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Principles of Nucleic Acid Structure

Principles of Nucleic Acid Structure. September 11, 2008. Components of Nucleic Acid Structures. Sugar Base Phosphate. Bases. Pyrimidines and purines Positions of hydrogens key to recognition. Tautomeric structures. Keto vs inol Different hydrogen bonding patterns. pK of nucleotides.

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Principles of Nucleic Acid Structure

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  1. Principles of Nucleic Acid Structure September 11, 2008

  2. Components of Nucleic Acid Structures • Sugar • Base • Phosphate

  3. Bases • Pyrimidines and purines • Positions of hydrogens key to recognition

  4. Tautomeric structures • Keto vs inol • Different hydrogen bonding patterns

  5. pK of nucleotides • Affects hydrogen bonding possibilities N1 adenine-3.5 N3 cytosine-4.2 N7 of adenine 1.0

  6. Geometry of Watson Crick base pairsA:T and G:C are isosteric

  7. Diversity of hydrogen bonding geometries

  8. Hydrogen bonding if WC base pair • Definition of Major and Minor groove • Mechanisms of recognition

  9. Basepair-base • C-G-C (C must be protonated) • T-A-T normal • Found in triple helices

  10. Amino acid - base pair

  11. Amino acid - base pair

  12. Amino acid - base pair

  13. Amino acid - base pair

  14. Base morphologyPropeller twist

  15. buckle

  16. Base pair twist

  17. roll

  18. Backbone conformation

  19. Anti vs. syn

  20. Change in sugar conformation affects the backbone

  21. Ribose ring is never flat

  22. C4’-C5’-g+

  23. Conformation wheel for nucleotides • -3 values • -3 values • -3 values • -two ranges • C3’ endo • C2’ endo • -trans,g- • -3 values

  24. Common building blocksSmall changes leading to big differences

  25. A DNAB DNA

  26. B-DNA

  27. A DNA

  28. Polymer Characteristics

  29. References Saenger, Wolfram. Principles of Nucleic Acid Structure. Springer-Verlag New York Inc., 1984, pp. 109, 113. Neidle, Stephen. Nucleic Acid Structure and Recognition. Oxford University Press, 2002, pp. 18, 21-22, 34, 36, 68, 90, 165-166. Voet, Donald and Judith G. Biochemistry. John Wiley & Sons, 1990, pp. 792, 797, 807-809.

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