Facile removal of new base protecting groups useful in oligonucleotide synthesis

Schulhof, J.C.; Molko, D.; Téoule, R.

doi:10.1016/s0040-4039(00)95646-6

Cited by 60 publications

(22 citation statements)

References 6 publications

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“…Assembling of the phosphoramidites building blocks on a solid support The phosphoramidite 4 was used, likewise each of the four 5'-O-(4,4'-dimethoxytrityl)-N-protected-2'-deoxynucleoside-3 '-O-(2-cyanoethyl-N,N-diisopropylamino)-phosphoramidites with labile base protection (N6-phenoxyacetyl adenine, N2-phenoxyacetyl guanine, N4-isobutyryl cytosine and thymine) described previously (16,17), for the synthesis of oligodeoxyribonucleotides on silica gel support. The protected phosphoramidite 4 was inserted using the standard phosphoramidite methodology (15,18,19), with the same high coupling efficiency (> 97%), as measured and calculated by the amount of released trityl cation.…”

Section: (A-cg0-a-c-t-t-a-g-c-g-a-g-g-f-t)3 6 D Y(acg0-a-c-t-t-a-0mentioning

confidence: 99%

Incorporation by chemical synthesis and characterization of deoxyribosylformylamine into DNA

Guy¹,

Duplaa²,

Ulrich³

et al. 1991

Nucl Acids Res

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2-deoxyribosylformylamine is a major oxidative DNA damage type which occurs upon the action of ionizing radiation on DNA. The protected 2-deoxyribosylformylamine phosphoramidite was synthesized and used in conjunction with previously reported alkali labile base protected phosphoramidites ('PAC phosphoramidites') for the preparation of oligodeoxyribonucleotides containing this lesion. Final deprotection of the oligonucleotides was performed under mild alkaline conditions to preserve the integrity of the fragile defect. The presence of formylamino deoxyribosyl residue was confirmed by FAB mass spectrometry sequencing. Oligonucleotides bearing deoxyribosyl formylamine were used as templates for studying in vitro replication. They direct the insertion of guanine or induce a deletion opposite the lesion.

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Section: (A-cg0-a-c-t-t-a-g-c-g-a-g-g-f-t)3 6 D Y(acg0-a-c-t-t-a-0mentioning

confidence: 99%

Incorporation by chemical synthesis and characterization of deoxyribosylformylamine into DNA

Guy¹,

Duplaa²,

Ulrich³

et al. 1991

Nucl Acids Res

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“…The plots show single-channel raw data for enzymatic dC reactions using 'Sequenase' performed under the conditions given in the text. (A) Tamra-primer synthesized using phosphoramidites with the labile base-protecting groups of Schulhof, et al (12,13) [dA(phenoxyacetyl), dG(phenoxyacetyl), dC(iso-butyryl)]; (B) Fain-primer synthesized using phosphoramidites with the standard baseprotecting groups [dA(benzoyl), dG(isobutyryl), dC(benzoyl)] (obtained from Applied Biosystems). Numbers above the peaks indicate the relative position in the M13 sequence and are presented only to aid in comparing the two traces.…”

Section: Resultsmentioning

confidence: 99%

“…al. (12,13). Protected nucleoside phosphoramidites were synthesized essentially as described in the above reference.…”

Section: Methodsmentioning

confidence: 99%

Specific-primer-directed DNA sequencing using automated fluorescence detection

et al. 1989

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Automated fluorescence-based DNA sequence analysis offers the possibility to undertake very large scale sequencing projects. Directed strategies, such as the specific-primer-directed sequencing approach ('gene walking'), should prove useful in such projects. Described herein is a study involving the use of this approach in conjunction with automated fluorescence detection on a commercial instrument (ABI 370A DNA sequencer). This includes procedures for the rapid chemical synthesis and purification of labeled primers, the design of primer sequences that are compatible with the commercial analysis software, and automated DNA sequence analysis using such primers. A set of four fluorophore-labeled primers can be reliably synthesized in a twenty-four hour period, and greater than 300 nucleotides of analyzed new sequence obtained using this set in an additional twenty-four hours. Scale-up of these procedures to take advantage of the full capabilities of the sequencer is, at present, too slow and costly to be suitable for routine sequencing, and therefore the use of specific-primers is best suited to the closure of gaps in extended sequence produced using random cloning and sequencing strategies.

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“…These results are interesting also in the context of recently introduced phenoxyacetyl (PAC) protections for amino group of guanine and adenine which are easily cleaved under moderate conditions (31). If PAC phosphoramidites would be used to prepare oligonucleotide 3'-phosphates on supports 1 treatment with ammonia at 50°C (2 hrs) or room temp.…”

Section: Synthesis Of Nucleoside 3'-phosphatesmentioning

confidence: 95%

Universal solid supports for the synthesis of oligonucleotides with terminal 3′-phosphates

Markiewicz

Wyrzykiewicz

1989

Nucl Acids Res

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The preparation of two types of supports based on controlled pore glass (CPG) is presented. These supports are compatible with established phosphoroamidite chemistry of oligonucleotides synthesis giving rise to an oligonucleotide with terminal 3'-phosphate function during final deprotection. CPG was modified with: (i) methacrylic acid derivatives and 2-mercaptoethanol (1) or (ii) aminoalkylsilane, succinic anhydride and benzidine (2). Support 2 can be also used for the synthesis of partially protected oligonucleotide 3'-phosphates.

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Facile removal of new base protecting groups useful in oligonucleotide synthesis

Cited by 60 publications

References 6 publications

Incorporation by chemical synthesis and characterization of deoxyribosylformylamine into DNA

Incorporation by chemical synthesis and characterization of deoxyribosylformylamine into DNA

Specific-primer-directed DNA sequencing using automated fluorescence detection

Universal solid supports for the synthesis of oligonucleotides with terminal 3′-phosphates

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