Phosphodiester modification by zinc metalated adenine polymer with carboxyl pendants

This report describes a novel carboxyl pendant containing adenylated polymeric template, its metalation with Zn (II), and manifestation of catalytic activity for the hydrolysis of model phosphodiester, bis(p-nitrophenyl) phosphate (bNPP), and plasmid cleavage. Observation of a bell-shaped pH-K(obs) profile suggested influence of pH variation over hydrolysis rate. This metalated polymer also afforded facile relaxation of pBR322 supercoiled DNA, with an interesting reusability feature intricately associated with heterogeneous catalysis.     

Facile cleavage of RNA via phosphodiester linkage fission by Co(III) complex.

Adenylyl (3'-5')adenosine (ApA) is effectively cleaved to two adenosine molecules by [Co(trien)(H2O)2]3+ complex (trien: triethylenetetramine). The complex (0.20 M) accelerates the cleavage by 10(5) fold, decreasing half-life of ApA from 4000 years to 9.3 days. The reaction involves general base catalysis by the hydroxide ion bound to the Co(III) ion for the formation of adenosine 2',3'-cyclic phosphate (A greater than p), followed by the prompt cleavage of the intermediate to adenosine.     

Chemical synthesis of 5''-pyrophosphate and triphosphate derivatives of 3''-5'' ApA, ApG, GpA and GpG. CD study of the effect of 5''-phosphate groups on the conformation of 3''-5'' GpG.

A simple, two-step method is described for the synthesis of the 5'-pyro- and triphosphate derivatives of 3'-5' ApA, ApG, GpA and GpG. The readily accessible 2'(3')-5' ApA, ApG, GpA and GpG were converted in one step to the corresponding 5'-phosphoramidate derivatives which were then transformed to the 5'-pyro- and triphosphates. CD spectra of 3'-5' pn GpG (n = 0,1,2 or 3) derivatives, measured at pH 1, indicated stabilization of the (syn) G+p (anti)G conformation by the 5'-phosphate groups.     

Molecular design of an acid–base cooperative catalyst for RNA cleavage based on a dizinc complex

The effects of donor groups of dizinc complexes, formed from a 2:1 mixture of Zn(II) and a dinucleating ligand, on adenylyl(3'-5')adenosine (ApA) cleavage have been studied. Two dinucleating ligands were used: one had two 2-pyridylmethyl and two 2-hydroxyethyl moieties on the 1,3-diamino-2-propanol linker moiety (2), and the other had two 2-pyridylmethyl and two carboxymethyl moieties on the 1,3-diamino-2-propanol linker moiety (3(2-)). The dizinc complex with2 [(Zn(2+))(2)-2] showed higher activities toward ApA cleavage than the dizinc complex using an analogous dinucleating ligand having four 2-pyridylmethyl donor moieties [(Zn(2+))(2)-1] at pH 5-8. The former showed a bell-shaped pH-rate constant profile, whereas the latter showed a sigmoidal pattern. The differences in the pH-rate constant profile are attributable to the various distributions of the monohydroxo-dizinc species, i.e. dideprotonated species, which are responsible for ApA cleavage. The monohydroxo species of (Zn(2+))(2)-2 has two acidic protons, which are not present in the corresponding monohydroxo species of (Zn(2+))(2)-1. The existence of both intracomplex acid (ROH or H(2)O) and base catalysts (RO(-) or OH(-)) in (Zn(2+))(2)-2 can explain its higher activity toward ApA cleavage than that of (Zn(2+))(2)-1. In contrast, (Zn(2+))(2)-3(2-) showed lower activity toward ApA cleavage at pH 7.0, which can be ascribed to the absence of the monohydroxo-dizinc species under these conditions.     

Hydrolysis of dinucleoside phosphates - mRNA 5' cap analogues - promoted by a binuclear copper(II)-zinc(II) complex

The hydrolysis of a 5' cap analogue, diadenosinyl-5',5'-triphosphate (ApppA), and two dinucleoside monophosphates: adenylyl(3',5')adenosine (ApA) and uridylyl(3',5')uridine (UpU) promoted by an imidazolate-bridged heterobinuclear copper(II)-zinc(II) complex, Cu(II)-diethylenetriamino-micro-imidazolato-Zn(II)- tris(aminoethyl)amine trisperchlorate (denoted as Cu,Zn-complex in the followings) has been investigated. Kinetic measurements were performed in order to explore the effects of pH, the total concentration of the Cu,Zn-complex and temperature on the cleavage rate. The catalytic activity of the Cu,Zn-complex was quantified by pseudo-first-order rate constants obtained in the excess of the cleaving agent. The results show that the Cu,Zn-complex and its deprotonated forms have phosphoesterase activity and with ApppA the metal complex promoted cleavage takes place selectively within the triphosphate bridge.     

A comparative conformational study of thymidylyl(3'----5')-thymidine, thymidylyl(3'----5')-5'-thio-5'- deoxythymidine and thymidinylacetamido-[3'(O)----5'(C)]-5'-deoxythymidine

A comparative 270 MHz NMR spectroscopic study on the solution structure of the dimer d(TpT) 1, and its two analogues, namely, d(TpST) 2, and NH2d(TcmT) 4 has been reported. Analysis of chemical shifts and coupling constants indicate that: (i) The sugar moieties of the constituent nucleotides are not affected by modification of the internucleotide linkages and adopt preferentially an S-type conformation. (ii) The C4'-C5' bond in the pT part of the modified dimers 2 and 4 shows a large conformational freedom (gamma+ = 32% and 35%, respectively) compared to 1 (gamma+ = 75%). (iii) The population of the trans conformer about C5'-O5' is less important in d(TpST) 2 compared to d(TpT) 1. (iv) The C3'-O3' bond in 2 adopts a trans conformation as in 1. (v) The glycosidic bonds in the modified dimers 2 and 4 showed preferential syn conformation. UV and CD data show that the modified dimers 2 and 4 have poor tendency to stack intramolecularly, they also base pair less efficiently with d(ApA) as compared to d(TpT) 1.     

Zn2+-dependent deoxyribozymes that form natural and unnatural RNA linkages

We report Zn(2+)-dependent deoxyribozymes that ligate RNA. The DNA enzymes were identified by in vitro selection and ligate RNA with k(obs) up to 0.5 min(-)(1) at 1 mM Zn(2+) and 23 degrees C, pH 7.9, which is substantially faster than our previously reported Mg(2+)-dependent deoxyribozymes. Each new Zn(2+)-dependent deoxyribozyme mediates the reaction of a specific nucleophile on one RNA substrate with a 2',3'-cyclic phosphate on a second RNA substrate. Some of the Zn(2+)-dependent deoxyribozymes create native 3'-5' RNA linkages (with k(obs) up to 0.02 min(-)(1)), whereas all of our previous Mg(2+)-dependent deoxyribozymes that use a 2',3'-cyclic phosphate create non-native 2'-5' RNA linkages. On this basis, Zn(2+)-dependent deoxyribozymes have promise for synthesis of native 3'-5'-linked RNA using 2',3'-cyclic phosphate RNA substrates, although these particular Zn(2+)-dependent deoxyribozymes are likely not useful for this practical application. Some of the new Zn(2+)-dependent deoxyribozymes instead create non-native 2'-5' linkages, just like their Mg(2+) counterparts. Unexpectedly, other Zn(2+)-dependent deoxyribozymes synthesize one of three unnatural linkages that are formed upon the reaction of an RNA nucleophile other than a 5'-hydroxyl group. Two of these unnatural linkages are the 3'-2' and 2'-2' linear junctions created when the 2'-hydroxyl of the 5'-terminal guanosine of one RNA substrate attacks the 2',3'-cyclic phosphate of the second RNA substrate. The third unnatural linkage is a branched RNA that results from attack of a specific internal 2'-hydroxyl of one RNA substrate at the 2',3'-cyclic phosphate. When compared with the consistent creation of 2'-5' linkages by Mg(2+)-dependent ligation, formation of this variety of RNA ligation products by Zn(2+)-dependent deoxyribozymes highlights the versatility of transition metals such as Zn(2+) for mediating nucleic acid catalysis.     

Synthesis and properties of ApA analogues with shortened phosphonate internucleotide linkage

A complete series of the 2 '-5 ' and 3 '-5 ' regioisomeric types of r(ApA) and 2 '-d(ApA) analogues with the α-hydroxy-phosphonate C3 '-O-P-CH(OH)-C4 ″ internucleotide linkage, isopolar but non-isosteric with the phosphodiester one, were synthesized and their hybridization properties with polyU studied. Due to the chirality on the 5 '-carbon atom of the modified internucleotide linkage bearing phosphorus and hydroxy moieties, each regioisomeric type of ApA dimer is split into epimeric pairs. To examine the role of the 5 '-hydroxyl of the α-hydroxy-phosphonate moiety during hybridization, the appropriate r(ApA) analogues with 3 '(2 ')-O-P-CH(2)-C4 ″ linkage lacking the 5 '-hydroxyl were synthesized. Nuclear magnetic resonance (NMR) spectroscopy study on the conformation of the modified sugar-phosphate backbone, along with the hybridization measurements, revealed remarkable differences in the stability of complexes with polyU, depending on the 5 '-carbon atom configuration. Potential usefulness of the α-hydroxy-phosphonate linkage in modified oligoribonucleotides is discussed.     

Rare earth metal ions for unprecedentedly fast RNA hydrolysis.

Adenylyl(3'-5')adenosine (ApA) and uridyl(3'-5')uridine (UpU) are hydrolyzed at unprecedentedly large rates by rare earth metal ions at pH 8, 30 degrees C. With 0.01 M Tm(III), the half-lives are 10 min and 51 min, respectively. Potentiality of these ions as catalytic center of artificial ribonuclease is proposed.     

Phosphate ester hydrolysis is catalyzed by a bacterial transferrin: potential implications for in vivo iron transport mechanisms

Two synergistic anions, p-nitrophenyl phosphate ester (NPP) and SO(4)(2-), were found to form new stable assemblies with Fe(3+) and a bacterial transferrin, FbpA (FbpA=ferric binding protein). Fe(3+)FbpA-SO(4) undergoes rapid anion exchange in the presence of NPP to form Fe(3+)FbpA-NPP. Formation of Fe(3+)FbpA-NPP was found to accelerate the rate of hydrolysis of the bound phosphate ester (k(hyd)=1.6 x 10(-6) s(-1) at 25 degrees C and pH 6.5) by >10(3) fold over the uncatalyzed reaction. These findings suggest a dual function for FbpA in vivo: transport of Fe(3+) across the periplasmic space to the inner membrane in certain gram-negative bacteria and hydrolysis of periplasmic polyphosphates.     

The stereochemical course of thiophosphoryl group transfer catalyzed by T4 polynucleotide kinase

The stereochemical course of the phosphoryl transfer reaction catalyzed by T4 polynucleotide kinase has been determined using the chiral ATP analog, (Sp)-adenosine-5'-(3-thio-3-[18O]triphosphate). T4 polynucleotide kinase catalyzes the transfer of the gamma-thiophosphoryl group of (Sp)-adenosine-5'-(3-thio-3-[18O]triphosphate) to the 5'-hydroxyl group of ApA to give the thiophosphorylated dinucleotide adenyl-5'-[18O]phosphorothioate-(3'-5')adenosine. A sample of adenyl-5'-[18O]phosphorothioate-(3'-5')adenosine was subjected to venom phosphodiesterase digestion. The resulting adenosine-5'-[18O]phosphorothioate was shown to have the Rp configuration, thus indicating that the thiophosphoryl transfer reaction occurs with overall inversion of configuration of phosphorus.     

Differentiation of a human monocyte-like cell line by (2′–5′) oligoisoadenylate

Treatment of a human monocyte-like cell line (U-937) by (2'-5')ApApA, the 5' dephosphorylated product of (2'-5')oligo-isoadenylate [oligo(A)] synthetase, an interferon-induced enzyme, was able to induce differentiation, mimicking the effect of interferon treatment. Treatment of U-937 cells with (2'-5')ApApA resulted in morphologic changes, new (monocyte-associated) membrane antigen expression, and acquisition of the capacity to mediate antibody-dependent cellular cytotoxicity (ADCC). (2'-5')ApA and (3'-5')ApApA were without effect. A myeloid cell line (HL-60) which differentiates in response to other agents, but not to alpha-interferon, was not able to differentiate in response to (2'-5')ApApA, despite the ability of interferon to induce (2'-5')oligo (A) synthetase.     

Determination of microscopic ionization constants and microscopic stacking equilibrium quotients of adenylyl(3' --> 5')adenosine

Using the basic ionization constants for a pair of isomers, m1ApA and Apm1A, and the measured values for the overlapping pK values of ApA, the microscopic ionization constants and intramolecular stacking quotients for the monoprotonated ApA were estimated. The results indicate that, in contrast to the case of GpG, ApA did not exhibit preferential protonation on either site of 3'- and 5'-linked nucleoside bases and neither enhanced nor diminished stacking was observed for ApA and ApA as compared to ApA.     

Nucleophilic reaction by carbonic anhydrase model zinc compound: characterization of intermediates for CO2 hydration and phosphoester hydrolysis

The partially hydrophilic and hydrophobic tripodal ligands, tris(hydroxy-2-benzimidazolylmethyl)amine L1h and tris(2-benzimidazolyl)amine L1 were used for the preparation of biomimetic complex of carbonic anhydrase. The CO(2) hydration using [L1hZn(OH)]ClO(4).1.5H(2)O provided the zinc-bound and free HCO(3)(-)s, which were formed by nucleophilic attack of Zn-OH toward CO(2) in dimethyl sulfoxide (DMSO). The phenolic OH in L1h can recognize water molecules through hydrogen bonds to facilitate the collection of the water molecules around a biomimetic zinc compound; the molecular structure of [L1hZn(OH)](+) was revealed. The packing diagram has demonstrated the all the water molecules are hydrogen bonded to each phenolic OH. The nucleophilic attack of zinc-bound OH(-) to substrate is used to catalyze the CO(2) hydration and phosphoester hydrolysis. The carbonic anhydrase model compound [L1Zn(OH(2))](2+) was applied for the hydrolysis of phosphoesters, parathion and bis(p-nitrophenyl)phosphate (BNPP(-)). The low reactivity of [L1Zn(OH)](+) for parathion hydrolysis is attributed to the stability of the intermediate [L1Zn(OP(S)(OEt)(2))](+). Since the structures of the intermediates [L1Zn(OH(2))](BNPP)(2) (1) and [L1Zn(OP(S)(OEt)(2))]ClO(4) (2) formed on the way of hydrolysis are too stable to realize the catalytic cycle and are not active for hydrolysis, carbonic anhydrase model compound [L1Zn(OH(2))](2+) was not suitable for phosphoester hydrolysis; the zinc model compound surrounded by three benzimidazolyl groups is used to have the steric hindrance for bulky substrate, such as parathion and BNPP(-).     

Investigation of activation of phosphate groups in mono- and oligonucleotides with mesitoyl chloride.

It has been demonstrated with the use of 31P NMR pulsed spectroscopy that the reaction of mesitoyl chloride (MsCOCl) both with terminal and internucleotide phosphate groups pA, d(MeOTr)TpT and dpTpT (Ac) proceeds in a quantitative fashion within less than 2 min at 0 degrees C with the respective mixed anhydrides being thereby formed. The anhydrides of phosphomonoesters are resistant, unlike those of phosphodiesters which may be readily split by water, alcohol or amine without the internucleotide bonds being broken. Treatment of poly(U) with an excess of MsCOCl leads to rapid cyclization followed by formation of phosphotriesters. A comparatively easy hydrolysis leads to partial cleavage and isomerization of internucleotide bonds. A similar treatment of UpC showed that about 20% of the internucleotide bonds are cleaved, the remaining UpC being a mixture of approximately equal amounts of 3'-5'- and 2'-5'-isomers.     

Rat intestinal phosphodiesterase II. Properties of the highly purified enzyme and its inactivation by iodoacetic acid.

A highly purifed preparation of rat intestinal phosphodiesterase II (oligonucleate 3'-nucleotidohydrolase, EC 3.1.4.18) has been studied using a synthetic substrate, thymidine 3'(2,4-dinitrophenyl) phosphate. The enzyme was most active between pH 6.1 and pH 6.7 and was inhibited by Cu2+ and Zn2+ but unaffected by EDTA, Mg2+, Co2+, and Ni2+. The reaction rate decreased at high levels of enzyme because of competitive inhibition by deoxythymidine 3'-phosphate, a reaction product, which showed a Ki of 2-10(-5) M. The molecular weight of the enzyme by gel-filtration was 150 000-170 000. In electrofocusing experiments multiple peaks of activity were found at pH 3.4, 4.2-4.5and 7.2. Polyacrylamide gel electrophoresis of freshly purified phosphodiesterase II showed up to 10 protein bands in the gels. If the preparations were stored at 4 degrees C for some time only one or two bands appeared. Investigation of the reaction of rat intestinal phosphodiesterase II with a number of possible phosphodiesterase substrates indicated that the enzyme required a nucleoside 3'-phosphoryl residue for the initiation of hydrolysis. Thus compounds such as NAD, ATP, bis-(p-nitrophenyl)phosphate, thymidine 5'-(p-nitrophenyl)phosphate, glycerylphosphorylcholine, guanylyl-(2' leads to 5')-adenosine and 3',5'-cyclic AMP which contain phosphodiester bonds, nevertheless were not substrates for the enzyme. The enzyme was inhibited reverisbly by p-chloromercuribenzoate and p-chloromercuriphenylsulfonate and inactivated irreversibly by iodoacetic acid. Activity of the phosphodiesterase II was reduced to 50% by incubation with 2.0-10(-3)--5.0-10(-3) M iodoacetate for 20--30 min at 24 degrees C at pH 5.0--6.1. Iodoacetamide had no effect. The degree of inactivation by iodoacetate was reduced by the presence of a substrate for the enzyme or, more effectively by deoxythymidine 3'-phosphate, a competitive inhibitor. It is concluded that iodoacetic acid alkylates an essential residue at the active centre of the enzyme.     

Inhibition of chloramphenicol binding to Escherichia coli 70S ribosomes by 2'(3')-O-aminoacyl-dinucleoside phosphates derived from the aminoacyl-tRNA acceptor terminus.

The effect of 2' and 3'-O-aminoacyl-dinucleoside phosphates cytidylyl(3'-5')-2'(3')-O-L-phenyl-alanyladenosine (I), cytidylyl(3'-5')-3'-deoxy-2'-O-L-phenylalanyladenosine (IIa), cytidylyl(3'-5')-2'-deoxy-3'-O-L-phenylalanyladenosine (IIIa), cytidylyl(3'-5')-3'-deoxy-2'-O-glycyladenosine (IIb), cytidylyl(3'-5')-2'-deoxy-3'-O-glycyladenosine (IIIb), cytidylyl(3'-5')-3'-deoxy-2'-O-L-leucyladenosine (IIc), cytidylyl(3'-5')-2'-deoxy-3'-O-L-leucyladenosine (IIIc), cytidylyl(3'-5')-3'-O-L-phenylalanyladenosine (IIId) as analogs of the 2'(3')-aminoacyl-tRNA termini, on chloramphenicol binding to 70S Excherichia coli ribosomes was investigated. The association constants (Kb) of the investigated compounds were determined by the equilibrium dialysis method. Based on the constancy of Kb over the range of inhibitor concentration, it was determined that the binding site of the 2' isomers IIa-IIc overlaps with the chloramphenicol site, whereas the variability of Kb for the 3' isomers IIIb, IIIc and especially IIIa seems to indicate that they do not achieve a complete fit. The consistently higher values of the Kb values for the 3' isomers IIIa-IIIc relative to that of the 2' isomers IIa-IIc also indicate a stabilization of the binding of the former due to a specific interaction between its amino acid portion and a ribosomal site.     

Derivatives of methanopterin, a coenzyme involved in methanogenesis

Degradational studies of methanopterin, a coenzyme involved in methanogenesis, are reported. The results of these studies are in full accordance with the proposed structure of methanopterin as N-[1'-(2'-amino-4'-hydroxy-7' -methyl-6'-pteridinyl)ethyl]-4-[2', 3', 4', 5'-tetrahydroxypent-1'-yl(5'-1' )O-alpha-ribofuranosyl-5'-phosphoric acid] aniline in which the phosphate group is esterified with alpha-hydroxyglutaric acid. Acid hydrolysis of methanopterin cleaved the 5'----1' glycosidic bond and yielded a 'hydrolytic product' which was identified as N-[1'-(2'-amino-4'-hydroxy-7' -methyl-6'-pteridinyl)ethyl]-4-[2', 3', 4', 5'-tetrahydroxypent-1'-yl]aniline. Alkaline permanganate oxidation of methanopterin yielded 7-methylpterin-6-carboxylic acid. Catalytic (or enzymatic) hydrogenation of methanopterin gave a mixture of 6-ethyl-7-methyl-7,8-dihydropterin, 6-ethyl-7-methylpterin and a third compound, named methaniline which was identified as 4-[2', 3', 4', 5'-tetrahydroxypent-1'-yl(5'----1')O-alpha -ribofuranosyl-5'-phosphoric acid]aniline, in which the phosphate group is esterified with alpha-hydroxyglutaric acid. Methanosarcina barkeri contains a closely related coenzyme called sarcinapterin, which was identified as a L-glutamyl derivative of methanopterin, where the glutamate moiety is attached to the alpha-carboxylic acid group of the alpha-hydroxyglutaric acid moiety of methanopterin via an amide linkage.     

Kinetics and activation parameter analyses of hydrolysis and interconversion of 2',5'- and 3',5'-linked dinucleoside monophosphate at extremely high temperatures

Kinetic analysis of hydrolytic stability of 2',5'- and 3',5'-linked dinucleoside monophosphate (N(2)'pN and N(3)'pN) was successfully performed in aqueous solution at 175-240 degrees C using a new real-time monitoring method for rapid hydrothermal reactions. The half-lives of NpN were in the range 2-8 s at 240 degrees C and apparent activation energy decreases in the order U(2)'pU>A(2)'pA>G(2)'pG>U(3)pU approximately C(3)'pC>A(3)pA. The stability of phosphodiester bond was dependent on the types of base moiety and phosphodiester linkages, but no systematic correlation was found between the structure and stability. The interconversion of 2',5'-adenylyladenosine monophosphate (A(2)'pA) and 3',5'-adenylyladenosine monophosphate (A(3)'pA) was enhanced in the presence of D- or L-histidine. The rate constants of degradation of NpN were dissected into the rate constants of hydrolysis and interconversion between N(2)'pN and N(3)'pN using a computer program SIMFIT. Kinetic analysis supports the mechanism that imidazolium ion and imidazole catalyze interconversion and hydrolysis even under hydrothermal environments. The activation parameters for the hydrolysis and interconversion of NpN were systematically determined for the first time from the temperature dependence of the rate constants, where both DeltaH(app)( not equal ) and DeltaS(app)( not equal ) for 2',5'-linked NpN are larger than those for 3',5'-linked NpN. These parameters support the pseudorotation mechanism through pentacoordinate intermediate from 2',5'- and 3',5'-linked NpN, where the average value of DeltaH( not equal ) (pseudorotation) was estimated to be 30+/-18 kJ mol(-1) at 175-240 degrees C.     

Ultraviolet irradiation of nucleic acids: formation, purification, and solution conformational analyses of oligothymidylates containing cis-syn photodimers

Acetone-photosensitized UV irradiation of three thymine oligomers, d(TpT), d(TpTpT), and d(TpTpTpT), forms predominantly cis-syn cyclobutyl photodimers. C-18 reverse-phase high-performance liquid chromatography is used to purify the following positional isomers: d(TpT[p]T), d(T[p]TpT), d(TpTpT[p]T), d(TpT[p]TpT), d(T[p]TpTpT), and d(T[p]TpT[p]T), where T[p]T represents the cis-syn photodimer. Conformational properties of the cis-syn dimers and adjacent thymine nucleotides have been investigated in solution by using 1H, 13C, and 31P NMR spectroscopy. These studies show that (1) the photodimer conformation in longer oligothymidylates is similar to that in the dinucleoside monophosphate and (2) the cis-syn dimer induces alterations to a greater degree on the 5' side than on the 3' side of the photodimer. Specifically, the photodimer distorts the exocyclic bonds epsilon(C3'-O3') in Tp- and gamma(C5'-C4') in -pT[p]- on the 5' side and slightly alters the furanose equilibrium of the -pT nucleotide on the 3' side of the dimer.