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