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General Reference

General Reference


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 mobility in gels

Gel % Bromophenol blue (BP) Xylene cyanole (XC)
3.5 100 460
5.0 65 260
8.0 45 160
12.0 20 70
20.0 12 45
Gel % Bromophenol blue (BP) Xylene cyanole (XC)
5.0 35 130
6.0 26 106
8.0 19 75
10.0 12 55
20.0 8 28

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

Enzyme Isoschizomers Buffer Temp Recognition Site Cloning sites
Aat II   med 37 GACGT/C Aat II
Acc I   med 37 GT/(AC)(GT)AC Acc I, Cla I
Aha III Dra I med 37 TTT/AAA blunt
Alu I   med 37 AG/CT blunt
Asu II     37 TT/CGAA Acc I, Cla I
Ava I   med 37 C/YCGRG Sal I, Xho I, Xma I
Ava II   med 37 G/G(AT)CC  
Bal I   low 37 TGG/CCA blunt
BamH1   med 37 G/GATCC BamH1, Bgl II
Bgl I   med 37 GCCN4/NGGC  
Bgl II   low 37 A/GATCT BamH1, Bgl II
BstE II   high 60 G/GTNACC  
BstN I   low 55 CC/(AT)GG  
Cla I   low 37 AT/CGAT Acc I, Cla I
Dra I Aha III low 37 TTT/AAA blunt
EcoR1   high 37 G/AATTC EcoR1
EcoR1*   low 37 /AATT EcoR1
EcoRV   med 37 GAT/ATC blunt
Hae I   low 37 (AT)GG/CC(TA) blunt
Hae II   low 37 RGCGC/Y  
Hae III   med 37 GG/CC blunt
Hha I Cfo I, HinP1 med 37 GCG/C Hha I
Hinc II   med 37 GTY/RAC blunt  
Hind III   med 37-55 A/AGCTT Hind III
Hinf I   med 37 G/ANTC  
HinP1 Cfo I, Hha I low 37 G/CGC Acc I, Cla I
Hpa I   low 37 GTT/AAC blunt
Hpa II Msp I low 37 C/CGG Acc I, Cla I
Kpn I   low 37 GGTAC/C Kpn I
Mbo I Sau3A med 37 /GATC BamH1, Bgl II
Msp I   med 37 C/CGG Acc I, Cla I
Mst I Fsp I high 37 TGC/GCA blunt
Mst II Bsu36 I high 37 CC/TNAGG  
Nae I   med 37 GCC/CCG blunt
Nco I   high 37 C/CATGG Nco I
Nde I   med 37 CA/TATG Nde I
Not I   high 37 GC/GGCCGC  
Nru I   med 37 TCG/CGA blunt
Pst I   med 21-37 CTGCA/G Pst I
Pvu I   high 37 CGAT/CG Pvu I
Pvu II   med 37 CAG/CTG blunt
Rsa I   med 37 GT/AC blunt
Sac I Sst I low 37 GAGCT/C Sac I, Sst I
Sal I   high 37 G/TCGAC Ava I, Sal I, Xho I
Sau3A I Mbo I med 37 /G*ATC BamH1, Bgl II
Sfi I     50 GGCCN4/NGGCC  
Sma I Xma I (1) 37 CCC/GGG blunt
Sph I   high 37 GCATG/C Sph I
Sst I Sac I med 37 GAGCT/C Sst I, Sac I
Sst II Sac II med 37 CCGC/GG Sst II
Taq I   low 37-55 T/CGA AccI, Cla I
Tha I FnuD II, Acc II low 37-60 CG/CG blunt
Xba I   high 37 T/CTAGA Xba I
Xho I Ccr I high 37 C/TCGAG Ava I, Cla I
Xma I Sma I low 37 C/CCGGG Ava I, Xma I

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 

Heat inactivation of restriction enzymes

Oligonucleotide universal primers used for DNA sequencing

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'



Listing of M13 (pUC) cloning sites

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