Solid-phase synthesis of base-sensitive oligonucleotides

Virta, Pasi

doi:10.3998/ark.5550190.0010.307

Cited by 7 publications

(6 citation statements)

References 61 publications

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“…Figure depicts the synthetic scheme that was developed for the preparation of BIBS protected 2′-deoxynucleoside 3′-phosphoramidites. Starting with 5′,3′-di- O -acetyl 2′-deoxynucleosides ( 1, 4 , or 7 ), silylation of the exocyclic amines was carried out using variations of the reported procedure . The reaction of 5′,3′-di- O -acetyl-2′-deoxycytidine ( 1 ) with BIBS-OTf (Tf = triflate) in the presence of base proceeded in 2 h at 50 °C with good yield (67%), whereas 5′,3′-di- O -acetyl-2′-deoxyadenosine ( 4 ) reacted more slowly and required heating at 60 °C for 3 days in order to obtain the product in 25–30% yield.…”

Section: Resultsmentioning

confidence: 99%

“…Starting with 5′,3′-di-O-acetyl 2′-deoxynucleosides (1, 4, or 7), silylation of the exocyclic amines was carried out using variations of the reported procedure. 65 The reaction of 5′,3′-di-O-acetyl-2′-deoxycytidine (1) with BIBS- OTf (Tf = triflate) in the presence of base proceeded in 2 h at 50 °C with good yield (67%), whereas 5′,3′-di-O-acetyl-2′deoxyadenosine (4) reacted more slowly and required heating at 60 °C for 3 days in order to obtain the product in 25−30% yield. These results are in accordance with the lower nucleophilicity of the adenine amine.…”

Section: ■ Resultsmentioning

confidence: 99%

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Silver Nanoassemblies Constructed from Boranephosphonate DNA

et al. 2013

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Spatially selective deposition of metal onto complex DNA assemblies is a promising approach for the preparation of metallic nanostructures with features that are smaller than what can be produced by top-down lithographic techniques. We have recently reported the ability of 2'-deoxyoligonucleotides containing boranephosphonate linkages (bpDNA) to reduce AuCl4(-), Ag(+), and PtCl4(2-) ions to the corresponding nanoparticles. Here we demonstrate incorporation of bpDNA oligomers into a two-dimensional DNA array comprised of tiles containing double crossover junctions. We further demonstrate the site-specific deposition of metallic silver onto this DNA structure which generates well-defined and preprogrammed arrays of silver nanoparticles. With this approach the size of the metallic features that can be produced is limited only by the underlying DNA template. These advances were enabled due to a new method for synthesizing bpDNA that uses a silyl protecting group on the DNA nucleobases during the solid-phase 2'-deoxyoligonucleotide synthesis.

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Section: Resultsmentioning

confidence: 99%

Section: ■ Resultsmentioning

confidence: 99%

Silver Nanoassemblies Constructed from Boranephosphonate DNA

et al. 2013

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“…Mechanism of Teoc deprotection using TBAF is shown in Figure 2.1.14. The fluoride-labile nucleobase protection strategy is detailed in a review by Virta (2009).…”

Section: Fluoride-labile Protectionmentioning

confidence: 99%

Nucleobase Protection of Deoxyribo‐ and Ribonucleosides

Meher

Iyer

2017

CP Nucleic Acid Chemistry

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Oligonucleotides carrying a variety of chemical modifications including conjugates are finding increasing applications in therapeutics, diagnostics, functional genomics, proteomics, and as research tools in chemical and molecular biology. The successful synthesis of oligonucleotides primarily depends on the use of appropriately protected nucleoside building blocks including the exocyclic amino groups of the nucleobases, the hydroxyl groups at the 2'-, 3'-, and 5'-positions of the sugar moieties, and the internucleotide phospho-linkage. This unit is a thoroughly revised update of the previously published version and describes the recent development of various protecting groups that facilitate reliable oligonucleotide synthesis. In addition, various protecting groups for the imide/lactam function of thymine/uracil and guanine, respectively, are described to prevent irreversible nucleobase modifications that may occur in the presence of reagents used in oligonucleotide synthesis. © 2017 by John Wiley & Sons, Inc.

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“…These applications frequently require modified ODNs that contain a wide variety of functional groups including those that cannot survive known ODN synthesis, cleavage and deprotection conditions. To meet these demands, some work on developing new technologies suitable for the synthesis of sensitive ODNs has been carried out [28,31]. A common method is to use more labile acyl functions such as the phenoxyacetyl group for amino protection and as linker to enable deprotection and cleavage under milder basic conditions [32].…”

Section: Introductionmentioning

confidence: 99%

Electrophilic oligodeoxynucleotide synthesis using dM-Dmoc for amino protection

Shahsavari¹,

Eriyagama²,

Halami³

et al. 2019

Beilstein J. Org. Chem.

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Solid-phase synthesis of electrophilic oligodeoxynucleotides (ODNs) was achieved using dimethyl-Dmoc (dM-Dmoc) as amino protecting group. Due to the high steric hindrance of the 2-(propan-2-ylidene)-1,3-dithiane side product from deprotection, the use of excess nucleophilic scavengers such as aniline to prevent Michael addition of the side product to the deprotected ODN during ODN cleavage and deprotection was no longer needed. The improved technology was demonstrated by the synthesis and characterization of five ODNs including three modified ones. The modified ODNs contained the electrophilic groups ethyl ester, α-chloroamide, and thioester. Using the technology, the sensitive groups can be installed at any location within the ODN sequences without using any sequence- or functionality-specific conditions and procedures.

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Solid-phase synthesis of base-sensitive oligonucleotides

Cited by 7 publications

References 61 publications

Silver Nanoassemblies Constructed from Boranephosphonate DNA

Silver Nanoassemblies Constructed from Boranephosphonate DNA

Nucleobase Protection of Deoxyribo‐ and Ribonucleosides

Electrophilic oligodeoxynucleotide synthesis using dM-Dmoc for amino protection

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