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Exploring Nucleic Acid Structures

Exploring Nucleic Acid Structures . Chemistry and Chemical Biology Rutgers University. Nucleic Acid Building Blocks: Nucleotides. Base. Sugar. Phosphate. Chemistry. Bases Purines and Pyrimidines Bases in DNA (dA, dT, dG, dC) Bases in RNA (A, U, G, C) Sugars

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Exploring Nucleic Acid Structures

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  1. Exploring Nucleic Acid Structures Chemistry and Chemical Biology Rutgers University

  2. Nucleic Acid Building Blocks: Nucleotides Base Sugar Phosphate

  3. Chemistry Bases Purines and Pyrimidines Bases in DNA (dA, dT, dG, dC) Bases in RNA (A, U, G, C) Sugars DNA has deoxy ribose sugar RNA has ribose sugar Phosphate deoxy-ribose ribose Bases C5’ C5’ C5’ P Phosphate Sugars

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

  5. Watson Crick Base Pairs Geometry of A:T and G:C base pairs are isosteric

  6. Diversity of hydrogen bonding geometries

  7. Base morphologyPropeller twist

  8. Base pair twist

  9. Backbone conformation

  10. Anti vs. syn Syn conformation Anti conformation

  11. Change in sugar conformation affects the backbone

  12. Ribose ring is never flat

  13. A DNA vs B DNA A-DNA B-DNA

  14. B DNA Voet, Donald and Judith G. Biochemistry, John Wiley & Sons, 1990, p. 802.

  15. A DNA Voet, Donald and Judith G. Biochemistry, John Wiley & Sons, 1990, p. 802.

  16. Z DNA • Left handed • Very deep minor groove • Major groove on outside Voet, Donald and Judith G. Biochemistry, John Wiley & Sons, 1990, p. 802.

  17. G pairing in quadruplex Top view 1l1H Side view 1L1H Close-up of G-pairing

  18. RNA • Double and single stranded • Double helix has A-form structure • Single stranded forms globular structure 1NYI Hammerhead ribozyme 387D RNA Pseudoknot 406D RNA double helix

  19. tRNA: Secondary and Tertiary Structures

  20. 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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