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

2. Nucleic Acid Building Blocks: Nucleotides
Base
Sugar
Sugar base phosphate
Phosphate 2

3. Chemistry Bases Sugars Phosphate 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
C5’
C5’
C5’ P
Phosphate
Sugars 3

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 5

6. Diversity of hydrogen bonding geometries

7. Base morphology Propeller 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
PDB ID 1L1H
Close-up of G-pairing

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

19. tRNA: Secondary and Tertiary Structures19

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,
Voet, Donald and Judith G. Biochemistry. John Wiley & Sons, 1990, pp. 792, 797,