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

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

• Migration of marker dyes in polyacrylamide denaturing gels

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

• 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

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

• 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.

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'

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

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

Listing of M13 (pUC) cloning sites

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