Enzymatic Cleavage of Type II Restriction Endonucleases on the 2′-O-Methyl Nucleotide and Phosphorothioate Substituted DNA

The effects of nucleotide analogue substitution on the cleavage efficiencies of type II restriction endonucleases have been investigated. Six restriction endonucleases (EcoRV, SpeI, XbaI, XhoI, PstI and SphI) were investigated respectively regarding their cleavage when substrates were substituted by 2′-O-methyl nucleotide (2′-OMeN) and phosphorothioate (PS). Substitutions were made in the recognition sequence and the two nucleotides flanking the recognition sequence for each endonuclease. The endonuclease cleavage efficiencies were determined using FRET-based assay. Results demonstrated a position-dependent inhibitory effect of substitution on the cleavage efficiency for all the six endonucleases. In general, the 2′-OMeN substitutions had greater impact than the PS substitutions on the enzymatic activities. Nucleotides of optimal substitutions for protection against RE cleavage were identified. Experimental results and conclusions in this study facilitate our insight into the DNA-protein interactions and the enzymatic cleavage mechanism, particularly for those whose detailed structure information is not available. In addition, the information could benefit the development of bioengineering and synthetic biology.     

Evaluation of Oligonucleotides Containing Two Novel 2′-O-Methyl Modified Nucleotide Monomers: A 3′-C-Allyl and a 2′-O-3′-C-Linked Bicyclic Derivative

Abstract

The two ribo-configured nucleosides 1-(3-C-allyl-2–0-methyl-β-D-ribo-pentofuranosyl)thymine 3 and (1S,5R,6R,8R)-5-hydroxy-6-(hydroxymethyl)-1-methoxy-8-(thymin-1-yl)-2,7-dioxabicyclo[3.3.0]octane 6 have been transformed into their corresponding phosphoramidites, 5 and 8 respectively, and used as building blocks for the synthesis of modified oligonucleotides. The oligonucleotides were shown to hybridize with decreased binding affinity towards complementary single stranded DNA and RNA.     

The Solution NMR Structure of 2′-O-Methyl CGCGCG RNA Duplex

Abstract

Complete assignments of nonexchangeable protons in ¹H NMR spectra of 2′-O-methyl-CGCGCG complemented by its analysis of ¹³C and ³¹P NMR spectra revealed A-RNA double helical structure in low salt solution.     

Synthesis and Biological Activities of 2′-Modified 4′-Thionucleosides

Abstract

We have synthesized 4′-thioDMDC, 4′-thiogemcitabine, and 4′-thioarabinonucleosides, as potential antitumor and antiviral agents, originated from D-glucose. Biological activities of these compounds are also described.     

2′-O-Methyl Thiomethyl Modifications in Hammerhead Ribozymes

Abstract

The synthesis of all four phosphoramidites of 2′-O-methylthiomethyl ribonucleosides and their incorporation into hammerhead ribozymes and influence on nuclease stability and catalytic activity is described.     

Synthesis and Properties of an Initiation Codon Analog Consisting of 2′-O-Methyl Nucleotides

Abstract

An initiation codon analog consisting of 2′-O-methyl nucleotides (AmUmG) was synthesized and examined for its binding efficiency to E. coli ribosomes with fMetRNA^fMet and also its stability in binding assay systems for comparison with those of r(AUG) and d(ATG). AmUmG was found completely resistant to nucleases under the conditions used.     

Effect of 2-Amino Substitution on the Antiviral Effects of 5-Ethyl-2′-Deoxyuridine and (E)-5-(2-bromovinyl)-2′-Deoxyuridine and Their Incorporation into DNA

Abstract

The 2-amino derivatives of 5-ethyl-2′-deoxyuridine (EDU) and (E)-5-(2-bromovinyl)-2′-deoxyuridine (BVDU) have been synthesized and evaluated for anti-herpesvirus activity. They were at least 1000-fold less effective against herpes simplex virus replication than the parent compounds EDU and BVDU. The 5′-triphosphates of the 2-amino substituted EDU, BVDU and thymidine derivatives were also synthesized and examined on their substrate/inhibitor properties against different DNA polymerases. None of the compounds proved markedly inhibitory to HSV-1 DNA polymerase or cellular DNA polymerase a. Nor were they incorporated into the growing DNA chain.     

Antileukemic Activities and Mechanism of Action of 2′-Deoxy-4′-methylcytidine and Related Nucleosides

Abstract

Antileukemic activity of several analogues containing 2′-deoxy-4′-methylcytidine and its araC counterpart were evaluated against murine leukemic P388 cells in vitro and in vivo. Both compounds showed significant cytostatic activity (both IC₅₀=0.4 μM) in vitro and the former compound administered intraperitoneally at a dose of 3 mg/kg/day × 5 showed high activity (T/C=175%) in vivo. The mechanism of action of these 5′-triphosphates on DNA polymerases in detail will be also described.     

Steric and Stereoelectronic Effects of 7-Deazapurine Bases on the Sugar Conformation of 2′-Deoxynucleosides

Abstract

Conformational analyses of the sugar moieties of a series of 7-(8)- substituted 7-deazapurine-2′-deoxynucleosides on the basis of vicinal [H,H] coupling constants is presented using the PSEUROT 6.0 program.     

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.     

Synthesis of Guanosine-3′-diphosphate- 5′-diphosphate by Nucleotide Pyrophosphotransferase

An α-glucosidase was purified from sweet corn seeds by fractionation with ammonium sulfate, chromatographies on CM-Sepharose and Sepharose 4B, and gel filtrations on Sephadex G-100. The enzyme was homogeneous in disc electrophoretic analysis. The molecular weight was estimated to be about 9.6 × 10⁴ by SDS-disc electrophoresis.

The enzyme showed high activities toward maltose, nigerose, phenyl-α-maltoside, and maltooligosaccharides. The ratios of maximum velocity for maltose, nigerose, kojibiose, isomaltose, phenyl-α-glucoside, phenyl-α-maltoside, panose, turanose, and soluble starch were estimated to be 100 : 78 : 17 : 11 : 28 : 100 : 31 : 3.4 : 126, and the Km values for these substrates, 1.5 mM, 1.4 mM, 0.48 mM, 14 mM, 4.2 mM, 1.1 mM, 5.0 mM, 0.28 mM and 52mg/ml, respectively. The maximum velocity for soluble starch was high, but this α-glucan was not a favorable substrate because the Km value was also very high. The V_max for maltooligosaccharides were somewhat dependent on the degree of polymerization (n). The Km values for substrates having four or more glucose units increased with the increase in n.     

Analysis of Endonuclease R·EcoRI Fragments of DNA from Lambdoid Bacteriophages and Other Viruses by Agarose-Gel Electrophoresis

By means of agarose-gel electrophoresis, endonuclease R.EcoRI-generated fragments of DNA from various viruses were separated, their molecular weights were determined, and complete or partial fragment maps for lambda, phi80, and hybrid phages were constructed.     

The Effects of Non-Synonymous Single Nucleotide Polymorphisms (nsSNPs) on Protein–Protein Interactions

Non-synonymous single nucleotide polymorphisms (nsSNPs) are single base changes leading to a change to the amino acid sequence of the encoded protein. Many of these variants are associated with disease, so nsSNPs have been well studied, with studies looking at the effects of nsSNPs on individual proteins, for example, on stability and enzyme active sites. In recent years, the impact of nsSNPs upon protein–protein interactions has also been investigated, giving a greater insight into the mechanisms by which nsSNPs can lead to disease.     

Effects of 5-fluoro-2′-deoxyuridine on bacterial growth its use for DNA labelling

Experiments on the action of 5-fluoro-2′-deoxyuridine on growth ofEscherichia coli B, CECT 101;Pseudomonas fluorescens, CECT 318;Pseudomonas savastanoi, CECT 93;Micrococcus luteus, ATCC 4698;Bacillus cereus, CIP 52.58;Bacillus macerans, ClP 52.58 andBacillus subtilis, ATCC 6633, are described. The inhibition of growth is reversed by thymine plus uracil in all cases except inPseudomonas strains in which uracil alone is active, and in which no exogenous thymine is taken up, not even in the presece of 2′-deoxyguanosine. Growth conditions for improved labelling of bacterial DNA are discussed in the light of the results.     

Antiviral Activities of β-Enantiomers of 3′-Substituted-3′-deoxythymidine Analogs

Abstract

Several β-L-3′-substituted-3′-deoxythymidine were stereospecifically synthesized. None of these analogs inhibited HIV-1 nor HBV replication in vitro suggesting that these β-L-pyrimidine derivatives may not be efficiently phosphorylated inside the cells.     

Activation of the Endonuclease that Defines mRNA 3′ Ends Requires Incorporation into an 8-Subunit Core Cleavage and Polyadenylation Factor Complex

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A Lipidomic Study of the Effects of N-methyl-N′-nitro-N-nitrosoguanidine on Sphingomyelin Metabolism

Systems biology is a new and rapidly developing research area in which,by quantitativelydescribing the interaction among all the individual components of a cell,a systems-level understanding of abiological response can be achieved.Therefore,it requires high-throughput measurement technologies forbiological molecules,such as genomic and proteomic approaches for DNA/RNA and protein,respectively.Recently,a new concept,lipidomics,which utilizes the mass spectrometry(MS)method for lipid analysis,has been proposed.Using this lipidomic approach,the effects of N-methyl-N'-nitro-N-nitrosoguanidine(MNNG)on sphingomyelin metabolism,a major class of sphingolipids,were evaluated.Sphingomyelin moleculeswere extracted from cells and analyzed by matrix-assisted laser desorption ionization-time of flight MS.Itwas found that MNNG induced profound changes in sphingomyelin metabolism,including the appearance ofsome new sphingomyelin species and the disappearance of some others,and the concentrations of severalsphmgomyelin species also changed.This was accompanied by the redistribution of acid sphingomyelinase(ASM),a key player in sphingomyelin metabolism.On the other hand,imipramine,an inhibitor of ASM,caused the accumulation of sphingomyelin.It also prevented some of the effects of MNNG,as well as theredistribution of ASM.Taken together,these data suggested that the lipidomic approach is highly effectivefor the systematic analysis of cellular lipids metabolism.     

Ring Cleavage and Modification at C-2 of a 3,5′-Cyclonucleoside Derivative of Adenosine

It was shown that under alkaline conditions the cyclonucleoside 1 was converted to an imidazole cyclonucleoside 2, and under milder conditions it was converted to an amidine 3, which reacted with N,N′-thiocarbonyldiimidazole and cyanogen bromide as well as phosgene affording the corresponding ring closure products 8, 9 and 10.     

Effects of Exogenous Adenosine 5′-triphosphate 3′-diphosphate on Growth and Sporulation of Bacillus subtilis

Exogenous adenosine 5′-triphosphate 3′-diphosphate (pppApp) had interesting effects on the cell cycle of B. subtilis IFO 3027. The growth rate was reduced by the addition of 1 mm pppApp, and the vegetative cell form was significantly changed. Moreover, the sporulation frequency was increased by 100 times or more as compared with the culture without pppApp. The sporulation process seemed to be stimulated around t₀. pppGpp and ppGpp also showed the same effects as pppApp. Among these effects, depression in growth rate was restored by Mg²⁺ and Ca²⁺, and stimulation of sporulation was inhibited by Mg²⁺, Ca²⁺ and certain carbon sources, such as glucose and glycerol. On the other hand, casamino acids or monovalent cations showed no influence on the pppApp effects. pppApp was not incorporated into cells in experiments with radioactive pppApp.