65 deg. C for 10 min.: Alu I, Apa I, Ava II, Bal I, Bgl I, Cvn I, Dpn I, Dra I, Eco R II, Eco RV, Hae II, Hha I, Hinc II, Kpn I, Mbo I, Msp I, Nar I, Nde II, Rsa I, Sau 3a, Sca I, Sfi I, Spe I, Sph I, Ssp I, Sst I, Stu I, and Sty I.
• The following enzymes are ONLY PARTIALLY heat inactivated by incubation at 65 deg.C for 10 min.: Ava I, Cfo I, Cla I, Cvn I, Eco RI, Mbo II, Mlu I, Nci I, Nru I, Pst I, Pvu II, Sma I and Xma III
• The following enzymes CANNOT be heat inactivated by incubation at 65 deg. C for 10 min.: Acc I, Bam HI, Bcl I, Bgl II, BstE II, Dde I, Hae III, Hind III, Hinf I, Hpa I, Hpa II Nde I, Nhe I, Nsi I, Pvu I, Sal I, Sau 96 I, Sst II, Taq I, Tha I, Xba I, Xho I, and Xor II.

M13 (-21) universal forward 5'-TGT-AAA-ACG-ACG-GCC-AGT-3'

M13 (-40) universal forward 5'-GTT-TTC-CCA-GTC-ACG-AC-3'

M13/pUC reverse primer 5'-CAG-GAA-ACA-GCT-ATG-ACC-3'

T7 primer 5'-TAA-TAC-GAC-TCA-CTA-TAG-GG-3'

SP6 primer 5'-ATT-TAG-GTG-ACA-CTA-TAG-3'

-16bs 5'-TCG-AGG-TCG-ACG-GTA-TCG-3'

+19bs 5'-GCC-GCT-CTA-GAA-CTA-GTG-3'

As they are read on DNA sequencing gels using the Universal primer:

 M13mp7 .......EcoR1....BamH1.SalI..PstI..SalI..BamH1....EcoR1 GGCCAGTGAATTCCCCGGATCCGTCGACCTGCAGGTCGACGGATCCGGGGAATTC  M13mp8 ..........HindIII.PstI.SalI...BamH1.SmaI.EcoR GGCCAGTGCCAAGCTTGGCTGCAGGTCGACGGATCCCCGGGAATTCGTAATCATG  M13mp9 .......EcoR1.SmaI.BamH1..SalI..PstI..HindIII GGCCAGTGAATTCCCGGGGATCCGTCGACCTGCAGCCAAGCTTGGCGTAATCATG  M13mp10 ...HindIII..PstI..SalI..XbaI..BamH1..SmaI..SstI..EcoR1 GCCAAGCTTGGGCTGCAGGTCGACTCTAGAGGATCCCCGGGCGAGCTCGAATTCG  M13mp11 ...EcoR1..SstI..SmaI..BamH1..XbaI..SalI..PstI..HindIII GTGAATTCGAGCTCGCCCGGGGATCCTCTAGAGTCGACCTGCAGCCCAAGCTTGG  M13mp18 HindIII.SphI..PstI..SalI.XbaI.BamH1.SmaI.KpnI.SstI.EcoR1 AAGCTTGCATGCCTGCAGGTCGACTCTAGAGGATCCCCGGGTACCGAGCTCGAATTC  M13mp19 EcoR1.SstI.KpnI.SmaI.BamH1.XbaI.SalI.PstI..SphI..HindIII GAATTCGAGCTCGGTACCCGGGGATCCTCTAGAGTCGACCTGCAGGCATGCAAGCTT