Phosphodiester cleavage

Scheme 14-1. General in-line monoanionic mechanism of phosphodiester cleavage transesterification catalyzed by hairpin ribozyme the first proton transfer (PT1), the nucleophilic attack (Nu), and the exocyclic cleavage (Cl) steps are shown, and the Oip and O2p pathways are indicated by blue and red colored hydrogens, respectively. For the uncatalyzed model reaction in solution, the Ojp and O2p pathways are energetically equivalent...

Figure 1. Generally accepted mechanism of phosphodiester cleavage by hydroxide.

Hydroxyl radicals attack the C4 position of the sugar resulting in sugar decomposition and phosphodiester cleavage. However, if nucleotides are protected... 

Another class of cofactor-dependent deoxyribozymes that use the amino acid histidine to promote phosphodiester cleavage was isolated recently by Roth and Breaker [113]. One of the isolated DNA requires L-histidine or a closely related analog to support RNA phosphodiester cleavage with a rate enhancement of nearly a million-fold over the basal substrate cleavage rate (Fig. 14). 

Wall et al. built a binuclear copper(II) complex 43 in order to see acceleration of phosphodiester cleavage (52). With the substrate (50 p.M) shown, the reaction might be considered as a model for the first step of the hydrolysis of RNA, in which the alcohol function of the side chain intramolecularly attacks the Cun-activated phosphate as a nucleophile for a ring closure reaction. Compared to an analogous mononuclear complex 44 (at 1 mM), a rate constant ca. 50 times larger for 43 (at 1 mM) was observed at 25°C and pH 7, implying that the two metal ions probably cooperate. An analogous zinc(II) complex 45 was reported only as a structural model for the active site of phospholi-... 

The above-mentioned mechanism suggests that positioning the two histidines appropriately would lead to artificial ribonuclease under optimized pH conditions. Figure 6.13 shows an example of an artificial ribonuclease created in this way, which has a cyclodextrin core as the hydrophobic pocket and two histidine residues as catalytic sites. This artificial enzyme catalyzed the second step of the phosphodiester cleavage. The hydrophobic part of the cyclic phosphodiester (substrate) was accommodated into the core of the cyclodextrin and the phosphodiester was exposed between the two histidines. The water molecule was activated through proton removal (performed by the neutral histidine, left), and the activated water performed a nucleophilic attack on the phosphate atom. The protonated histidine (right) assisted this nucleophilic attack by protonating of the phosphodiester. Because of the cooperation between... 

V. Jubian, R.P. Dixon, A.D. Hamilton, Molecular Recognition and Catalysis - Acceleration of Phosphodiester Cleavage by a Simple Hydrogen-Bonding Receptor , J. Am. Chem. Soc., 114, 1120 (1992)... 

A pentacoordinate oxorhenium(V) metallochelate elicits anti- 72. body catalysts for phosphodiester cleavage. J. Am. Chem. Soc. 

Vrkic et al. [34] studied the fragmentation reactions of [M+H] of all 64 protonated ohgodeoxynucleotide trimers and of the 16 isomeric mixed-base tetramers in ion-trap MS-MS. Similar to negative-ion MS-MS, the first loss involves a nncleobase. The relative abundance of the resnlting fragment depends on the nncleobase (C G>A T) and its position (5 >3 >intemal). Fnrther MS experiments on the [M+H-BnH]" fragment ion result in 3 -C-0 phosphodiester cleavage to w- and (a-B)- ions. 

Another dinuclear Zn complex with A(,A/ ,A(, N -tetrakis[(2-pyridyl) methyl]-2-hydroxy-l,3-diaminopropane was shown to be able to achieve phosphodiester cleavage of diribonucleotide ApA at 50°C and neutral pH 355) (16, Fig. 17). The hydrol5dic cleavage of ApA was significantly accelerated by the cooperation of two metals in the binu-clear complex because the mononuclear complex was inactive in comparable experimental conditions. The pseudo-first-order rate constant is 1.9 X 10 sec (half-life 10 hr) (ApA, 100 /aM ZnCL, 5 mM ligand, 2.5 mM). Deprotonation of 2 -OH by a metal hydroxo would be involved in the mechanism of reaction because the products of cleavage were adenosine, adenosine 2 - or 3 -phosphate, and 2, 3 -cAMP. 

Jubian. V. Dixou. R.P. Hamilton, A.D. Molecular recognition and catalysis. Acceleration of phosphodiester cleavage by a simple hydrogen-bonding receptor. J. Am. Chem. Soc. 1992, 114 (3). 1120-1121. 

Catalysis of phosphodiester cleavage by the charge-relay system of DNase I. Transfer of a proton from water to generates a positive... 

Mechanisms of enzyme catalyzed phosphodiester cleavage studied to date often follow an in-line associative Sn2 mechanism (6). This mechanism... 

Add a solution of bis(2,4-dinitrophenyl)phosphate to each mixture, and monitor the change in absorbance at 400 nm due to the release of 2,4-dinitrophenoxide. The rate of change is proportional to the rate of phosphodiester cleavage. Correct the rates of the asymmetric complexes by subtracting the contributions by the symmetric complexes. Each mixture contains 25% of each symmetric complex and 50% of the asymmetric complex (see Note 6). 

Receptors 12 and 13 are well-suited for the catalysis of phosphodiester cleavage. They possess a dicationic trigonal binding cavity that should be complementary both in terms of shape and electrostatics to the dianionic trigonal bipyramidal intermediate for nucleophilic attack on a phosphodiester. 

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