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Permanent or reversible conjugation of 2'-O- or 5'-O-aminooxymethylated nucleosides with functional groups as a convenient and efficient approach to the modification of RNA and DNA sequences.

Cieslak J, Grajkowski A, Ausín C, Gapeev A, Beaucage SL - Nucleic Acids Res. (2011)

Bottom Line: The reaction of these novel ribonucleosides with 1-pyrenecarboxaldehyde results in the efficient formation of stable and yet reversible ribonucleoside 2'-conjugates in yields of 69-82%.Although the versatility and uniqueness of 2'-O-aminooxymethyl ribonucleosides in the preparation of modified RNA sequences is demonstrated by the single or double incorporation of a reversible pyrenylated uridine 2'-conjugate into an RNA sequence, the conjugation of 2'-O-aminooxymethyl ribonucleosides with aldehydes, including those generated from their acetals, provides reversible 2'-O-protected ribonucleosides for potential applications in the solid-phase synthesis of native RNA sequences.The synthesis of a chimeric polyuridylic acid is presented as an exemplary model.

View Article: PubMed Central - PubMed

Affiliation: Division of Therapeutic Proteins, Center for Drug Evaluation and Research, Food and Drug Administration, 8800 Rockville Pike, Bethesda, MD 20892, USA.

ABSTRACT
2'-O-Aminooxymethyl ribonucleosides are prepared from their 3',5'-disilylated 2'-O-phthalimidooxymethyl derivatives by treatment with NH(4)F in MeOH. The reaction of these novel ribonucleosides with 1-pyrenecarboxaldehyde results in the efficient formation of stable and yet reversible ribonucleoside 2'-conjugates in yields of 69-82%. Indeed, exposure of these conjugates to 0.5 M tetra-n-butylammonium fluoride (TBAF) in THF results in the cleavage of their iminoether functions to give the native ribonucleosides along with the innocuous nitrile side product. Conversely, the reaction of 5-cholesten-3-one or dansyl chloride with 2'-O-aminooxymethyl uridine provides permanent uridine 2'-conjugates, which are left essentially intact upon treatment with TBAF. Alternatively, 5'-O-aminooxymethyl thymidine is prepared by hydrazinolysis of its 3'-O-levulinyl-5'-O-phthalimidooxymethyl precursor. Pyrenylation of 5'-O-aminooxymethyl thymidine and the sensitivity of the 5'-conjugate to TBAF further exemplify the usefulness of this nucleoside for modifying DNA sequences either permanently or reversibly. Although the versatility and uniqueness of 2'-O-aminooxymethyl ribonucleosides in the preparation of modified RNA sequences is demonstrated by the single or double incorporation of a reversible pyrenylated uridine 2'-conjugate into an RNA sequence, the conjugation of 2'-O-aminooxymethyl ribonucleosides with aldehydes, including those generated from their acetals, provides reversible 2'-O-protected ribonucleosides for potential applications in the solid-phase synthesis of native RNA sequences. The synthesis of a chimeric polyuridylic acid is presented as an exemplary model.

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Synthesis of 2′-O-pyrenylated ribonucleosides derivatives. (i) DMSO, Ac2O, AcOH, 50°C, 16 h; (ii) silica gel chromatography; (iii) SO2Cl2, CH2Cl2, 25°C, 2 h; (iv) N-hydroxyphthalimide, DBU, CH2Cl2, 25°C, 24 h; (v) NH4F, MeOH, 25°C, 16 h; (vi) concd aq NH3, 55°C, 1 h; (vii) 1-pyrenecarboxaldehyde, MeOH, 55°C, 1 h; (viii) DMTrCl, pyridine, 25°C, 16 h; (ix) 2-cyanoethyl N,N-diisopropylchlorophosphoramidite, Et3N, CH2Cl2, 25°C, 2 h. Abreviations. BP: a, uracil-1-yl; b, N4-acetylcytosin-1-yl; c, N6-isobutyryladenin-9-yl; d, N2-phenoxyacetylguanin-9-yl; B: a, uracil-1-yl; b, cytosin-1-yl; c, adenin-9-yl; d, guanin-9-yl; DMTr, 4,4′-dimethoxytrityl.
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gkr896-SCH1: Synthesis of 2′-O-pyrenylated ribonucleosides derivatives. (i) DMSO, Ac2O, AcOH, 50°C, 16 h; (ii) silica gel chromatography; (iii) SO2Cl2, CH2Cl2, 25°C, 2 h; (iv) N-hydroxyphthalimide, DBU, CH2Cl2, 25°C, 24 h; (v) NH4F, MeOH, 25°C, 16 h; (vi) concd aq NH3, 55°C, 1 h; (vii) 1-pyrenecarboxaldehyde, MeOH, 55°C, 1 h; (viii) DMTrCl, pyridine, 25°C, 16 h; (ix) 2-cyanoethyl N,N-diisopropylchlorophosphoramidite, Et3N, CH2Cl2, 25°C, 2 h. Abreviations. BP: a, uracil-1-yl; b, N4-acetylcytosin-1-yl; c, N6-isobutyryladenin-9-yl; d, N2-phenoxyacetylguanin-9-yl; B: a, uracil-1-yl; b, cytosin-1-yl; c, adenin-9-yl; d, guanin-9-yl; DMTr, 4,4′-dimethoxytrityl.


Permanent or reversible conjugation of 2'-O- or 5'-O-aminooxymethylated nucleosides with functional groups as a convenient and efficient approach to the modification of RNA and DNA sequences.

Cieslak J, Grajkowski A, Ausín C, Gapeev A, Beaucage SL - Nucleic Acids Res. (2011)

Synthesis of 2′-O-pyrenylated ribonucleosides derivatives. (i) DMSO, Ac2O, AcOH, 50°C, 16 h; (ii) silica gel chromatography; (iii) SO2Cl2, CH2Cl2, 25°C, 2 h; (iv) N-hydroxyphthalimide, DBU, CH2Cl2, 25°C, 24 h; (v) NH4F, MeOH, 25°C, 16 h; (vi) concd aq NH3, 55°C, 1 h; (vii) 1-pyrenecarboxaldehyde, MeOH, 55°C, 1 h; (viii) DMTrCl, pyridine, 25°C, 16 h; (ix) 2-cyanoethyl N,N-diisopropylchlorophosphoramidite, Et3N, CH2Cl2, 25°C, 2 h. Abreviations. BP: a, uracil-1-yl; b, N4-acetylcytosin-1-yl; c, N6-isobutyryladenin-9-yl; d, N2-phenoxyacetylguanin-9-yl; B: a, uracil-1-yl; b, cytosin-1-yl; c, adenin-9-yl; d, guanin-9-yl; DMTr, 4,4′-dimethoxytrityl.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3300013&req=5

gkr896-SCH1: Synthesis of 2′-O-pyrenylated ribonucleosides derivatives. (i) DMSO, Ac2O, AcOH, 50°C, 16 h; (ii) silica gel chromatography; (iii) SO2Cl2, CH2Cl2, 25°C, 2 h; (iv) N-hydroxyphthalimide, DBU, CH2Cl2, 25°C, 24 h; (v) NH4F, MeOH, 25°C, 16 h; (vi) concd aq NH3, 55°C, 1 h; (vii) 1-pyrenecarboxaldehyde, MeOH, 55°C, 1 h; (viii) DMTrCl, pyridine, 25°C, 16 h; (ix) 2-cyanoethyl N,N-diisopropylchlorophosphoramidite, Et3N, CH2Cl2, 25°C, 2 h. Abreviations. BP: a, uracil-1-yl; b, N4-acetylcytosin-1-yl; c, N6-isobutyryladenin-9-yl; d, N2-phenoxyacetylguanin-9-yl; B: a, uracil-1-yl; b, cytosin-1-yl; c, adenin-9-yl; d, guanin-9-yl; DMTr, 4,4′-dimethoxytrityl.
Bottom Line: The reaction of these novel ribonucleosides with 1-pyrenecarboxaldehyde results in the efficient formation of stable and yet reversible ribonucleoside 2'-conjugates in yields of 69-82%.Although the versatility and uniqueness of 2'-O-aminooxymethyl ribonucleosides in the preparation of modified RNA sequences is demonstrated by the single or double incorporation of a reversible pyrenylated uridine 2'-conjugate into an RNA sequence, the conjugation of 2'-O-aminooxymethyl ribonucleosides with aldehydes, including those generated from their acetals, provides reversible 2'-O-protected ribonucleosides for potential applications in the solid-phase synthesis of native RNA sequences.The synthesis of a chimeric polyuridylic acid is presented as an exemplary model.

View Article: PubMed Central - PubMed

Affiliation: Division of Therapeutic Proteins, Center for Drug Evaluation and Research, Food and Drug Administration, 8800 Rockville Pike, Bethesda, MD 20892, USA.

ABSTRACT
2'-O-Aminooxymethyl ribonucleosides are prepared from their 3',5'-disilylated 2'-O-phthalimidooxymethyl derivatives by treatment with NH(4)F in MeOH. The reaction of these novel ribonucleosides with 1-pyrenecarboxaldehyde results in the efficient formation of stable and yet reversible ribonucleoside 2'-conjugates in yields of 69-82%. Indeed, exposure of these conjugates to 0.5 M tetra-n-butylammonium fluoride (TBAF) in THF results in the cleavage of their iminoether functions to give the native ribonucleosides along with the innocuous nitrile side product. Conversely, the reaction of 5-cholesten-3-one or dansyl chloride with 2'-O-aminooxymethyl uridine provides permanent uridine 2'-conjugates, which are left essentially intact upon treatment with TBAF. Alternatively, 5'-O-aminooxymethyl thymidine is prepared by hydrazinolysis of its 3'-O-levulinyl-5'-O-phthalimidooxymethyl precursor. Pyrenylation of 5'-O-aminooxymethyl thymidine and the sensitivity of the 5'-conjugate to TBAF further exemplify the usefulness of this nucleoside for modifying DNA sequences either permanently or reversibly. Although the versatility and uniqueness of 2'-O-aminooxymethyl ribonucleosides in the preparation of modified RNA sequences is demonstrated by the single or double incorporation of a reversible pyrenylated uridine 2'-conjugate into an RNA sequence, the conjugation of 2'-O-aminooxymethyl ribonucleosides with aldehydes, including those generated from their acetals, provides reversible 2'-O-protected ribonucleosides for potential applications in the solid-phase synthesis of native RNA sequences. The synthesis of a chimeric polyuridylic acid is presented as an exemplary model.

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Related in: MedlinePlus