Exploring Nucleic Acid Structures Chemistry and Chemical Biology Rutgers University
Nucleic Acid Building Blocks: Nucleotides Base Sugar Sugar base phosphate Phosphate 2
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
Tautomeric structures Keto vs inol Different hydrogen bonding patterns
Watson Crick Base Pairs Geometry of A:T and G:C base pairs are isosteric 5
Diversity of hydrogen bonding geometries
Base morphology Propeller twist
Base pair twist
Backbone conformation
Anti vs. syn Syn conformation Anti conformation
Change in sugar conformation affects the backbone
Ribose ring is never flat
A DNA vs B DNA A-DNA B-DNA
B DNA Voet, Donald and Judith G. Biochemistry, John Wiley & Sons, 1990, p. 802.
A DNA Voet, Donald and Judith G. Biochemistry, John Wiley & Sons, 1990, p. 802.
Z DNA Left handed Very deep minor groove Major groove on outside Voet, Donald and Judith G. Biochemistry, John Wiley & Sons, 1990, p. 802.
G pairing in quadruplex Top view 1l1H Side view 1L1H PDB ID 1L1H Close-up of G-pairing
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
tRNA: Secondary and Tertiary Structures 19
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