Nucleases of the Metallo-β-lactamase Family and Their Role in DNA and RNA Metabolism

ABSTRACT

Proteins of the metallo-β-lactamase family with either demonstrated or predicted nuclease activity have been identified in a number of organisms ranging from bacteria to humans and has been shown to be important constituents of cellular metabolism. Nucleases of this family are believed to utilize a zinc-dependent mechanism in catalysis and function as 5′ to 3′ exonucleases and or endonucleases in such processes as 3′ end processing of RNA precursors, DNA repair, V(D)J recombination, and telomere maintenance. Examples of metallo-β-lactamase nucleases include CPSF-73, a known component of the cleavage/polyadenylation machinery, which functions as the endonuclease in 3′ end formation of both polyadenylated and histone mRNAs, and Artemis that opens DNA hairpins during V(D)J recombination. Mutations in two metallo-β-lactamase nucleases have been implicated in human diseases: tRNase Z required for 3′ processing of tRNA precursors has been linked to the familial form of prostate cancer, whereas inactivation of Artemis causes severe combined immunodeficiency (SCID). There is also a group of as yet uncharacterized proteins of this family in bacteria and archaea that based on sequence similarity to CPSF-73 are predicted to function as nucleases in RNA metabolism. This article reviews the cellular roles of nucleases of the metallo-β-lactamase family and the recent advances in studying these proteins.     

Synthesis and Properties of the Oligonucleotide N3′ →P5′ Phosphoramidates

Abstract

Uniformly modified oligonucleotide N3′ → P5′ phosphoramidates were synthesized. The prepared N3′ → P5′ phosphoramidates form extremely stable duplexes and triplexes with complementary nucleic acids. Moreover, these compounds are highly resistant to enzymatic hydrolysis by snake venom phosphodiesterase and cellular nucleases and they show high antisense activity in vitro and in vivo.     

Synthesis and Incorporation of 5″-Amino- and 5′-Mercapto-5′-Deoxy-2′-O-Methyl Nucleosides Into Hammerhead Ribozymes

Abstract

Novel 5′-amino-5′-deoxy-2′-O-methyl uridine, guanosine and adenosine 3′-O-phosphoramidites 5, 11, and 20, as well as protected 5′-mercapto-5′-deoxy-2′-O-methyl uridine 3′-O-phosphoramidite 23 were synthesized from 2′-O-methyl nucleosides. These analogs were incorporated at the 5′-ends of hammerhead ribozymes to evaluate achiral bridging 5′-N- phosphoramidates and 5′-S-phosphorothioates as alternatives for non- bridging phosphorothioates commonly used for end stabilization against nucleases. Oligonucleotide synthesis and deprotection conditions were optimized for better yields of these modified ribozymes.     

Dinucleotides Incorporating Isomeric Nucleosides: Synthesis,Structural and Stereochemical Characterization,and Enzymology

Abstract

The synthesis, stability toward nucleases, and conformational properties of 3′→5′ and 5′→5′ dinucleotides bearing an isomeric nucleoside component is described.     

Substrate Properties of Adenosine- and Uridine- 3′, 5′-bisphenylphosphonates for 3′-Nucleotidase/Nucleases

Abstract

3′, 5′-Bisphenylphosphonate and 5′-phenylphosphonate esters of adenosine and uridine were synthesized to investigate the substrate properties of the 3′, 5′-bisphenylphosphonates for 3′-nucleotidase/nucleases. The V _max/apparent K _m, values of the enzymes for them were found to be 9 to 21-fold higher than those for the corresponding nucleoside 3′-phenylphosphonates.     

Substrate Properties of Adenosine- and Uridine- 3′- Phenylphosphonates for 3′-Nucleotidase/Nucleases

Abstract

Adenosine- and uridine- 3′-phenylphosphonates have been synthesized and evaluated as substrates of 3′-nucleotidase/nucleases. No other nucleases hydrolyzed these compounds. Since V_max values for the adenosine derivative were comparable to those for 3 -AMP and the apparent K_m were 1.4–2.6 mM, it may be a useful substrate.

     

NOVEL NUCLEOSIDE TRIPHOSPHATE ANALOGS FOR THE ENZYMATIC LABELING OF NUCLEIC ACIDS

We have evaluated several novel nucleotide analogs suitable for enzymatic labeling of nucleic acid targets for a variety of array-based assays. Two new reagents in particular, a C4-labeled 1-(2′,3′-dideoxy-β-D-ribofuranosyl) imid- azole-4-carboxamide 5′-triphosphate 5 and an N1-labeled 5-(β-D- ribofuranosyl)-2,4(1H,3H)-pyrimidinedione 5′-triphosphate 3, were found to be excellent substrates for labeling with terminal deoxynucleotidyl transferase and T7 RNA polymerase, respectively.     

Determination of some nuclear deoxyribonucleases in X-irradiated rat thymocytes

Summary The spectrum of nuclear nucleases in control and irradiated (4 Gy) thymocytes has been investigated. Using the method of SDS electrophoresis of nuclear proteins in³H - DNA-polyacrylamide gels a number of polypeptides of MW. 35, 32, 17.7, 17.2 and 16.4 kDa possessing nuclease activity were found. The 35 kDa enzyme is only active in the presence of Ca²⁺ and Mg²⁺ ions. In response to cycloheximide injection (3 mg/100 g body weight) and irradiation, we did not detect the 35 kDa nuclease activity. Nucleases of 32, 17.7, 17.2 and 16.4 kDa are active in the presence of Ca²⁺ ions. The activities of these nucleases increases 60 min after irradiation. These nucleases were also found in the fraction of polydeoxyribonucleotide (PDN).     

Index to Subjects,Vol. 27

Abstract

A constrained model building procedure is used to generate nucleic acid structures of the familiar A-, B-, and Z-DNA duplexes. Attention is focused upon the multiple structural solutions associated with the arrangements of nucleic acid base pairs rather than the optimum sugar-phosphate structure. The glycosyl (χ) and sugar torsions (both the ring puckering and the exocyclic C5′-C4′ (ψ) torsion) are treated as independent variables and the resulting O3′…O5′ distances are used as closure determinants. When such distances conform to the known geometry of phosphate chemical bonding, an intervening phosphorus atom with correct C-O-P valence angles can be located. Four sequential torsion angles- φ,ω,ω,ω and φ about the C3′-O3′-P-O5′-C5′ bonds are then obtained as dependent variables. The resulting structures are categorized in terms of conformation, ranked in potential energy, and analyzed for torsional correlations. The numerical results are quite interesting with implications regarding nucleic acid models constructed to fit less than ideal experimental data. The multiple solutions to the problem are useful for comprehending the conformational complexities of thelocal sugar-phosphate backbone and for understanding the transitions between different helical forms. According to these studies, unique characterization of a nucleic acid duplex involves more than the determination of its base pair morphology, its sugar puckering preferences, or its groove binding features.     

The occurrence of the syn-C3′ endo conformation and the distorted backbone conformations for C4′-C5′ and P-O5′ in oligo and polynucleotides

Abstract

The nucleoside constituents of nucleic acids prefer the anti conformation (1). When the sugar pucker is taken into account the nucleosides prefer the C2′endo-anti conformation. Of the nearly 300 nucleosides known, about 250 are in the anti conformation and 50 are in the syn-conformation, i.e., anti to syn conformation is 5:1. The nucleotide building blocks of nucleic acids show the same trend as nucleosides. Both the deoxy-guanosine and ribo- guanosine residues in nucleosides and nucleotides prefer the syn-C2′endo conformation with an intra-molecular hydrogen bond (for nucleosides) between the O5′- H and the N3 of the base and, a few syn-C3′endo conformations are also observed. Evidence is presented for the occurrence of the C3′endo-syn conformation for guanines in mis-paired double helical right-handed structures with the distorted sugar phosphate C4′-C5′ and P-O5′ bonds respectively, from g+ (gg) and g- to trans. Evidence is also provided for guanosine nucleotides in left-handed double-helical (Z-DNA) oligo and polynucleotides which has the same syn-C3′endo conformation and the distorted backbone sugar-phosphate bonds (C4′-C5′ and P- O5′) as in the earlier right-handed case.     

Conformational Studies of Nucleic Acids: III. Empirical Multiple Correlation Functions for Nucleic Acid Torsion Angles

Abstract

There are seven significantly variable torsion angles in each monomer unit of a polynucleotide. Because of this, it is computationally infeasible to consider the energetics of all conformations available to a nucleic acid without the use of simplifications. In this paper, we develop functions suggested by and regression fit to crystallographic data which allow three of these torsion angles, α (03′-P-05′-C5′), δ (C5′-C4′-C3′-03′) and ε (C4′-C3′-03′-P), to be calculated as dependent variables of those remaining. Using these functions, the seven independent torsions are reduced to four, a reduction in complexity sufficient to allow an examination of the global conformational energetics of a nucleic acid for the remaining independent torsion angles. These functions are the first to quantitatively relate a dependent nucleic acid torsion angle to several different independent angles. In all three cases the data are fit reasonably well, and in one case, α, the fit is exceptionally good, lending support for the suitability of the functions in conformational searches. In addition, an examination of the most significant terms in each of the correlation functions allows insight into the physical basis for the correlations.     

Oligodeoxyribonucleotides Covalently Linked via Nucleic Bases with 3′-5′ and 5′-5′ Polarities

Abstract

The solid-phase preparation of oligodeoxyribonucleotides covalently linked via nucleic bases with normal (3′-5′) or inverted (5′-5′) polarities is reported. The key-step of these syntheses is the preparation of the tethered dimers.     

Use of 5-Nitroindole-2′-deoxyribose-5′-triphosphate for Labelling and Detection of Oligonucleotides†

Abstract

The 5′-triphosphate of 5-nitroindole-2′-deoxyriboside has been shown to be a good substrate for terminal deoxynucleotidyl transferase (TdT). An antibody has been prepared for the detection of 5-nitroindole and has been used for the detection of 5-nitroindole tailed DNA both in single-stranded form and after hybridisation to a template. This is therefore a new method for the detection of nucleic acid probes.

     

用于核酸递送的GSH响应型纳米粒构建

摘要 目的：核酸治疗近年来越来越受到关注,但是核酸药物易被快速清除、易被核酸酶降解、非特异性生物分布、以及不易被细胞摄取的缺点使其在体内难以发挥效果。本文提供了一种具有谷胱甘肽（GSH）响应性释放的纳米粒,能够进行有效核酸药物递送。方法：使用十六烷基三甲基氯化铵（CTAC）制备介孔硅纳米粒,在介孔硅纳米粒表面进行巯基修饰并活化,使其与巯基修饰的聚丙烯亚胺和聚乙二醇反应,形成具有GSH响应的介孔硅纳米粒,通过静电吸附进行核酸荷载。马尔文粒度仪测量表面电位、粒径,透射电镜观察纳米粒形态。核酸电泳检测其核酸负载效率,通过体外检测GSH响应释放聚乙烯亚胺（PEI）情况,共聚焦显微镜观察细胞摄取以及溶酶体逃逸情况。结果：成功构建了具有GSH响应的纳米粒,粒径为76.44±1.68 nm,表面电位为33.93±0.59 mV;通过透射电镜观察到纳米粒呈圆形带孔颗粒状;琼脂糖核酸负载试验观察到当氮磷比大于20时,能够有效进行核酸负载。共聚焦显微镜显示该纳米粒能够成功被MDA-MB-231乳腺癌细胞摄取。在溶酶体逃逸试验中观察到纳米粒进入细胞后3 h,Cy5-siRNA与溶酶体的荧光分离,证明构建的纳米粒成功从溶酶体逃脱。结论：成功构建了具有GSH响应的介孔硅纳米粒,能够有效用于核酸递送。     

3′-(N-Hydroxyimino)-2′,3-dideoxynucleosides and Their Derivatives: Synthesis,Broad Spectrum Antiviral Properties and Synthetical Application for the Preparation of Other Nucleoside Analogues

Abstract

A series of 3′-(N-hydroxyimino)-2′,3′-dideoxynucleosides bearing different nucleic bases has been prepared. In vitro antiviral activity studies showed that among these compounds the thymine derivative possesses significant activity against HIV, HSV, EBV and HBV. Conveniently 5′-protected 3′-(N-hydroxyimino)-2′,3′-dideoxythymidine was further used as a synthon for the preparation of other nucleoside analogues.     

Pyranosyl - Oligonucleotides

Abstract

Pentopyranosyl-oligonucleotides, constitutional isomers of RNA containing the aldopentose units in the pyranose (instead of furanose) form and the phosphodiester bridges between the positions 4′ and 2′ (instead of 5′ and 3′) are being studied in our laboratories in the context of a systematic investigation directed towards a chemical etiology of nucleic acid structure. The primary aim of these studies is to collect factual information that may bear on the problem of why Nature, in evolving a genetic system, had chosen RNA and not some alternative system, such as one from RNA′s close structural neighborhood. In addition, investigations of this type are expected to extend insights into the relationships between structure and base pairing properties of the natural nucleic acids.     

Interference of Nucleases in Cyanobacterium Ferredoxin Purification

Abstract

Isolation of cyanobacterial ferredoxin is normally carried out using nucleases in order to degrade the nucleic acids that accompany this protein during the purification procedure. However, this practice presents the inconvenience that these proteins remain in trace amounts in the purified ferredoxin preparations, although they are not visible by electrophoretical techniques. Evidence of that fact is shown in this report and an alternative procedure is described for the rapid preparation of ferredoxin from crude extracts of Anabaena PCC 7119. The method involves a treatment of the crude extract with streptomycin sulphate, a high molecular weight polication that precipitates the nucleic acids in the beginning of the purification.     

The identification of Ca2+-dependent nucleases activated in the nuclei of rat thymocytes under the action of glucocorticoids

Spectra of thymocyte's nuclear nucleases of control and glucocorticoid treated (5 mg/kg body weight) adrenalectomized rats have been investigated. Using the method of SDS-electrophoresis of nuclear proteins in 3H-DNA-polyacrylamide gel (PAAG) the authors managed to discover a number of polypeptides of 35, 32, 17.7, 17.0, 16.4 kDa molecular mass possessing a nuclease activity. The enzyme of 35 kDa is only active in the presence of Ca2+ and Mg2+ ions and inhibited by cycloheximide. Nucleases of 32, 17.7, 17.0, 16.4 kDa are active in the presence of Ca2+ ions. The enzymic activity of these nucleases increases 60 min after steroid treatment. Nuclease of 17.7, 17.0, 16.4 kDa are poly(ADP-ribosylated). Glucocorticoid mediated activation don't blocked by poly(ADP-ribosylation). Possible role and mechanism of discovered nucleases are discussed.     

Biocatalytic synthesis of 2′-deoxynucleotide 5′-triphosphates from bacterial genomic DNA: Proof of principle

2′-deoxynucleoside 5′-triphosphates (dNTPs) are the building blocks of DNA and are key reagents which are incorporated by polymerase enzymes during nucleic acid amplification techniques, such as polymerase chain reaction (PCR). These techniques are of high importance, not only in molecular biology research, but also in molecular diagnostics. dNTPs are generally produced by a bottom-up technique which relies on synthesis or isolation of purified small molecules like deoxynucleosides. However, the disproportionately high cost of dNTPs in low- and middle-income countries (LMICs) and the requirement for cold chain storage during international shipping makes an adequate supply of these molecules challenging. To reduce supply chain dependency and promote domestic manufacturing in LMICs, a unique top-down biocatalytic synthesis method is described to produce dNTPs. Readily available bacterial genomic DNA provides a crude source material to generate dNTPs and is extracted directly from Escherichia coli (step 1). Nuclease enzymes are then used to digest the genomic DNA creating monophosphorylated deoxynucleotides (dNMPs) (step 2). Design and recombinant production and characterization of E. coli nucleotide kinases is presented to further phosphorylate the monophosphorylated products to generate dNTPs (step 3). Direct use of the in-house produced dNTPs in nucleic acid amplification is shown (step 4) and their successful use as reagents in the application of PCR, thereby providing proof of principle for the future development of recombinant nucleases and design of a recombinant solid-state bioreactor for on-demand dNTP production.