Synthesis of Building Blocks and Oligonucleotides Containing {T}O4‐Alkylene‐O4{T} Interstrand Cross‐Links
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Abstract
This protocol describes the preparation of O 4 ?thymidine?alkylene?O 4 ?thymidine dimer bis?phosphoramidites and precursors for incorporation into DNA sequences to produce site?specific DNA interstrand cross?links. Linkers are introduced at the 4?position of thymidine by reacting the sodium salt of a diol with a pyrimidinyl?convertible nucleoside to produce mono?adducts, which then undergo reaction with a stoichiometric equivalent of a pyrimidinyl?convertible nucleoside under basic conditions to form O 4 ?thymidine?alkylene?O 4 ?thymidine dimers. Bis?phosphoramidites are incorporated into oligonucleotides by solid?phase synthesis, and mild conditions for deprotection and cleavage from the solid support are employed to prevent degradation of the thymidine modifications. Purification of these cross?linked oligonucleotides is performed by denaturing polyacrylamide gel electrophoresis. This approach allows for the preparation of cross?linked DNA substrates in quantities and purity sufficient for a wide range of biophysical experiments and biochemical studies as substrates to investigate DNA repair pathways. Curr. Protoc. Nucleic Acid Chem . 55:5.13.1?5.13.19. © 2013 by John Wiley & Sons, Inc.
Keywords: DNA interstrand cross?link; chemically modified oligonucleotide; oligonucleotide synthesis; solid?phase synthesis; DNA damage; DNA repair
GO TO THE FULL PROTOCOL: PDF or HTML at Wiley Online Library Table of Contents
- Introduction
- Basic Protocol 1: Synthesis of O4‐Hydroxyalkyl‐Thymidine‐3′‐O‐Phosphoramidites
- Basic Protocol 2: Synthesis of O4‐Thymidine‐Alkylene‐O4‐Thymidine‐3‐O‐Bis‐Phosphoramidites
- Basic Protocol 3: Solid‐Phase Synthesis and Deprotection of Oligonucleotides Containing O4‐Hydroxyalkyl‐Thymidine Mono‐Adducts and O4‐Thymidine‐Alkylene‐O4‐Thymidine Cross‐Link Modifications
- Basic Protocol 4: Purification of Oligonucleotides Containing O4‐Alkylene‐Thymidine Mono‐Adducts and O4‐Thymidine‐Alkylene‐O4‐Thymidine Cross‐Link Modifications
- Commentary
- Literature Cited
- Figures
GO TO THE FULL PROTOCOL: PDF or HTML at Wiley Online Library Materials
Basic Protocol 1: Synthesis of O4‐Hydroxyalkyl‐Thymidine‐3′‐O‐Phosphoramidites Materials
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GO TO THE FULL PROTOCOL: PDF or HTML at Wiley Online Library Figures
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Figure 5.13.1 Chemical structure of (A ) the O 4 ‐hydroxyalkyl‐thymidine mono‐adduct and (B ) the O 4 ‐thymidine‐alkylene O 4 ‐thymidine cross‐link. -
Figure 5.13.2 Preparation of 6 . (a) 1,2,4‐triazole, TEA, POCl3 , MeCN:DCM (1:1 v/v); (b) sodium salt of 1,7‐heptanediol, dioxane; (c) Pac‐Cl, TEA, THF; (d) TBAF (1 M in THF), THF; (e) Cl‐P(OCE)N i Pr2 , DIPEA, THF. Abbreviations: TEA, triethylamine; POCl3 , phosphorus(V) oxychloride; MeCN, acetonitrile; DCM, dichloromethane; Pac‐Cl, phenoxyacetyl chloride; THF, tetrahydrofuran; TBAF, tetrabutylammonium fluoride; Cl‐P(OCE)N i Pr2 , N,N‐diisopropylamino cyanoethyl phosphonamidic chloride; DIPEA, diisopropylethylamine; DMT, 4,4′‐dimethoxytrityl; TBDMS, tert ‐butyldimethylsilyl; Pac, phenoxyacetyl. -
Figure 5.13.3 Preparation of 9 . (a) DBU, pyridine; (b) TBAF (1 M in THF), THF; (c) Cl‐P(OCE)N i Pr2 , DIPEA, THF. Abbreviations: DBU, 1,8‐Diazabicyclo[5.4.0]undec‐7‐ene; TBAF, tetrabutylammonium fluoride; THF, tetrahydrofuran; Cl‐P(OCE)N i Pr2 , N,N‐diisopropylamino cyanoethyl phosphonamidic chloride; DIPEA, diisopropylethylamine; DMT, 4,4′‐dimethoxytrityl; TBDMS, tert ‐butyldimethylsilyl. -
Figure 5.13.4 Mono‐phosphoramidite approach for assembly of oligonucleotides containing a O 4 ‐hydroxyalkyl‐thymidine by solid‐phase synthesis. (a) Oligonucleotide synthesis with 2′‐deoxyribonucleoside‐3′‐ O ‐phosphoramidites; (b) coupling with phosphoramidite 6 (labeled as T* ); (c) chain extension with 2′‐deoxyribonucleoside 3′‐phosphoramidites; (d) cleavage from the solid‐support and deprotection with 10% DBU in 1,7‐heptanediol for oligonucleotides containing 6 . -
Figure 5.13.5 Bis‐phosphoramidite approach for assembly of oligonucleotides containing an O 4 ‐ thymidine‐alkylene‐ O 4 ‐thymidine cross‐link by solid‐phase synthesis in a (A ) directly opposing fashion and in a (B ) staggered fashion. (a) Oligonucleotide synthesis with 2′‐deoxyribonucleoside 3′‐phosphoramidites; (b) coupling with bis‐phosphoramidite 9 (labeled as T‐T ); (c) chain extension with 2′‐deoxyribonucleoside 3′‐phosphoramidites; (d) cleavage from the solid support and deprotection with 10% DBU in anhydrous ethanol.
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