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2 article(s) from Lönnberg, Tuomas

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

Full text

Nucleic acids through condensation of nucleosides and phosphorous acid in the presence of sulfur

Tuomas Lönnberg

Beilstein J. Org. Chem. 2016, 12, 670–673, doi:10.3762/bjoc.12.67

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Graphical Abstract

Figure 1: ³¹P NMR spectrum (162 MHz, D₂O) of the crude product mixture after refluxing equimolar amounts of t...

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Figure 2: IE HPLC trace of the crude product mixture after refluxing equimolar amounts of thymidine and triet...

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Figure 3: Possible structures of the most abundant product.

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Figure 4: IE HPLC traces of (A) a mixture of tetrameric products, (B) the product mixture after desulfurizati...

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Scheme 1: Phosphitylation and subsequent dimerization of thymidine.

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Published 11 Apr 2016

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