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