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It should however be understood that our findings are aimed at improving the current methods for the synthesis of oligonucleotides on microarrays. In this regard, replacement of the DMTr group with an aminosulfinyl group should not be viewed as a loss of a color-producing indicator for phosphoramidite coupling efficiency given that the DMTr assay is not sensitive enough to reliably assess phosphoramidite coupling efficiency on microarrays.
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3N (3 mol equiv) in MeCN under an inert atmosphere at 5 °C.
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36
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3543091225
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3N (3.3 mol equiv) in MeCN under an atmosphere of argon gas.
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37
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3543087694
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Alternatively, 2,2,5,5-tetramethyl-3-pyrroline-3-carboxamide is inexpensively prepared in two steps from 2,2,6,6-tetramethylpiperidin-4-one.25a
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The most important parameters investigated were (i) phosphoramidite coupling time and coupling efficiency, and (ii) time required for oxidative 5′-O-deprotection relative to the concentration of the acidic salt being used in the reaction.
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The details of this complex deprotection mechanism are still being investigated.
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Skipping the 1 min treatment with a commercial iodine solution leads to premature cleavage of the internucleoside phosphite triester linkage caused by the acidity of the 0.1 M iodine solution.
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51
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3543058418
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2O (9:1 v/v) results in a noticeably slower deprotection of the 5′-O-sulfinyl group and thus underscores the synergistic participation of iodine in the cleavage of the protecting group.
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PST) is provided in the Supporting Information and compared with a chromatogram of the same oligonucleotide synthesized from standard 5′-O-DMTr-deoxyribonucleoside phosphoramidites under similar conditions.
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These additional extractions are required only to optimize the recovery of 7b.
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3. These signals are consistent with the four diastereomers emerging from the asymmetry of the phosphorus and sulfur atoms.
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