GeneralReference

Units

• 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

Formulas

• 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

DNA mobility in gels

• 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.

Amino acid symbols

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

Commonly used restriction enzymes and assay buffers