Z-DNA Left handed Helix Occurs in DNA sequences with stretches of consecutive G-C base pairs jagged backbone G nucleotides: Switch C2’endo -> C3’ endo anti -> Syn Requires high salt in vitro PDB ID: 1DCG C nucleotides: No change
on bases Helical Pitch = 34 A (10 residues/turn) Rise/ residue = 3.4 AĬomplementary sets of donors and acceptor groups on basesĪ comparison of the Watson-Crick model (1953) and of the first B-DNA structure solved (1980) The Dickerson Dodecamer X-ray structure (CGCGAATTCGCG) PDB ID: 1BNA Watson-Crick ModelĭNA Double Helix Definitions Bases Orientationīase pairs seen from above the helix (helical projection) Helical Axis Major Groove >180° H O H N N7 N1 H N3 N9 N1 N3 O H N dR dR H Minor Groove B DNA H20 A B A water spine (green dots) has been proposed to exist in the minor groove of B-DNA that would stabilize the B-form This concept is controversial and will not be detailed further. Antiparallel right-handed double helix. The original model for DNA structure Watson and Crick (1953) Nature 171, 964-967 Franklin DNA fibers X-ray diffraction data 2) bases are in the keto conformation Maltese Cross Indicates an Helical pattern Spacing between Phosphates = 3.4A enol Helical Pitch = 34A keto Bragg’s Law: 2dsinQ = nl used to interpret X-ray diffraction pictures 4) Density measurements: ~2 polymers/helix 3) Chargaff’s rules: (G+C)/(A+T) can vary But (G+A)/(C+T) = G/C = A/T =1 5) C2’ endo sugar pucker conformationīragg's Law = repeated atomic features in the crystal or fiber Bragg’s law indicates an inverse relationship between diffraction angle and actual distances between repeated features in crystal/fiber 
Information that Watson and Crick used to propose the double helix model: 1) R. Watson and Crick (1953) Watson and Crick (1953): “It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material”. 1950: “It is, however, noteworthy -whether this is more than accidental, cannot yet be said-that in all deoxypentose nucleic acids examined thus far the molar ratios of total purines to total pyrimidines, and also of adenine to thymine and of guanine to cytosine, were not far from 1”.
Rosalind Franklin (1950 or 1951) Chargaff.
Links 3’-O of preceding nucleotide to 5’ of next nucleotide ->5’-3’ polarity. DNA Sequencing 6- Principles of Nucleic Acids Denaturation. Nucleic Acids Structures 1-Discovery of DNA structure 2- A, B and Z conformations of dsDNA/dsRNA 3- DNA tertiary Structures Nucleosome, G-quadruplex 4- Secondary and tertiary Structure of RNA 5- Principles of DNA Recognition by sequence-specific DNA binding proteins
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