Synthesis of 1-Deazaadenosine Analogues of (2′→5′) ApApA

Abstract

Synthesis of (2′ → 5′)ApApA analogues containing 1-deazaadenosine at different positions is described (32–34). The approach used the phosphotrieer methodology in solution and utilized 3′-O-benzoylated derivatives of the N⁶-protected 5′-O-monomethoxytrityl-1-deazaadenosine as starting material.

     

Two-dimensional 1H NMR study of two cyclobutane type photodimers of thymidylyl-(3′→5′)-thymidine

2D NMR spectroscopy and J coupling constant analysis are applied to resolve the structure of two photoproducts of thymidylyl-(35)-thymidine. These products are cyclobutane type thymine dimers possessing the cis-syn (the predominant one) and trans-syn geometry. The cis-syn is formed in an ANTI-ANTI conformation about the N-glycosyl linkages and resembles the normal base-stacked configuration. The glycosidic conformation in solution of the 5 terminal fragment differs from the crystal in which the less common SYN conformation is observed. In this isomer only the sugar pucker of the 3 terminal fragment is changed substantially with respect to the dinucleotide. The trans-syn isomer is formed in a SYN-ANTI glycosidic conformation. In this isomer the sugar puckers of both deoxyribose rings are affected and a preference for a pure 2-endo conformation is observed.Abbreviations dTpdT 2-deoxythymidylyl-(35)-2-deoxythymidine - dTp[]dT cyclobutane type photodimers of dTpdT - dTp- and dTp[]- their 5' terminal fragments (fragment A) - -pdT and-[]pdT their 3 terminal fragments (fragment B) - RP-HPLC reversed-phase high-performance liquid chromatography - COSY two-dimensional correlated spectroscopy - 2D NOE two-dimensional nuclear Overhauser spectroscopy     

2′-5′寡聚腺苷酸衍生物的研究——Ⅱ.pppA~(2′)p~(5′)A~(2′)p~(5′)A~(3′)p~(5′)Cp的合成及生物活性的观察

本文研究了以T_4RNA连接酶为工具,合成pppA2p~(5′)A~(2′)p~(5′)A~(3′)p~(5′)Cp(2′-5′P_3A_3-Cp)的条件,建立了分离产物的方法,连接得率可达83.1%,获得了紫外水平的量。初步研究了它的一些性质。2′-5′P_3A_3-Cp的分子结构与2′-5′P_3A_3不同,但在体外它也能抑制蛋白质的生物合成,有抗病毒等生物作用,它激活巨噬细胞的能力比2′-5′P_3A_3强。说明将pCp加到2′-5′P_3A_3的3′末端对其生物活性并无大的影响。     

Properties of autonomous 3′→5′ exonucleases

Autonomous 3′→5′ exonucleases (AE) are not bound covalently to DNA polymerases, but they are often included into the replicative complexes. Intracellular AE overproduction in bacteria results in sharp suppression of mutagenesis, whereas inactivation of these enzymes in bacteria and fungi leads to an increase in mutagenesis frequency by 2–3 orders of magnitude. Correction of DNA polymerase errors in vitro occurs after addition of AE to the incubation medium. This correction is clearly manifested under conditions of mutational stress (during induced but not spontaneous mutagenesis), for instance, with an imbalance of dNTPs — error-prone conditions. At equimolar dNTP (error-free conditions), the correction is relatively weak. The gene knockout of both alleles of the major AE gene in mice does not influence spontaneous mutagenesis though a substantial increase could be expected. The frequency of induced mutagenesis has not been yet measured, though the inactivation of AE could increase the frequency of mutagenesis. Complete inactivation of the major AE leads to inflammatory myocarditis and a 5-fold reduction of life span of mice. Dominant heterozygous mutations were found in various loci of the AE gene, which caused the development of Aicardi-Goutieres (autosomal recessive encephalopathy) syndrome, familial chilblain lupus, systemic lupus erythematosus, retinal vasculopathy, and cerebral leukodystrophy. In the nucleus, AE have a corrective function, but after transition into cytoplasm these enzymes destroy aberrant DNA that appears during replication and thereby save the cells from autoimmune diseases. Depending on their intracellular localization, AE carry out various biological functions but employ the same mechanism of the catalyzed reactions.     

Hydrolytic Reactions of 3′-Deoxy-3′-thioinosylyl-(3′→ >5′)-uridine; An RNA Dinucleotide Containing a 3′-S-Phosphorothiolate Linkage

Abstract

The course of hydrolysis of 3′-deoxy-3′-thioinosylyl-(3′ → 5′)-uridine (IspU) has been followed by HPLC over a wide pH-range. Two reactions of the internucleosidic thiophosphate linkage compete: (i) cleavage yielding thioinosine monophosphates and uridine, and (ii) isomerization to the 2′,5′-isomer of IspU. Under very acidic conditions, even acid-catalyzed depurination of the inosine moiety is observed. The stability of the thiophosphate linkage and the mechanisms of its rupture are discussed.     

pppA_(2′)p_(5′)A_(2′)p_(5′)A 对甲胎蛋白抑制巨噬细胞功能的对抗作用

干扰素是一类由干扰素诱生剂诱导生物机体有关细胞产生的糖蛋白,具有广泛的生物学活性,能抗病毒、抗癌肿、及免疫调节等功能。pppA_(2′)p_(5′)A_(2′)p_(5′)A(简称2′-5′P_3A_3)是由干扰素作用于细胞以后诱导产生的一种寡聚腺苷酸,它能表现干扰素的许多生物学功     

Interaction of (2′ -5′) and (3′ -5′) Linked 2-Aminoadenylyl-3-aminoadenosines with Polyuridylic Acid

Abstract

2′-5′ and 3′-5′ linked 2-aminoadenylyl-2-aminoadenosines [(2′-5′)n²Apn²A (1) and (3′-5′)n²Apn²A (2)] were synthesized by condensation of 5′-O-monomethoxytrityl-N ² N ⁶-dibenzoyl-2-aminoadenosine and N ²,N ⁶,2′,3′-O-tetrabenzoyl-2-aminoadenosine 5′-phosphate using dicyclohexylcarbodiimide (DCC). The conformational properties of these dimers 1 and 2 were examined by UV, NMR and CD spectroscopy. The results reveal that the 2′-5′-isomer 1 takes a stacked conformation, which contains a larger base-base overlap and is more stable against thermal perturbation with respect to the 3′-5′-isomer 2. Interactions of 1 and 2 with polyuridylic acid (Poly (U)) were also examined by Tm, mixing curves, UV and CD spectra. Both the dinucleoside isomers 1 and 2 formed a complex of 1 : 2 stoichiometry with poly(U), which was much more stable than that of the corresponding ApA isomer     

Thermodynamic and NMR Study of Proton Complex Formation of 2′-Deoxyadenylyl-(3′→5′)-2′-Deoxyadenosine in Aqueous Solution

Abstract

A thermodynamic and proton NMR study has been carried out in order to characterize the behaviour of 2′-deoxyadenylyl-(3′→5′)-2′-deoxyadenosine towards the protonation. Conformational changes occurring following two protonation steps are discussed.     

Reversed(5′-3′)Oligonucleotide Synthesis on Oxalyl-CPG Support

Abstract

A solid-phase reversed(5′-3′) oligodeoxyribonucleotide synthesis on oxalyl and succinyl aminopropyl controlled-pore glass (CPG) is presented. Oxalyl linked oligomers are deprotected without cleavage fiom the support.     

SYNTHESIS of 2′-DEOXY-2′-FLUOROGUANYL-(3′,5′)-GUANOSINE

ABSTRACT

The protected analogue of 2-amnio-6-chloropurine arabinoside (3b) was subjected to reaction with diethylaminosulfur trifluoride (DAST) and subsequently treated with NaOAc in Ac₂O/AcOH to give N ²,O ^3′,O ^5′-triacetyl-2′-deoxy-2′-fluoroguanosine (5a). After deacetylation of the sugar moiety and protection of 5′-OH by a 4,4′-dimethoxytrityl group, this nucleoside component was converted to 2′-deoxy-2′-fluoroguanyl-(3′,5′)-guanosine (6c, GfpG).     

The 3′→5′ exonuclease associated with HeLa DNA polymerase epsilon

The 3′→5′ exonuclease activity of highly purified large form of human DNA polymerase epsilon was studied. The activity removes mononucleotides from the 3′ end of an oligonucleotide with a non-processive mechanism and leaves 5′-terminal trinucleotide non-hydrolyzed. This is the case both with single-stranded oligonucleotides and with oligonucleotides annealed to complementary regions of M13DNA. However, the reaction rates with single-stranded oligonucleotides are at least ten-fold when compared to those with completely base-paired oligonucleotides. Conceivably, mismatched 3′ end of an oligonucleotide annealed to M13DNA is rapidly removed and the hydrolysis is slown down when double-stranded region is reached. The preferential removal of a non-complementary 3′ end and the non-processive mechanism are consistent with anticipated proofreading function. In addition to the 3′→5′ exonuclease activity, an 5′→3′ exonuclease activity is often present even in relatively highly purified DNA polymerase epsilon preparates suggesting that such an activity may be an essential com-ponent for the action of this enzymein vivo. Contrary to the 3′→5′ exonuclease activity, the 5′→3′ exonuclease is separable from the polymerase activity.     

The 3′→5′ exonuclease associated with HeLa DNA polymerase epsilon

The 3′→5′ exonuclease activity of highly purified large form of human DNA polymerase epsilon was studied. The activity removes mononucleotides from the 3′ end of an oligonucleotide with a non-processive mechanism and leaves 5′-terminal trinucleotide non-hydrolyzed. This is the case both with single-stranded oligonucleotides and with oligonucleotides annealed to complementary regions of M13DNA. However, the reaction rates with single-stranded oligonucleotides are at least ten-fold when compared to those with completely base-paired oligonucleotides. Conceivably, mismatched 3′ end of an oligonucleotide annealed to M13DNA is rapidly removed and the hydrolysis is slown down when double-stranded region is reached. The preferential removal of a non-complementary 3′ end and the non-processive mechanism are consistent with anticipated proofreading function. In addition to the 3′→5′ exonuclease activity, an 5′→3′ exonuclease activity is often present even in relatively highly purified DNA polymerase epsilon preparates suggesting that such an activity may be an essential com-ponent for the action of this enzymein vivo. Contrary to the 3′→5′ exonuclease activity, the 5′→3′ exonuclease is separable from the polymerase activity.     

Inhibition of the peptidyltransferase acceptor site by 2′(3′)-O-cycloleucyl- and α-aminoisobutyryl derivatives of cytidylyl-(3′–5′)adenosine

2′(3′)-O-(N-Benzyloxycarbonylcycloleucyl)adenosine (1a) was prepared by esterification of 5′-O-(4-methoxytrityl)adenosine with N-benzyloxycarbonylcycloleucine in the presence of dicyclohexylcarbodiimide and subsequent deprotection in acidic medium. The compound 1a was separated into pure 2′- and 3′-isomers using HPLC; these isomers were found to undergo an easy interconversion. Compound 1a was coupled with N-dimethylaminomethylene-2′,5′-di-O-tetrahydropyranylcytidine 3′-phosphate in the presence of dicyclohexylcarbodiimide to give, after subsequent deblocking, cytidylyl(3′→5′)2′(3′)-O-cycloleucyladenosine (1c). Compound 1c, as well as the related cytidylyl(3′→5′)2′(3′)-O-(α-aminoisobutyryl)adenosine (1d), inhibited the peptidyltransferase catalyzed transfer of an AcPhe residue to puromycin in the Ac[¹⁴C]Phe-tRNA·poly(U)·70 S E. coli ribosome system. A half of the maximum inhibition of AcPhe-puromycin formation (at 10^?5 M puromycin) was achieved at 9.5·10^?6 M of compound 1c and 9·10^?5 M of compound 1d, respectively. The inhibition of the puromycin reaction by compound 1d shows a mixed-type of inhibition kinetics. Further, none of the compounds 1c and 1d was an acceptor in the peptidyltransferase reaction. Both compounds 1c and 1d inhibited the binding of C-A-C-C-A[¹⁴C]Phe to the A site of peptidyltransferase in a system containing tRNA^Phe·poly(U)·70 S E. coli ribosomes, in which compound 1d was a much stronger inhibitor than 1c. These results indicate that the derivatives such as compounds 1c and 1d which contain an anomalous amino acid with a substituent in lieu of α-hydrogen can interfere with the peptidyltransferase A site; however, they are not acceptors in the peptidyltransferase reaction probably due to a misfit of the α-substituent.     

p53 in cytoplasm exerts 3′→5′ exonuclease activity with dsRNA

Double-stranded RNA (dsRNA) is a biologically active molecule that plays important roles in normal cell growth and function. Accordingly, the cell uses multiple mechanisms to control its level. The tumor suppressor protein p53 possesses intrinsic 3′→5′ exonuclease activity. The aim of the present study was to elucidate the degradation of dsRNA by the exonuclease activity of p53. The results show that recombinant, purified wtp53 and endogenous protein in cytoplasmic fractions of cells remove nucleotides from 3’-ends of dsRNA. Several lines of evidence support a connection between p53 and dsRNase activity in cytoplasm: (1) this activity parallels the status of endogenous cytoplasmic p53; (2) the endogenous exonuclease displays a similar dsRNA excision profile characteristic for purified wtp53; (3) cytoplasmic fractions of HCT116(p53+/+) cells exert higher levels of exonuclease activity compared to those of HCT116(p53-/-) cells; (4) transfection of the wtp53, but not exonuclease-deficient mutant p53-R175H, into HCT116 (p53-/-) cells induced high levels of dsRNase activity in cytoplasm; (5) the accumulation of p53 in cytoplasm following the γ-irradiation stress stimuli correlates with the increase in the excision of dsRNA and (6) the dsRNA forms a complex with a protein that can be disrupted by an anti-p53 antibody. Our data suggest that the degradation of dsRNA by p53 protein may direct either the complete degradation of and decrease in the level of dsRNA or incomplete degradation and the generation of short dsRNA products. The possible roles of p53 dsRNase activity in cytoplasm in the inhibition of translation and induction of cell apoptosis, is discussed.     

NMR Investigations of the Solution Conformations of Deoxynucleotidyl (3′-5′) Arabinonucleosides

Abstract

The solution conformations of all eight deoxynucleotidyl (3′-5′) arabinonucleosides containing 9-B-D-arabinofuranosyladenine and 1-B-D-arabinonfuranosylcytosine have been analyzed by NMR methods and compared to dinucleoside monophosphates containing the corresponding deoxyriboside units.     

Inhibition of 5-α-Reductase (TYPE-II) Expression by Antisense 3′-Deoxy-(2′-5′) Oligonucleotide Chimeras

Abstract

ABSTRACT: 3′-Deoxy-(2′-5′) oligonucleotides bind selectively to complementary RNA but not to DNA. 3′-Deoxy-(2′-5′) phosphorothioate ODN chimeras embedded with a short stretch of 3′-5′ phosphorothioate cassette are potent inhibitors of steroid 5-α-reductasc expression with significantly less non-specific interactions in cell culture.     

Cytldlne Cyclic (3′, 5′) Monophosphate: Cyclic Nucleotide With a Non-Characteristic Ribose Ring Conformation

Abstract

Cytidine 3′,-5′-cyclic phosphate (cCMP) occurs in nature and has growth stimulatory activity on L-1210 cells. The initiation of cell growth by cCMP, under conditions where CAMP, cGMP and cUMP delay the onset of proliferation suggests that cCMP may play a regulatory role in the cell metabolism. It has been reported that in 3′,5′-cyclic nucleotides, the phosphate ring fused to the furanose ring resuicts the conformation of the furanose ring to the twist form C(3′) endo C(4′) exo (³T₄), in contrast to the C(2′) endo C(3′) endo (²T₃) and C(3′) endo C(2′) exo (³T₂) twist forms normally found in nucleotides and nucleosides. We have carried out an accurate crystal structure of cCMP and found that the furanose ring in cCMP has the C(3′) endo C(2′) exo conformation (³T₂), with a pseudo rotation amplitude (P) of 44° and phase angle τ_m of 12°. cCMP is in low anti conformation (X_CN = 15.4°) and O(5′) has the fixed g conformation. The phosphate ring is constrained to the chair conformation, as in other cyclic nucleotides. The two exocyclic P-O bond distances are short (1.489, 1.476Å) and the ring angle at N(3) is large (125.2°) suggesting that the molecule in the solid state is a zwitterion with a plus charge on N(3). The crystals are hydrated and highly unstable. The three water molecules are highly disordered in ten locations. The crystals of cCMP 3H₂O are hexagonal, a = 16.294(3), b = c = 11.099(4)Å, space group P6₁, final R value is 0.067 for 1620 reflections 230.     

Synthesis of (2′,5′)-Oligoadenylate Antisense Chimeras Targeting Steroid 5α-Reductase

Abstract

2–5A antisense chimeras have been synthesized which target human steroid 5α-reductase mRNA. To enhance the stability of the chimera towards degradative enzymes the terminal phosphodiester bond was isomerized from 3′,5′ to 3′,3′ and the 5′-phosphate group was thiolated.     

干扰素的功能表达机理——Ⅹ、pppA_(2′p5′)A_(2′p5′)A抗病毒作用的条件

本工作说明pppA2′p5′A2′p5′A(2′-5′p_3A_3)能使Lpa小鼠细胞对新城鸡瘟病毒或水泡性口腔炎病毒的攻击起一定的保护作用,进一步支持2′-5′p_3A_3抗病毒作用的普遍性。本文还证明在无Ca~(++)存在下,2′-5′p_3A_3于病毒攻击前数小时处理细胞,也能得到抗病毒效果。     

Partial Protection of Carbohydrate Derivatives. Part 24.1 Synthesis of Adenylyl-(2′–5′)-Adenylyl-(2′–5′)-Adenosine Using a 3′-O-(Tetrahydropyran-2-YL) Adenosine Derivative

Abstract

The synthesis of the title compound was performed using a 3′-O-(tetrahydropyran-2-yl) adenosine derivative as the starting material, i.e., a coupling reaction of triethylammonium N ⁶-benzoyl-5′-O-dimethoxytrityl-3′-O-(tetrahydropyran-2-yl) adenosine 2′-(4-chlorophenyl)phosphate with N ⁶-benzoyl-2′,3′-di-O-benzoyladenosine, followed by a sequence of reactions, O-dedimethoxytritylation, a coupling reaction with the former triethylammonium salt, and complete deblocking of the resultant 2′, 5′-triadenylic acid derivative.