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Biochemist’s View of the DNA Double Helix

Biochemist’s View of the DNA Double Helix. Minor groove. Major groove. 2. Representative Nucleotides. 5’. 3’. Chemist’s View. Contrast with Nucleic Acid Bases (A, T, C, G, U) – Specific!. Evidence for specificity? Why are these interactions specific? e.g. G-C & A-T. Evidence?

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Biochemist’s View of the DNA Double Helix

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  1. Biochemist’s View of the DNA Double Helix Minor groove Major groove

  2. 2 Representative Nucleotides 5’ 3’

  3. Chemist’s View

  4. Contrast with Nucleic Acid Bases (A, T, C, G, U) – Specific! • Evidence for specificity? • Why are these interactions specific? e.g. G-C & A-T

  5. Evidence? • If mix G & C together → exothermic reaction occurs; change in 1H chemical shift in NMR; other changes  reaction occurring • Also occurs with A & T • Other combinations → no change! e.g. Guanine-Cytosine: • Why? • In G-C duplex, 3 complementary H-bonds can form: donors & acceptors = molecular recognition

  6. Mechanism?

  7. Properties of Pyridine • We’ve seen it as an acid & an H-bond acceptor • Lone pair can act as a nucleophile:

  8. Another example of N-Alkylation of Pyridines This is an SN2 reaction with stereospecificity

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