215F07-notes-12-7-07 - Chem 215 F07 Notes — Dr Masato...

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Unformatted text preview: Chem 215 F07 Notes — Dr. Masato Koreeda — Page 1 of 3. Date: December 7, 2007 Polynucelotides: DNA and RNA (Chapter 23.9) (1) Nucleosides: the bicyclic purine (adenine or guanine) or monocyclic pyrimidine base (thymine, uracil, or cytosine) joined from a ring nitrogen to carbon 1 of a pentose sugar; in the ribonucleic acid (RNA) system, the pentose is D—ribose which is locked into a five- membered furanose ring and in the deoxyribonucleic acid (DNA) system the pentose is 2- deoxy—D-ribose. Nucleotides: the phosphate esters of nucleosides. Sugars Nucleosides HO HO HO O OH 0 -Base 0 IE] HO OH HO OH HO Ribose 2-Deoxyribose A ribonucleogide A deoxyribonucleogide (no oxygen at the 2—position) Nucleotides o o _ ll _ ll o—ila—o o—T—o The sugars ribose and deoxyribose, and 0. ° ' 0_ 0 the corresponding nucleosides and nucleotides, phosphorylated nucleos1des. HO OH I HO Structures of the five major purine and pyrimidine bases of nucleic acids NH2 0 NH2 0 O N 6 N s A\N Me NH \ (97 l JN (97 l 3% el 1% l 1% These bases N 3N/ N N/ NHz N 0 N O can be different / / ' l ' l in RNAand H A H a" H C H T adenine guanine cytosine thymine This OH at the 2-position is present in RNA, but absent in DNA Nucleic acids (DNA and RNA) are polymeric collection of nucleotides Chem 215 F07 Notes — Dr. Masato Koreeda - Page 2 of 3. Date: December 7, 2007 (2) The H—bonding between nucleic acid bases and the double helix structure of DNA H ,H N—H O N\7 2 o'wH—N N\ /C\N-HHH_N N —N 01 N—< \=N 01 0/1 OH'H-—N\ of, o H Watson—Crick base—pairing for C—G (left) and T—A (right). strand 1: strand II: 5’end ‘ 3’end ‘Azzz'll'i —T==:A¥‘—:. ——GE':5C EL—CESZG V —A:::T Double helix of DNA. Two GWC complementary strands are __T..;;;_a 34,; joined by hydrogen—bonds '1 between the base pairs. This double strand coils into a .C'ggggi helical arrangement. 3—A‘“T—‘—g t—TzzzA +GESEC —T:::A-.-“-”" strand 1: strand II: 3’end Send (3) Synthesis of ribonucleosides With heavy metal salts of bases: 0 JL 0 HN Ph L <N I \ N HN Ph NH2 / N \ N \ A00 ‘11 J NHS | J 90‘ N M OH N WBr 1 A00 N 6 HO N xy ene O 0 A00 OAc 120 °C 0 AC = A (acetyl) ACO OAC HO OH H3C Chem 215 F07 Notes — Dr. Masato Koreeda - Page 3 of 3. Date: December 7, 2007 (4) Synthesis of 2—deoxyribonucleosides Cl CI N \ N N N N N N/J TolO ONa/> ToIO ' CH3 0 ’ o % aw 8N2! 71% Tol: 3‘ T IO 0' 0 ToIO (5) Formation of oligonucleotide bonds phosphodiester method 0 “300 HNJLPh N \ N O </N l A i O N H300 HN Ph H300 0 Ph #0:} 1' O O (NIKN || S—Cl N N/) HO ('5 O + i H3CO Ph 0 i HN Ph pyridine HN Ph N \ O O N </ I N 2. aqueous workup \\p/ </ [\N o /) eO/\ é! o—P—o O | O 0 e o deprotection of 4,4'-dimethoxytriphenylmethyl ACO group Aco I. C|3CC(=O)OH (trichloroacetic acid) 2. NH3-CH30H ...
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