A practical and efficient approach to PNA monomers compatible with Fmoc-mediated solid-phase synthesis protocols

European Journal of Organic Chemistry

Volumn , Issue 34, 2008, Pages 5786-5797

  Porcheddu, Andrea ^a   Giacomelli, Giampaolo ^a   Piredda, Ivana ^a   Carta, Mariolino ^a   Nieddu, Giammario ^a  

^a UNIVERSITY OF SASSARI   (Italy)

Author keywords

Guanine; Peptide nucleic acids; Protecting groups; Solid phase synthesis

Indexed keywords

EID: 56749178599     PISSN: 1434193X     EISSN: 10990690     Source Type: Journal    
DOI: 10.1002/ejoc.200800891     Document Type: Article

References (79)

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53. DMF has been linked to cancer in humans, and it is thought to cause birth defects. In some sectors of industry women are banned from working with DMF. For a DMF chronic toxicity summary, see: http://www.oehha.org/air/chronic_rels/ pdf/68122.pdf.
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57. The synthesis of thyminylacetic acid, which does not require an additional base protecting group, can be prepared either by alkylation of thymine with halogenoacetic acid esters followed by saponification or by direct alkylation with bromoacetic acid. This latter method is better because of its simplicity.
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66. This procedure was conducted in duplicate and did not always give reproducible results.
67. From our experience, most displacement reactions with alkoxide from 2-amino-6-chloropurine are rather elaborate and give the desired guanine in low yields. Hudson and Wojciechowski (a team with a deep experience in PNA synthesis) in their seminal paper suggest the procedure outline by Kunz (C. Barth, O. Seitz, H. Z. Kunz, Naturforsch. 2004, 59b, 802) to climb this obstacle. Honestly, we have no direct experience with this last procedure.
68. After several attempts and two years of unsuccessful research we still were at a dead end.
69. Trimethylammonium is a better leaving group than chloride in the addition-elimination mechanism leading to displacement of the 6-substituent by a nucleophile.
70. 2O, 95:5).
71. The structure of the collected solid was confirmed by detailed spectroscopic, mass and elemental analysis. The same reaction was conducted in duplicate and with increasing quantities of the substrate (up to 2 g); we never observed the presence of a 6-dimethylamino byproduct. For a closer examination, see the NMR spectroscopic analysis in the Supporting Information.
72. In the protocol outlined by Winssinger to prepare N-Boc-protected guanine, the exocyclic nitrogen atom was converted into an isocyanate, which was then treated with tBuOH. Unlike other nucleobases, the lower reactivity of 6-amino-2-chloropurine necessitated the use of triphosgene for isocyanate formation.
73. This procedure was successfully applied for final quantities of monomers up to 5 g.
74. 2 and isobutyl alcohol (two volatile compounds). Moreover, IBC and pivaloyl chloride are cheap and couple easily to the acid. These last points of view are not marginal if our goal is the preparation of all monomers on macroscale.
75. Used protocols were based on those provided in: R. Casale, I. S. Jensen, M. Egholm, "Synthesis of PNA Oligomers by Fmoc Chemistry" in Peptide Nucleic Acids: Protocols and Applications (Eds.: P. E. Nielsen), 2nd ed., Garland Science, 2003.
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77. [33]
78. The residue was put under high vacuum for at least 2-3 h to remove all traces of tBuOH.
79. An off-white solid started to precipitate just after 30 min.