Synthesis of new terminator substrates for DNA-polymerases-- nucleoside-5'-triphosphates with modified carbohydrate residue

Synthesis of 3'-chloro- and 3'-cyanothio-2',3'-dideoxythymidine by the reaction of 2,3'-anhydro-2'-deoxythymidine with ammonium chloride and lithium thiocyanate, respectively, has been developed. In addition, 3'-methanesulphonylamido- and 3'-sulphonylamido-2',3'-dideoxythymidines were synthesized starting from 3'-amino-2',3'-dideoxythymidine. All these compounds along with 2',3'-anhydroriboadenosine,2',3'-anhydrolyxoadenosine, 2',3'-O-isopropylidenecytidine, and 2,3'-anhydro-2'-deoxythymidine were transformed into 5'-triphosphates by treatment with phosphoryl tris-1,2,4-triazolide and then with bis(tri-n-butylammonium)pyrophosphate. All 5'-triphosphates of nucleoside analogues were tested as termination substrates in cell-free systems with various DNA polymerases.     

Human milk lactoferrin hydrolyzes nucleoside-5'-triphosphates

Lactoferrin (LF) is a main iron-transfering glycoprotein of human barrier body fluids, blood and milk. LF, a protein of the acute phase, is responsible for nonspecific cells defense against microbial and viral infection and cancer diseases. LF is an important component of the passive immunity of newborns system. LF, an extremely polyfunctional protein, is the object of intensive investigations. In this work electrophoretically homogeneous LF from human milk was prepared. Affinity chromatography of LF on Blue Sepharose separated the protein into several distinct isoforms with different affinities to this resin. Two of this isoforms possess nucleoside-5'-triphosphate-hydrolyzing activity. Using several methods including in-gel ATPase activity assays, we show that ATP (and others NTP) hydrolysis is an intrinsic property of LF, and that LF is the major ATPase of human milk. It was shown that ATP-hydrolyzing site is located in C-lobe of LF.     

DNA helicase and nucleoside-5'-triphosphatase activities of polyoma virus large tumor antigen

Polyoma virus large tumor antigen (PyV T antigen) has been purified to near homogeneity by immunoaffinity column chromatography. We have detected DNA helicase and ATPase (nucleoside-5'-triphosphatase) activities in the purified PyV T antigen fraction and characterized these activities. The ATPase activity was stimulated about 2-fold by poly(dT), which was the most effective stimulator among the synthetic polynucleotides tested. Natural nucleic acids, such as calf thymus native and heat-denatured DNA, and single-stranded circular fd DNA were also effective, but the degree of stimulation was less than 1.5-fold. The basal and poly(dT)-stimulated ATPase activities showed similar preference for nucleoside 5'-triphosphates, requirement for divalent cations, and pH optima. The preference for nucleoside 5'-triphosphates was ATP, dATP greater than CTP, UTP much greater than GTP. The only difference observed between the two activities was salt sensitivity. The basal ATPase activity was resistant to KC1 up to 300 mM. In contrast, poly-(dT)-stimulated activity was reduced to the level of basal activity at 300 mM KC1. DNA helicase activity required divalent cations and was dependent on hydrolysis of ATP. The activity showed similar preference for nucleoside 5'-triphosphates, requirement for divalent cations, and pH optimum as the two ATPase activities, and the salt sensitivity of DNA helicase activity was similar to that of poly(dT)-stimulated ATPase activity. The helicase activity was inhibited competitively by the addition of single-stranded or double-stranded DNA, and a relatively high inhibitory activity was observed with poly [d(A-T)]. The PyV T antigen helicase was found to migrate in the 3' to 5' direction along the DNA strand to which the protein bound.     

Indirect inactivation of rat brain cytosolic diacylglycerol kinase by nucleoside-5'-monophosphate

Cytosolic diacylglycerol kinase was inhibited drastically by nucleoside monophosphate. The inhibition was relatively specific for adenosine-5'-monophosphate (5'-AMP), although uridine-5'-monophosphate was also effective. The effect of 5'-AMP on diacylglycerol kinase appeared to be indirect since the degree of inhibition lessened with the dilution of the cytosol and the more purified enzyme failed to respond to 5'-AMP. A 5'-AMP-dependent mediator is proposed to be involved in the inactivation of diacylglycerol kinase.     

Revised UV extinction coefficients for nucleoside-5′-monophosphates and unpaired DNA and RNA

Ultraviolet absorption provides the nearly universal basis for determining concentrations of nucleic acids. Values for the UV extinction coefficients of DNA and RNA rely on the mononucleotide values determined 30–50 years ago. We show that nearly all of the previously published extinction coefficients for the nucleoside-5′-monophosphates are too large, and in error by as much as 7%. Concentrations based on complete hydrolysis and the older set of values are too low by ~4% for typical RNA and 2–3% for typical DNA samples. We also analyzed data in the literature for the extinction coefficients of unpaired DNA oligomers. Robust prediction of concentrations can be made using 38 µg/A₂₆₀ unit for single-stranded DNA (ssDNA) having non-repetitive sequences and 40–80% GC. This is superior to currently used predictions that account for nearest-neighbor frequency or base composition. The latter result in concentrations that are 10–30% too low for typical ssDNA used as primers for PCR and other similar techniques. Methods are described here to accurately measure concentrations of nucleotides by nuclear magnetic resonance. NMR can be used to accurately determine concentrations (and extinction coefficients) of biomolecules within 1%.     

Revised UV extinction coefficients for nucleoside-5'-monophosphates and unpaired DNA and RNA

Ultraviolet absorption provides the nearly universal basis for determining concentrations of nucleic acids. Values for the UV extinction coefficients of DNA and RNA rely on the mononucleotide values determined 30-50 years ago. We show that nearly all of the previously published extinction coefficients for the nucleoside-5'-monophosphates are too large, and in error by as much as 7%. Concentrations based on complete hydrolysis and the older set of values are too low by approximately 4% for typical RNA and 2-3% for typical DNA samples. We also analyzed data in the literature for the extinction coefficients of unpaired DNA oligomers. Robust prediction of concentrations can be made using 38 microg/A260 unit for single-stranded DNA (ssDNA) having non-repetitive sequences and 40-80% GC. This is superior to currently used predictions that account for nearest-neighbor frequency or base composition. The latter result in concentrations that are 10-30% too low for typical ssDNA used as primers for PCR and other similar techniques. Methods are described here to accurately measure concentrations of nucleotides by nuclear magnetic resonance. NMR can be used to accurately determine concentrations (and extinction coefficients) of biomolecules within 1%.     

Smart conferring of nuclease resistance to DNA by 3′-end protection using 2′,4′-bridged nucleoside-5′-triphosphates

Incorporation of 2′,4′-bridged nucleotides into the 3′-end of oligodeoxyribonucleotide (ODN) was examined using terminal deoxynucleotidyl transferase (TdT). The three types of 2′,4′-bridged nucleoside-5′-triphospates with different bridging structures used were incorporated efficiently into the 3′-end of DNA by TdT, although only single nucleotide incorporation was observed. Nuclease resistance was conferred on DNA, depending on the types of bridging nucleotides added.     

Nucleotide release from tubulin and nucleoside-5'-diphosphate kinase action in microtubule assembly.

ATP and UTP support microtubule assembly through the action of brain nucleoside-5'-diphosphate kinase on GDP. Penningroth and Kirschner (1977) J. Mol. Biol. 115, 643-673) have proposed that microtubule assembly may occur by either of two mechanisms: indirectly, through nucleoside-5'-diphosphate kinase-catalyzed phosphorylation of uncomplexed GDP and directly by nucleoside-5'-diphosphate kinase-mediated transphosphorylation of tubulin-bound GDP at low tubulin concentrations. We find the rates of GDP and GTP release (0.68 and 0.32 min-1, respectively) are sufficiently fast relative to assembly to permit GDP release, phosphorylation, and GTP binding as the sole mechanism of nucleoside-5'-diphosphate kinase action in microtubule assembly. Computer simulation studies accord with the conclusion that GDP release is rapid relative to microtubule assembly. The specific activity of the nucleoside-5'-diphosphate kinase is 1.7 nmol/min/mg of microtubular protein under the conditions studied. Pulse-chase experiments with tubulin . [14C]GDP complex and the rapidity of GDP phosphorylation by the kinase are in agreement with this scheme. Finally, it was observed that the extent and rate of microtubule assembly depends upon the [ATP]/[ADP] ratio.     

Large scale enzymatic synthesis of nucleoside-5'-monophosphates using a phosphotransferase from carrots

The enzymatic synthesis of nucleoside-5′-monophosphates from purineriboside, 6-mercapto-purine riboside, 6-methylmercapto-purine riboside, 6-chloro-purine riboside, tubercidin, 8-aza-adenosine, and 3′-deoxy-adenosine is described in gram scale. The synthesis is catalyzed by a phosphotransferase from carrots and uses phenylphosphate as phosphate donor. The reaction products are purified on QAE-Sephadex A25 columns. The large scale preparation of the enzyme is also reported.     

Novel approach to nucleoside-5'-(1-hydroxymethylene-1, 1-bisphosphonates): synthesis of new AZT analogues

An efficient synthetic method of nucleoside-5'-(1-hydroxymethylene-1,1-bisphosphonates) is reported here. The procedure was optimized with 3'-protected thymidine and then applied to synthesis of new AZT analogues.     

Fractionation of nucleosides and nucleoside-5'-mono-, di and triphosphates by thin layer chromatography in silufol]

New solvent systems--dioxane--isopropanol--water--ammonium (4:2:4:1) and dioxane--water--ammonium (6:4:1)--for rapid qualitative and quantitative estimation of nucleosides, nucleoside-5'-mono-, di- and triphosphates by thin layer chromatography is Silufol UV-254 are proposed. The Rf values for 40 ribo- and deoxyribonucleotides of these systems are given.     

31P NMR studies on the putative chemoselective activation of nucleoside-3'-thiophosphate-O-esters

P-diastereomerically pure O-esters of N(Bz)-5'-DMT-dA-3'-monothiophosphate, having charged S=P-O(-) moiety, have been synthesized. Chemoselectivity of their activations by formation of different mixed anhydrides, followed by couplings with N(Bz)-3'-levulinyl-dA, were studied by 31P NMR spectroscopy.     

Effect of nucleoside-5'-phosphates on collagen-induced in vitro mineralization

Nucleoside triphosphates (NTPs) at 4-10 microM concentrations were found to inhibit the rates of collagen-induced in vitro mineralization and ion exchange reactions. The sequential removal of the terminal phosphate groups caused a step-wise decrease in their inhibitory potency. The results suggest that NTPs inhibit the rates of ion uptake and exchange reactions at concentrations much lower than their intracellular physiological concentrations. Thus NTPs may be involved in the control of biological mineralization and the tissues which mineralize under physiological conditions develop a system to locally convert NTPs to NDPs and NMPs.     

Acceptor specificity of ATP:nucleoside-5'-phosphate pyrophosphotransferase from Streptomyces adephospholyticus. Synthesis of the 3'-pyrophosphates of pyrimidine nucleotides, some oligoribonucleotides, 5'-diphosphonucleosidic coenzymes and mG-5'-ppp-5'-Am.

ATP: nucleoside-5'-phosphate pyrophosphotransferase [EC 2.7.6.4] of Streptomyces adephospholyticus synthesizes not only 3'-pyrophosphates of 5'-purine ribomononucleotides but also those of pyrimidine mononucleotides, some short oligonucleotides, a variety of 5'-diphosphonucleosidic coenzymes and mG-5'-ppp-5'-Am.     

Inhibitory effect of various analogs of nucleoside-5'-triphosphates on DNA synthesis catalyzed by DNA polymerase from herpes simplex virus type I

The effect of nucleoside-5-triphosphates analogues on the DNA polymerase of herpes simplex virus (HSV) has been investigated. Evidence is obtained that 3-amino-2,3-dideoxythymidine triphosphate selectively inhibits the DNA synthesis, catalyzed by HSV DNA polymerase. 3-amino-2,3-dideoxythymidine exhibits antiherpetic effect in single cells cultures. It may be phosphorylated by cellular thymidine kinase. The nuclei of Vero cells infected by HSV are an adequate system for antiherpetic compounds screening.     

Structural bases for substrate recognition and activity in Meaban virus nucleoside-2'-O-methyltransferase

Viral methyltransferases are involved in the mRNA capping process, resulting in the transfer of a methyl group from S-adenosyl-L-methionine to capped RNA. Two groups of methyltransferases (MTases) are known: (guanine-N7)-methyltransferases (N7MTases), adding a methyl group onto the N7 atom of guanine, and (nucleoside-2'-O-)-methyltransferases (2'OMTases), adding a methyl group to a ribose hydroxyl. We have expressed and purified two constructs of Meaban virus (MV; genus Flavivirus) NS5 protein MTase domain (residues 1-265 and 1-293, respectively). We report here the three-dimensional structure of the shorter MTase construct in complex with the cofactor S-adenosyl-L-methionine, at 2.9 angstroms resolution. Inspection of the refined crystal structure, which highlights structural conservation of specific active site residues, together with sequence analysis and structural comparison with Dengue virus 2'OMTase, suggests that the crystallized enzyme belongs to the 2'OMTase subgroup. Enzymatic assays show that the short MV MTase construct is inactive, but the longer construct expressed can transfer a methyl group to the ribose 2'O atom of a short GpppAC(5) substrate. West Nile virus MTase domain has been recently shown to display both N7 and 2'O MTase activity on a capped RNA substrate comprising the 5'-terminal 190 nt of the West Nile virus genome. The lack of N7 MTase activity here reported for MV MTase may be related either to the small size of the capped RNA substrate, to its sequence, or to different structural properties of the C-terminal regions of West Nile virus and MV MTase-domains.     

Synthesis and purification of fluorinated benzimidazole and benzene nucleoside-5'-triphosphates

The expression "universal base" is very often used to express hybridization properties and recognition patterns of nucleosides. Their behaviour in biological applications, however, is of great interest regarding, e.g.,' their incorporation by polymerases. The 4,6-difluorobenzimidazole and the 2,4-difluorobenzene nucleoside analogues have proven to be universal bases that do not discriminate between the four natural nucleobases in RNA duplexes. Therefore, we synthesized the corresponding triphosphates to evaluate their behavior in polymerase catalyzed reactions and to investigate their ability to serve as substrates for the T7 RNA polymerase.