An An Austrian chemist StudiedStudied chemistry chemistry inin

ViennaVienna UniversityUniversity, , YaleYale UniversityUniversity

He worked at the He worked at the University of BerlinUniversity of Berlin

A professor at the A professor at the Columbia UniversityColumbia University

What we can understandWhat we can understand How double-stranded DNA became an intracellular How double-stranded DNA became an intracellular

alarm signalalarm signalHow potentially recombining nucleic acids can How potentially recombining nucleic acids can

distinguish between "self" and "not-self" so leading to distinguish between "self" and "not-self" so leading to the origin of speciesthe origin of species

How isochores evolved to facilitate gene replicationHow isochores evolved to facilitate gene replicationHow unlikely it is that any mutation can ever How unlikely it is that any mutation can ever

remain truly neutralremain truly neutral

First Parity RuleFirst Parity RuleSecond Parity Rule Second Parity Rule GC Rule GC Rule Cluster Rule Cluster Rule

• A. Chargaff used quantitative chromatography to separate A. Chargaff used quantitative chromatography to separate DNA basesDNA bases

(1) Purines (1) Purines ((adenineadenine & & guanineguanine) )

(2) Pyrimidines(2) Pyrimidines ((cytosinecytosine & & thyminethymine))• B. Looked at DNA from many different speciesB. Looked at DNA from many different species• C. Looked at DNA from different individuals within speciesC. Looked at DNA from different individuals within species• D. Chargaff's basic observations, stated as Chargaff's Rules: D. Chargaff's basic observations, stated as Chargaff's Rules:

(1) Individuals within species had same % of 4 bases (1) Individuals within species had same % of 4 bases (a) % Didn't vary with tissue, age, nutrition or environment (a) % Didn't vary with tissue, age, nutrition or environment

(2) Different species had different % of 4 bases (2) Different species had different % of 4 bases

(3) Closely related species had similar % of 4 bases (3) Closely related species had similar % of 4 bases

(4) Also noted that %A = %T and %C = %G (4) Also noted that %A = %T and %C = %G

% of A = % of T % of A = % of T % of C = % of G% of C = % of GSum of A+G Sum of A+G (purines)(purines) = Sum = Sum of C+T of C+T (pyrimidines)(pyrimidines) % of C+G ≠ % of A+T in the % of C+G ≠ % of A+T in the DNADNA

Less well known is the fact that Chargaff's rules apply Less well known is the fact that Chargaff's rules apply approximately and separately to each of the two approximately and separately to each of the two strands of dsDNAstrands of dsDNA

Aw=Tc , Tw=Ac , Cc= Gw , Gc=Cw Aw=Tc , Tw=Ac , Cc= Gw , Gc=Cw (where the letters represent the molar fraction of a (where the letters represent the molar fraction of a base on one strand)base on one strand)

Ac ≈ Tc , Aw ≈ Tw , Cc ≈ Gc , Cw ≈ GwAc ≈ Tc , Aw ≈ Tw , Cc ≈ Gc , Cw ≈ GwComplementary strands are approximately symmetric Complementary strands are approximately symmetric

in nucleotide content. If they are truein nucleotide content. If they are trueAw=Ac , Tw=Tc , Cw=Cc , Gw= GcAw=Ac , Tw=Tc , Cw=Cc , Gw= Gc

Equality — even in the separated DNA strands — of 6-Equality — even in the separated DNA strands — of 6-amino [A + C] and 6-keto [G + T] nucleotides, in the amino [A + C] and 6-keto [G + T] nucleotides, in the absence of all other pairing regularitiesabsence of all other pairing regularities

Departures from strand symmetry or Chargaff asymmetries Departures from strand symmetry or Chargaff asymmetries can be expressed by differences:can be expressed by differences:

((A-TA-T)/()/(A+TA+T) and () and (C-GC-G)/()/(C+GC+G) for each strand ) for each strand Strand symmetry originates from identical

mutation/substitution processes affecting each strandFor examplesame probability of changingAcAc Tc and Tc and Aw TwAw TwHowever, some mutation processes are known to be strand

asymmetric. Furthermore, nucleotide substitution is subjected to selection which may depend on information contained in only one strand.

The ratio of C + G to the total bases (A+C+G+T) tends to The ratio of C + G to the total bases (A+C+G+T) tends to be constant in a particular speciesbe constant in a particular species

But varies between species But varies between species

DNA base composition is a reflection of phylogenetic DNA base composition is a reflection of phylogenetic relationshiprelationshipIt is evident that those strains which mate with one It is evident that those strains which mate with one another another (i.e. strains within the same 'variety')(i.e. strains within the same 'variety') have similar have similar base compositionsbase compositionsThus strains of variety 1 ..., which are freely intercrossed, Thus strains of variety 1 ..., which are freely intercrossed, have similar mean GC contenthave similar mean GC contentThe organismal phenotype comprises two componentsThe organismal phenotype comprises two components

the classical phenotype, corresponding to the 'gene products the classical phenotype, corresponding to the 'gene products the genome phenotype which is defined by [base] the genome phenotype which is defined by [base] compositional constraintscompositional constraints

Erwin Chargaff provides more evidence that DNA = genetic Erwin Chargaff provides more evidence that DNA = genetic material material

Analysis of base composition of DNA compared between different Analysis of base composition of DNA compared between different organismsorganisms

Nitrogenous basesNitrogenous basesAdenine Adenine (A)(A)Thymine Thymine (T)(T)Guanine Guanine (G)(G)Cytosine Cytosine (C)(C)

Conclusions of ChargaffConclusions of ChargaffDNA composition is species specificDNA composition is species specificThe amounts of A,G,C and T are not the same between speciesThe amounts of A,G,C and T are not the same between species

Ratios of nitrogenous bases vary between speciesRatios of nitrogenous bases vary between species

Fourth observation was critical to Watson and Crick as Fourth observation was critical to Watson and Crick as they deduced the structure of DNA they deduced the structure of DNA