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4 article(s) from Lönnberg, Harri

Phosphodiester models for cleavage of nucleic acids

Satu Mikkola,
Tuomas Lönnberg and
Harri Lönnberg

Beilstein J. Org. Chem. 2018, 14, 803–837, doi:10.3762/bjoc.14.68

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Graphical Abstract

Figure 1: Enzymatic cleavage of phosphodiester linkages of DNA and RNA.

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Figure 2: Energy profiles for a concerted A_ND_N (A) and stepwise mechanisms (A_N + D_N) with rate-limiting break...

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Figure 3: Pseudorotation of a trigonal bipyramidal phosphorane intermediate by Berry pseudorotation [20].

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Figure 4: Protolytic equilibria of phosphorane intermediate of RNA transesterification.

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Figure 5: Structures of acyclic analogs of ribonucleosides.

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Figure 6: First-order rate constants for buffer-independent partial reactions of uridyl-3´,5´-uridine at pH 5...

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Scheme 1: pH- and buffer-independent cleavage and isomerization of RNA phosphodiester linkages. Observed firs...

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Scheme 2: Mechanism for the pH- and buffer-independent cleavage of RNA phosphodiester linkages.

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Scheme 3: Hydroxide-ion-catalyzed cleavage of RNA phosphodiester linkages.

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Scheme 4: Anslyn's and Breslow's mechanism for the buffer-catalyzed cleavage and isomerization of RNA phospho...

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Scheme 5: General base-catalyzed cleavage of RNA phosphodiester bonds.

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Scheme 6: Kirby´s mechanism for the buffer-catalyzed cleavage of RNA phosphodiester bonds [65].

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Figure 7: Guanidinium-group-based cleaving agents of RNA.

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Scheme 7: Tautomers of triazine-based cleaving agents and cleavage of RNA phosphodiester bonds by these agent...

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Figure 8: Bifunctional guanidine/guanidinium group-based cleaving agents of RNA.

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Scheme 8: Cleavage of HPNP by 1,3-distal calix[4]arene bearing two guanidine groups [80].

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Figure 9: Cyclic amine-based cleaving agents of RNA.

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Scheme 9: Mechanism for the pH-independent cleavage and isomerization of model compound 12a in the pH-range 7...

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Scheme 10: Mechanism for the pH-independent cleavage of guanylyl-3´,3´-(2´-amino-2´-deoxyuridine) at pH 6-8 [89].

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Scheme 11: Cleavage of uridine 3´-dimethyl phosphate by A) intermolecular attack of methoxide ion and B) intra...

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Scheme 12: Transesterification of group I introns and hydrolysis of phosphotriester models proceed through a s...

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Scheme 13: Cleavage of trinucleoside 3´,3´,5´-monophosphates by A) P–O3´ and B) P–O5´ bond fission.

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Figure 10: Model compounds (23–25) and metal ion binding ligands used in kinetic studies of metal-ion-promoted...

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Figure 11: Zn²⁺-ion-based mono- and di-nuclear cleaving agents of nucleic acids.

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Figure 12: Miscellaneous complexes and ligands used in kinetic studies of metal-ion-promoted cleavage of nucle...

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Figure 13: Azacrown ligands 34 and 35 and dinuclear Zn²⁺ complex 36 used in kinetic studies of metal-ion-promo...

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Figure 14: Metal ion complexes used for determination of β_lg values of metal-ion-promoted cleavage of RNA mode...

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Figure 15: Metal ion complexes used in kinetic studies of medium effects on the cleavage of RNA model compound...

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Scheme 14: Alternative mechanisms for metal-ion-promoted cleavage of phosphodiesters.

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Figure 16: Nucleic acid cleaving agents where the attacking oxyanion is not coordinated to metal ion.

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Review

Published 10 Apr 2018

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Synthesis of oligonucleotides on a soluble support

Harri Lönnberg

Beilstein J. Org. Chem. 2017, 13, 1368–1387, doi:10.3762/bjoc.13.134

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Figure 1: General principle of oligonucleotide synthesis.

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Scheme 1: Alternative coupling methods used in the synthesis of oligonucleotides.

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Scheme 2: Synthesis of ODNs on a precipitative PEG-support by phosphotriester chemistry using MSNT/NMI activa...

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Scheme 3: Synthesis of ODNs on a precipitative tetrapodal support by phosphotriester chemistry using 1-hydrox...

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Scheme 4: Synthesis of ODNs on a precipitative PEG-support by conventional phosphoramidite chemistry [51].

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Scheme 5: Synthesis of ODNs on a precipitative tetrapodal support by conventional phosphoramidite chemistry [43].

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Scheme 6: Synthesis of ODNs by an extractive strategy on an adamant-1-ylacetyl support [57].

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Scheme 7: Synthesis of ODNs by a combination of extractive and precipitative strategy [58].

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Scheme 8: Synthesis of ODNs by phosphoramidite chemistry on a N¹,N³,N⁵-tris(2-aminoethyl)benzene-1,3,5-tricar...

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Scheme 9: Synthesis of ORNs by phosphoramidite chemistry on a hydrophobic support [61].

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Scheme 10: Synthesis of ORNs by the phosphoramidite chemistry on a precipitative tetrapodal support using 2´-O...

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Scheme 11: Synthesis of ORNs by phosphoramidite chemistry on a precipitative tetrapodal support from commercia...

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Scheme 12: Synthesis of ODNs on a precipitative PEG-support by H-phosphonate chemistry [65].

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Scheme 13: Synthesis of 2´-O-methyl ORN phosphorothioates by phosphoramidite chemistry by making use of nanofi...

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Review

Published 12 Jul 2017

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Preparation of a disulfide-linked precipitative soluble support for solution-phase synthesis of trimeric oligodeoxyribonucleotide 3´-(2-chlorophenylphosphate) building blocks

Amit M. Jabgunde,
Alejandro Gimenez Molina,
Pasi Virta and
Harri Lönnberg

Beilstein J. Org. Chem. 2015, 11, 1553–1560, doi:10.3762/bjoc.11.171

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Scheme 1: Synthesis of soluble support. Reagents and conditions: (i) CuI, sodium ascorbate, DMAC, 50 °C, 12 h...

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Scheme 2: Activation of nucleosides. Reagents and conditions: (i) pyridine, dry dioxane, room temperature, 3 ...

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Scheme 3: Synthesis of oligonucleotides. Reagents and conditions: (i) 4–6, 1-methylimidazole, dioxane, under N...

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Figure 1: (A) HPLC traces for the precipitated support bearing phosphate-protected 3’-T-5’ monomer having the...

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Figure 2: (A) HPLC traces for the precipitated support bearing phosphate-protected 3’-pTpdC^Bz-5’-O-DMTr (8a) ...

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Figure 3: (A) HPLC traces for the precipitated support bearing phosphate-protected 3’-pTpdC^Bz-5’-OH dimer 8b,...

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Scheme 4: Cleavage of oligonucleotides from support. Reagents and conditions: (i) tris(2-carboxyethyl)phosphi...

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Published 07 Sep 2015

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Solution phase synthesis of short oligoribonucleotides on a precipitative tetrapodal support

Alejandro Gimenez Molina,
Amit M. Jabgunde,
Pasi Virta and
Harri Lönnberg

Beilstein J. Org. Chem. 2014, 10, 2279–2285, doi:10.3762/bjoc.10.237

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Scheme 1: Synthesis of building blocks of the oligoribonucleotide synthesis. (i) TFA, aq THF, 0 °C; (ii) 2-me...

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Scheme 2: (i) 6a, CuI, sodium ascorbate, DMAc; (ii) HCl in dioxane/MeOH 2:1, (iii) 5a', 4,5-dicyanoimidazole,...

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Figure 1: HPLC traces referring to precipitation of the tetrapodal support bearing fully protected UU-dimers (...

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Figure 2: HPLC traces referring to precipitation of the tetrapodal support bearing 5'-O-deprotected UU-dimers...

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Figure 3: Negative ion ESIMS and HPLC traces of the isolated 3'-UUGCA-5'. For the MS over a wider mass range,...

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Published 29 Sep 2014

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