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Nucleic Acids Research 2005Triplex-forming oligonucleotides (TFOs) bind DNA in a sequence-specific manner at polypurine/polypyrimidine sites and mediate targeted genome modification. Triplexes are...
Triplex-forming oligonucleotides (TFOs) bind DNA in a sequence-specific manner at polypurine/polypyrimidine sites and mediate targeted genome modification. Triplexes are formed by either pyrimidine TFOs, which bind parallel to the purine strand of the duplex (pyrimidine, parallel motif), or purine TFOs, which bind in an anti-parallel orientation (purine, anti-parallel motif). Both purine and pyrimidine TFOs, when linked to psoralen, have been shown to direct psoralen adduct formation in cells, leading to mutagenesis or recombination. However, only purine TFOs have been shown to mediate genome modification without the need for a targeted DNA-adduct. In this work, we report the ability of a series of pyrimidine TFOs, with selected chemical modifications, to induce repair and recombination in two distinct episomal targets in mammalian cells in the absence of any DNA-reactive conjugate. We find that TFOs containing N3'-->P5' phosphoramidate (amidate), 5-(1-propynyl)-2'-deoxyuridine (pdU), 2'-O-methyl-ribose (2'-O-Me), 2'-O-(2-aminoethyl)-ribose, or 2'-O, 4'-C-methylene bridged or locked nucleic acid (LNA)-modified nucleotides show substantially increased formation of non-covalent triplexes under physiological conditions compared with unmodified DNA TFOs. However, of these modified TFOs, only the amidate and pdU-modified TFOs mediate induced recombination in cells and stimulate repair in cell extracts, at levels comparable to those seen with purine TFOs in similar assays. These results show that amidate and pdU-modified TFOs can be used as reagents to stimulate site-specific gene targeting without the need for conjugation to DNA-reactive molecules. By demonstrating the potential for induced repair and recombination with appropriately modified pyrimidine TFOs, this work expands the options available for triplex-mediated gene targeting.
Topics: Animals; Binding Sites; CHO Cells; COS Cells; Chlorocebus aethiops; Cricetinae; Cricetulus; DNA; DNA Repair; Deoxyribonucleases; HeLa Cells; Humans; Oligonucleotides; Pyrimidine Nucleotides; Recombination, Genetic
PubMed: 15961731
DOI: 10.1093/nar/gki659 -
Methods in Enzymology 2014RNAs are an important class of cellular regulatory elements, and they are well characterized by X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy...
RNAs are an important class of cellular regulatory elements, and they are well characterized by X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy in their folded or bound states. However, the apo or unfolded states are more difficult to characterize by either method. Particularly, effective NMR spectroscopy studies of RNAs in the past were hampered by chemical shift overlap of resonances and associated rapid signal loss due to line broadening for RNAs larger than the median size found in the PDB (~25 nt); most functional riboswitches are bigger than this median size. Incorporation of selective site-specific (13)C/(15)N-labeled nucleotides into RNAs promises to overcome this NMR size limitation. Unlike previous isotopic enrichment methods such as phosphoramidite, de novo, uniform-labeling, and selective-biomass approaches, this newer chemical-enzymatic selective method presents a number of advantages for producing labeled nucleotides over these other methods. For example, total chemical synthesis of nucleotides, followed by solid-phase synthesis of RNA using phosphoramidite chemistry, while versatile in incorporating isotope labels into RNA at any desired position, faces problems of low yields (<10%) that drop precipitously for oligonucleotides larger than 50 nt. The alternative method of de novo pyrimidine biosynthesis of NTPs is also a robust technique, with modest yields of up to 45%, but it comes at the cost of using 16 enzymes, expensive substrates, and difficulty in making some needed labeling patterns such as selective labeling of the ribose C1' and C5' and the pyrimidine nucleobase C2, C4, C5, or C6. Biomass-produced, uniformly or selectively labeled NTPs offer a third method, but suffer from low overall yield per labeled input metabolite and isotopic scrambling with only modest suppression of (13)C-(13)C couplings. In contrast to these four methods, our current chemo-enzymatic approach overcomes most of these shortcomings and allows for the synthesis of gram quantities of nucleotides with >80% yields while using a limited number of enzymes, six at most. The unavailability of selectively labeled ribose and base precursors had prevented the effective use of this versatile method until now. Recently, we combined an improved organic synthetic approach that selectively places (13)C/(15)N labels in the pyrimidine nucleobase (either (15)N1, (15)N3, (13)C2, (13)C4, (13)C5, or (13)C6 or any combination) with a very efficient enzymatic method to couple ribose with uracil to produce previously unattainable labeling patterns (Alvarado et al., 2014). Herein we provide detailed steps of both our chemo-enzymatic synthesis of custom nucleotides and their incorporation into RNAs with sizes ranging from 29 to 155 nt and showcase the dramatic improvement in spectral quality of reduced crowding and narrow linewidths. Applications of this selective labeling technology should prove valuable in overcoming two major obstacles, chemical shift overlap of resonances and associated rapid signal loss due to line broadening, that have impeded studying the structure and dynamics of large RNAs such as full-length riboswitches larger than the ~25 nt median size of RNA NMR structures found in the PDB.
Topics: Carbon Isotopes; Cytidine Triphosphate; Nitrogen Isotopes; Nuclear Magnetic Resonance, Biomolecular; RNA; Transcription, Genetic; Uracil; Uridine Triphosphate
PubMed: 25432748
DOI: 10.1016/B978-0-12-801122-5.00007-6 -
The Journal of Biological Chemistry Jun 1953
Topics: Nucleic Acids; Nucleotides; Orotic Acid; Phosphates; Pyrimidine Nucleotides
PubMed: 13061497
DOI: No ID Found -
Current Opinion in Immunology Oct 1996Among all the new immunosuppressive molecules being investigated either preclinically or clinically, four stand out: tacrolimus (FK506), sirolimus (rapamycin),... (Review)
Review
Among all the new immunosuppressive molecules being investigated either preclinically or clinically, four stand out: tacrolimus (FK506), sirolimus (rapamycin), mycophenolate mofetil and leflunomide (and its malononitriloamide analogs). Each drug has distinct mechanisms of immunosuppressive action, and in the past year significant advances have been made in our understanding of the actions of these drugs at the molecular and even atomic levels. Data from recent clinical trials demonstrate that these drugs very effectively suppress graft rejection or autoimmune diseases, validating the pivotal role played by each of their distinct molecular targets in the normal functioning of immune cells.
Topics: Animals; Autoimmune Diseases; Graft Rejection; Humans; Immunosuppressive Agents; Isoxazoles; Leflunomide; Mycophenolic Acid; Polyenes; Pyrimidine Nucleotides; Sirolimus; Tacrolimus; Xenobiotics
PubMed: 8902398
DOI: 10.1016/s0952-7915(96)80090-2 -
Emerging Microbes & Infections 2019The ability of Mycobacterium tuberculosis (Mtb) to adopt a slowly growing or nongrowing state within the host plays a critical role for the bacilli to persist in the...
The ability of Mycobacterium tuberculosis (Mtb) to adopt a slowly growing or nongrowing state within the host plays a critical role for the bacilli to persist in the face of a prolonged multidrug therapy, establish latency and sustain chronic infection. In our previous study, we revealed that genome maintenance via MazG-mediated elimination of oxidized dCTP contributes to the antibiotic tolerance of nongrowing Mtb. Here, we provide evidence that housecleaning of pyrimidine nucleotide pool via MazG coordinates metabolic adaptation of Mtb to nongrowing state. We found that the ΔmazG mutant fails to maintain a nongrowing and metabolic quiescence state under dormancy models in vitro. To investigate bacterial metabolic changes during infection, we employed RNA-seq to compare the global transcriptional response of wild-type Mtb and the ΔmazG mutant after infection of macrophages. Pathway enrichment analyses of the differentially regulated genes indicate that the deletion of mazG in Mtb not only results in DNA instability, but also perturbs pyrimidine metabolism, iron and carbon source uptake, catabolism of propionate and TCA cycle. Moreover, these transcriptional signatures reflect anticipatory metabolism and regulatory activities observed during cell cycle re-entry in the ΔmazG mutant. Taken together, these results provide evidence that pyrimidine metabolism is a metabolic checkpoint during mycobacterial adaptation to nongrowing state.
Topics: Adaptation, Physiological; Bacterial Proteins; Carbon; Drug Therapy, Combination; Gene Expression Profiling; Gene Expression Regulation, Bacterial; Humans; Iron; Macrophages; Mutation; Mycobacterium tuberculosis; Pyrimidine Nucleotides; Pyrimidines; Pyrophosphatases; Sequence Analysis, RNA; THP-1 Cells
PubMed: 30866758
DOI: 10.1080/22221751.2018.1559706 -
Nucleic Acids Research Mar 2010Cytokinins are important plant hormones, and their biosynthesis most begins with the transfer of isopentenyl group from dimethylallyl diphosphate (DMAPP) to the N6-amino...
Crystal structure and substrate specificity of plant adenylate isopentenyltransferase from Humulus lupulus: distinctive binding affinity for purine and pyrimidine nucleotides.
Cytokinins are important plant hormones, and their biosynthesis most begins with the transfer of isopentenyl group from dimethylallyl diphosphate (DMAPP) to the N6-amino group of adenine by either adenylate isopentenyltransferase (AIPT) or tRNA-IPT. Plant AIPTs use ATP/ADP as an isopentenyl acceptor and bacterial AIPTs prefer AMP, whereas tRNA-IPTs act on specific sites of tRNA. Here, we present the crystal structure of an AIPT-ATP complex from Humulus lupulus (HlAIPT), which is similar to the previous structures of Agrobacterium AIPT and yeast tRNA-IPT. The enzyme is structurally homologous to the NTP-binding kinase family of proteins but forms a solvent-accessible channel that binds to the donor substrate DMAPP, which is directed toward the acceptor substrate ATP/ADP. When measured with isothermal titration calorimetry, some nucleotides displayed different binding affinities to HlAIPT with an order of ATP > dATP approximately ADP > GTP > CTP > UTP. Two basic residues Lys275 and Lys220 in HlAIPT interact with the beta and gamma-phosphate of ATP. By contrast, the interactions are absent in Agrobacterium AIPT because they are replaced by the acidic residues Asp221 and Asp171. Despite its structural similarity to the yeast tRNA-IPT, HlAIPT has evolved with a different binding strategy for adenylate.
Topics: Alkyl and Aryl Transferases; Aspartic Acid; Catalytic Domain; Crystallography, X-Ray; Humulus; Models, Molecular; Purine Nucleotides; Pyrimidine Nucleotides; RNA, Transfer; Rhizobium; Substrate Specificity
PubMed: 20007608
DOI: 10.1093/nar/gkp1093 -
The Journal of Biological Chemistry Dec 1980We have measured the pyrimidine nucleotide contents of the culture fluid, acid-soluble fraction, and acid-insoluble fraction of cultures of hamster embryo fibroblasts...
We have measured the pyrimidine nucleotide contents of the culture fluid, acid-soluble fraction, and acid-insoluble fraction of cultures of hamster embryo fibroblasts (third subculture) through the final two divisions of growth in culture. The cells show a growth delay between the penultimate and ultimate division periods and a concomitant biochemical synchrony of pyrimidine metabolism. The cells exhibit normal excretion of pyrimidine nucleotides beginning with the ultimate division cycle. This excretion results from the net breakdown of ribonucleic acid and a cell-regulated maximum for pyrimidine mononucleoside polyphosphate content. This upper limit for the pyrimidine nucleoside polyphosphate content is not a steady state phenomenon but rather an absence of both synthesis and utilization. The hamster embryo fibroblast exhibits a directed flow of salvage uridine for ribonucleic acid synthesis. We show that de novo synthetic uridine 5'-monophosphate also can be used for ribonucleic acid synthesis without prior entry into the cytoplasmic uridine nucleoside polyphosphate pool. During attachment and first division salvage uridine does enter the cytoplasmic nucleotide pool. The properties of the cytidine pools differ from the uridine pools in specific activity and levels of cytidine, due to turnover of the terminal C-C-A of cytoplasmic transfer ribonucleic acid and the delay in conversion of of nonradioactive de novo synthetic uridine 5'-monophosphate to cytidine 5'-triphosphate. The partial synchrony in these cultures has been used as a temporal marker of the observed events.
Topics: Animals; Cell Cycle; Cells, Cultured; Cricetinae; Embryo, Mammalian; Female; Fibroblasts; Interphase; Kinetics; Pregnancy; Pyrimidine Nucleotides
PubMed: 7440538
DOI: No ID Found -
Nucleic Acids Research Mar 2021We recently reported the synthesis of 2'-fluorinated Northern-methanocarbacyclic (2'-F-NMC) nucleotides, which are based on a bicyclo[3.1.0]hexane scaffold. Here, we...
siRNAs containing 2'-fluorinated Northern-methanocarbacyclic (2'-F-NMC) nucleotides: in vitro and in vivo RNAi activity and inability of mitochondrial polymerases to incorporate 2'-F-NMC NTPs.
We recently reported the synthesis of 2'-fluorinated Northern-methanocarbacyclic (2'-F-NMC) nucleotides, which are based on a bicyclo[3.1.0]hexane scaffold. Here, we analyzed RNAi-mediated gene silencing activity in cell culture and demonstrated that a single incorporation of 2'-F-NMC within the guide or passenger strand of the tri-N-acetylgalactosamine-conjugated siRNA targeting mouse Ttr was generally well tolerated. Exceptions were incorporation of 2'-F-NMC into the guide strand at positions 1 and 2, which resulted in a loss of the in vitro activity. Activity at position 1 was recovered when the guide strand was modified with a 5' phosphate, suggesting that the 2'-F-NMC is a poor substrate for 5' kinases. In mice, the 2'-F-NMC-modified siRNAs had comparable RNAi potencies to the parent siRNA. 2'-F-NMC residues in the guide seed region position 7 and at positions 10, 11 and 12 were well tolerated. Surprisingly, when the 5'-phosphate mimic 5'-(E)-vinylphosphonate was attached to the 2'-F-NMC at the position 1 of the guide strand, activity was considerably reduced. The steric constraints of the bicyclic 2'-F-NMC may impair formation of hydrogen-bonding interactions between the vinylphosphonate and the MID domain of Ago2. Molecular modeling studies explain the position- and conformation-dependent RNAi-mediated gene silencing activity of 2'-F-NMC. Finally, the 5'-triphosphate of 2'-F-NMC is not a substrate for mitochondrial RNA and DNA polymerases, indicating that metabolites should not be toxic.
Topics: Animals; Argonaute Proteins; COS Cells; Cells, Cultured; Chlorocebus aethiops; DNA Polymerase gamma; DNA-Directed RNA Polymerases; Mice; Mitochondria; Mitochondrial Proteins; Models, Molecular; Nucleotides; Organophosphorus Compounds; Prealbumin; Pyrimidine Nucleotides; RNA Interference; RNA, Small Interfering; Uridine
PubMed: 33577685
DOI: 10.1093/nar/gkab050 -
The Journal of Biological Chemistry Nov 1986Acivicin (NSC 163501) and dichloroallyl lawsone (NSC 126771) are potent inhibitors of nucleotide biosynthesis with consequent anti-cancer activity against certain...
Acivicin (NSC 163501) and dichloroallyl lawsone (NSC 126771) are potent inhibitors of nucleotide biosynthesis with consequent anti-cancer activity against certain experimental tumors. To determine in detail the metabolic events induced by each inhibitor, we have devised a new two-dimensional chromatographic procedure for measurement of the concentrations of all pyrimidine intermediates and some purine nucleotides from 100 microliter of an extract of cells grown in the presence of [14C]bicarbonate. Addition of acivicin (25 microM) to mouse L1210 leukemia cells causes severe depletion in the cellular levels of CTP and GTP, accumulation of uridine nucleotides, and abrupt but transient increases in the concentrations of the early intermediates of both the pyrimidine and purine pathways. Addition of dichloroallyl lawsone (25 microM) results in a rapid depletion of uridine and cytidine nucleotides; carbamyl aspartate and dihydroorotate accumulate to high levels in an equilibrium ratio of 20.5:1, and orotate, orotidine, and UMP increase transiently before decreasing to levels approaching their original steady states. The predominant inhibitory effects of acivicin are upon the reactions UTP----CTP and XMP----GMP, but there is also an initial transient activation of both the pyrimidine and purine pathways by acivicin. The data obtained with dichloroallyl lawsone are consistent with inhibition of the conversion of UMP----UDP initially followed by potent inhibition of dihydroorotate----orotate.
Topics: Animals; Bicarbonates; Carbon Radioisotopes; Cytidine Triphosphate; Guanosine Triphosphate; Isoxazoles; Kinetics; Leukemia L1210; Mice; Naphthoquinones; Oxazoles; Pyrimidines; Uracil Nucleotides
PubMed: 3771555
DOI: No ID Found -
The Journal of Biological Chemistry Jul 1955
Topics: Nucleotides; Phosphates; Pyrimidine Nucleotides; Uracil Nucleotides; Uridine
PubMed: 14392174
DOI: No ID Found