The 3-(<i>N</i>-<i>tert</i>-Butylcarboxamido)-1-propyl Group as an Attractive Phosphate/Thiophosphate Protecting Group for Solid-Phase Oligodeoxyribonucleotide Synthesis

Wilk, Andrzej; Chmielewski, Marcin K.; Grajkowski, Andrzej; Phillips, L.; Beaucage, Serge L.

doi:10.1021/jo0258608

Cited by 40 publications

(44 citation statements)

References 22 publications

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“…The half-time of thiophosphate deprotection is estimated to be 73 h at 37°C, and complete deprotection is achieved within 600 h. Fully deprotected CpG ODN fma 1555 exhibited a t R (23 min) identical to that of CpG ODN 1555 under identical chromatographic conditions (Figure 1). The thermolytic deprotection mechanism presumably proceeds through a cyclodeesterification mechanism (Scheme 3) that is typically observed with many of the thermosensitive phosphate/thiophosphate protecting groups investigated earlier (2,4,6,7). …”

Section: Resultsmentioning

confidence: 86%

Thermolytic CpG-containing DNA oligonucleotides as potential immunotherapeutic prodrugs

Grajkowski

Pedras-Vasconcelos²,

Wang³

et al. 2005

Nucleic Acids Research

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A CpG-containing DNA oligonucleotide functionalized with the 2-(N-formyl-N-methyl)aminoethyl thiophosphate protecting group (CpG ODN fma1555) was prepared from phosphoramidites 1a–d using solid-phase techniques. The oligonucleotide behaved as a prodrug by virtue of its conversion to the well-studied immunomodulatory CpG ODN 1555 through thermolytic cleavage of the 2-(N-formyl-N-methyl)aminoethyl thiophosphate protecting group. Such a conversion occurred at 37°C with a half-time of 73 h. The immunostimulatory properties of CpG ODN fma1555 were evaluated in two in vivo assays, one of which consisted of mice challenged in the ear with live Leishmania major metacyclic promastigotes. Local intradermal administration of CpG ODN fma1555 was as effective as that of CpG ODN 1555 in reducing the size of Leishmania lesions over time. In a different infectious model, CpG ODN 1555 prevented the death of Tacaribe-infected mice (43% survival) when administered between day 0 and 3 post infection. Administration of CpG ODN fma1555 three days before infection resulted in improved immunoprotection (60–70% survival). Moreover, co-administration of CpG ODN fma1555 and CpG ODN 1555 in this model increased the window for therapeutic treatment against Tacaribe virus infection, and thus supports the use of thermolytic oligonucleotides as prodrugs in the effective treatment of infectious diseases.

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Section: Resultsmentioning

confidence: 86%

Thermolytic CpG-containing DNA oligonucleotides as potential immunotherapeutic prodrugs

Grajkowski

Pedras-Vasconcelos²,

Wang³

et al. 2005

Nucleic Acids Research

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“…A similar route was used to prepare MAF-modified 3′-phosphoramidites. Although faster deprotecting PTE groups, such as 3-( N -tert-butylcarboxamido)-1-propyl (TBCA) and 4-methylthio-1-butyl (MTB) (72,75) were examined, their low stability during preparation and isolation limited their development.…”

Section: Resultsmentioning

confidence: 99%

Hot Start PCR with heat-activatable primers: a novel approach for improved PCR performance

Lebedev

Paul

Yee

et al. 2008

Nucleic Acids Research

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The polymerase chain reaction (PCR) is widely used for applications which require a high level of specificity and reliability, such as genetic testing, clinical diagnostics, blood screening, forensics and biodefense. Great improvements to PCR performance have been achieved by the use of Hot Start activation strategies that aim to prevent DNA polymerase extension until more stringent, higher temperatures are reached. Herein we present a novel Hot Start activation approach in PCR where primers contain one or two thermolabile, 4-oxo-1-pentyl (OXP) phosphotriester (PTE) modification groups at 3′-terminal and 3′-penultimate internucleotide linkages. Studies demonstrated that the presence of one or more OXP PTE modifications impaired DNA polymerase primer extension at the lower temperatures that exist prior to PCR amplification. Furthermore, incubation of the OXP-modified primers at elevated temperatures was found to produce the corresponding unmodified phosphodiester (PDE) primer, which was then a suitable DNA polymerase substrate. The OXP-modified primers were tested in conventional PCR with endpoint detection, in one-step reverse transcription (RT)–PCR and in real-time PCR with SYBR Green I dye and Taqman® probe detection. When OXP-modified primers were used as substitutes for unmodified PDE primers in PCR, significant improvement was observed in the specificity and efficiency of nucleic acid target amplification.

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“…The CH 2 signals at 46.8 ( 13 C) and 3.77-3.72 ( 1 H) ppm are characteristic for the CH 2 N group [14], whereas the CH 2 O signals of 11' would be expected at ca. 62 and 4.2 ppm, respectively [15] [16]. The formation of 11 may be rationalized by the cyclization of intermediate 12.…”

Section: Methodsmentioning

confidence: 96%

Reactions with 4‐Hydroxy‐2‐methylbutananilides: Unexpected Formation of a Cyclopropanecarboxamide

Mekhael

Linden

Heimgartner

2011

Helvetica Chimica Acta

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The successive treatment of the N,N‐disubstituted 4‐hydroxy‐2‐methylbutanamide 2a with lithium diisopropylamide (LDA) and diphenyl phosphorochloridate (DPPCl) led to the 1‐methylcyclopropanecarboxamide 10 in good yield. This base‐catalyzed cyclization offers a new approach to cyclopropanecarboxamides. Under similar conditions, the N‐monosubstituted 4‐hydroxy‐2‐methylbutanamide 2b gave the 3‐methylpyrrolidin‐2‐one 11. The structure of the cyclopropanecarboxamide 10 was established by X‐ray crystallography.

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The 3-(N-tert-Butylcarboxamido)-1-propyl Group as an Attractive Phosphate/Thiophosphate Protecting Group for Solid-Phase Oligodeoxyribonucleotide Synthesis

Cited by 40 publications

References 22 publications

Thermolytic CpG-containing DNA oligonucleotides as potential immunotherapeutic prodrugs

Thermolytic CpG-containing DNA oligonucleotides as potential immunotherapeutic prodrugs

Hot Start PCR with heat-activatable primers: a novel approach for improved PCR performance

Reactions with 4‐Hydroxy‐2‐methylbutananilides: Unexpected Formation of a Cyclopropanecarboxamide

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