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CONSTANTS & EQUATIONS

equations gif

Molecular Structure of Amino Acids
amino acid #1 
 amino acid #2
 amino acid #3
 amino acid #4
 amino acid #5

amino acid chart
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The Genetic Code

genetic code
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Nucleic Acid Data

1 µg of 1000 bp DNA = 1,52 pmol = 9.1 x 1011 molecules
1 µg of pUC18/19 DNA (2686 bp) = .057 pmol = 3.4 x 1011 molecules
1 µg of pBR322 DNA (4361 bp) = 0.35 pmol = 2.1 x 1011 molecules
1 µg of M13mp18/19 DNA (7250 bp) = 0.21 pmol = 1.3 x 1011 molecules
1 µg of l DNA (48502 bp) = 0.03 pmol 1.8 x 1010 molecules

1 pmol of 1000 bp DNA = 0.66 µg
1 pmol of pUC18/19 DNA (2686 bp) = 1.77 µg
1 pmol of l DNA (48502 bp) = 32.01 µg

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Spectrophotometric Conversions

1 A 260 unit of double-stranded DNA = 50 µg/ml
1 A 260 unit of single-stranded DNA = 33 µg/ml
1 A 260 unit of single-stranded RNA = 40 µg/ml
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Picomole Ends per Microgram of Double-Stranded Linear DNA

(2 x 106)/(660 x Number of bases) = pmol ends/µg double-stranded DNA
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Tm Factors Influencing the Tm of Nucleic Acid Hybrids2
Factor Influence on Tm
Ionic strength Tm increses 16.6° C for each onefold increase in monovalent cations, between 0.01 and 0.40M NaCl
Base 
composition		 AT base pairs are less stable than GC base pairs in aqueous solutions containing NaCI. The difference is negligible in tetramenthyl ammoniuum chloride.
Destablizing 
agents		 Each 1% formamide reduces the Tm by about 0.6°C, 6M urea reduces the Tm by about 30°C.
Mismatched 
base pairs 		 The Tm is reduced by 1°C for each 1% of mismatching.
Duplex length  Negligble effect with probes > 500 bp.
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Equations for Calculating Tm
System Equationa
DNA-DNA hybridsb  Tm = 81.5°C + 16.6(logM) + 0.41(%GC) - .61(%form) -500/bp 
DNA-RNA hybridsb  Tm = 79.8°C + 18.5(logM) + 0.58(%GC) + 11.8(%GC)2 - 0.50(%form) - 820/L
RNA-RNA hybridsb  Tm = 79.8°C + 18.5(logM) + 0.58(%GC) + 11.8(%GC)2 - 0.35(%form) - 820/L 
Oligonucleotide probes  Tm = 2(# AT bp) + 4(#GC bp) 
a M, molarity of monovalent cations (Na+ concentration, % GC, percentage of G and C nucleotides in the DNA, % form, percentage of Formamide in the hybridization solutions; L, length of the duplex in base pairs.
b These equations hold for Na+ concentrations between 0.01 and 0.40M and %GC values of 30-75%.
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References

1. Brown, T.A. Molecular Biology LabFax, Bios Scientific Publishers, Academic Press, 1991.

2. Dyson, N.J. (1991) In Essential Molecular Biology: A Practical Approach. T.A. Brown (ed) Vol. 2 Oxford University Press, Oxford, in press.

3. Meinkoth, J. and Wahl G. (1984) Anal. Biochem., 138:267.

4.Casey, J. and Davidson, N. (1977) Nucleic Acids Res., 4:1539.

5. Bodkin, D.K. and Knudson, D.L. (1985) J. Virol. Methods, 10:45.

6. Wallace, R.B., et al. (1979) Nucleic Acids Res., 6:3543.

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