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
Graphical Abstract
Figure 1: Enzymatic cleavage of phosphodiester linkages of DNA and RNA.
Figure 2: Energy profiles for a concerted ANDN (A) and stepwise mechanisms (AN + DN) with rate-limiting break...
Figure 3: Pseudorotation of a trigonal bipyramidal phosphorane intermediate by Berry pseudorotation [20].
Figure 4: Protolytic equilibria of phosphorane intermediate of RNA transesterification.
Figure 5: Structures of acyclic analogs of ribonucleosides.
Figure 6: First-order rate constants for buffer-independent partial reactions of uridyl-3´,5´-uridine at pH 5...
Scheme 1: pH- and buffer-independent cleavage and isomerization of RNA phosphodiester linkages. Observed firs...
Scheme 2: Mechanism for the pH- and buffer-independent cleavage of RNA phosphodiester linkages.
Scheme 3: Hydroxide-ion-catalyzed cleavage of RNA phosphodiester linkages.
Scheme 4: Anslyn's and Breslow's mechanism for the buffer-catalyzed cleavage and isomerization of RNA phospho...
Scheme 5: General base-catalyzed cleavage of RNA phosphodiester bonds.
Scheme 6: Kirby´s mechanism for the buffer-catalyzed cleavage of RNA phosphodiester bonds [65].
Figure 7: Guanidinium-group-based cleaving agents of RNA.
Scheme 7: Tautomers of triazine-based cleaving agents and cleavage of RNA phosphodiester bonds by these agent...
Figure 8: Bifunctional guanidine/guanidinium group-based cleaving agents of RNA.
Scheme 8: Cleavage of HPNP by 1,3-distal calix[4]arene bearing two guanidine groups [80].
Figure 9: Cyclic amine-based cleaving agents of RNA.
Scheme 9: Mechanism for the pH-independent cleavage and isomerization of model compound 12a in the pH-range 7...
Scheme 10: Mechanism for the pH-independent cleavage of guanylyl-3´,3´-(2´-amino-2´-deoxyuridine) at pH 6-8 [89].
Scheme 11: Cleavage of uridine 3´-dimethyl phosphate by A) intermolecular attack of methoxide ion and B) intra...
Scheme 12: Transesterification of group I introns and hydrolysis of phosphotriester models proceed through a s...
Scheme 13: Cleavage of trinucleoside 3´,3´,5´-monophosphates by A) P–O3´ and B) P–O5´ bond fission.
Figure 10: Model compounds (23–25) and metal ion binding ligands used in kinetic studies of metal-ion-promoted...
Figure 11: Zn2+-ion-based mono- and di-nuclear cleaving agents of nucleic acids.
Figure 12: Miscellaneous complexes and ligands used in kinetic studies of metal-ion-promoted cleavage of nucle...
Figure 13: Azacrown ligands 34 and 35 and dinuclear Zn2+ complex 36 used in kinetic studies of metal-ion-promo...
Figure 14: Metal ion complexes used for determination of βlg values of metal-ion-promoted cleavage of RNA mode...
Figure 15: Metal ion complexes used in kinetic studies of medium effects on the cleavage of RNA model compound...
Scheme 14: Alternative mechanisms for metal-ion-promoted cleavage of phosphodiesters.
Figure 16: Nucleic acid cleaving agents where the attacking oxyanion is not coordinated to metal ion.
