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Ouyang Y, Dong J, Willner I. Dynamic DNA Networks-Guided Directional and Orthogonal Transient Biocatalytic Cascades. J Am Chem Soc 2023; 145:22135-22149. [PMID: 37773962 PMCID: PMC10571085 DOI: 10.1021/jacs.3c08020] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Indexed: 10/01/2023]
Abstract
DNA frameworks, consisting of constitutional dynamic networks (CDNs) undergoing fuel-driven reconfiguration, are coupled to a dissipative reaction module that triggers the reconfigured CDNs into a transient intermediate CDNs recovering the parent CDN state. Biocatalytic cascades consisting of the glucose oxidase (GOx)/horseradish peroxidase (HRP) couple or the lactate dehydrogenase (LDH)/nicotinamide adenine dinucleotide (NAD+) couple are tethered to the constituents of two different CDNs, allowing the CDNs-guided operation of the spatially confined GOx/HRP or LDH/NAD+ biocatalytic cascades. By applying two different fuel triggers, the directional transient CDN-guided upregulation/downregulation of the two biocatalytic cascades are demonstrated. By mixing the GOx/HRP-biocatalyst-modified CDN with the LDH/NAD+-biocatalyst-functionalized CDN, a composite CDN is assembled. Triggering the composite CDN with two different fuel strands results in orthogonal transient upregulation of the GOx/HRP cascade and transient downregulation of the LDH/NAD+ cascade or vice versa. The transient CDNs-guided biocatalytic cascades are computationally simulated by kinetic models, and the computational analyses allow the prediction of the performance of transient biocatalytic cascades under different auxiliary conditions. The concept of orthogonally triggered temporal, transient, biocatalytic cascades by means of CDN frameworks is applied to design an orthogonally operating CDN for the temporal upregulated or downregulated transient thrombin-induced coagulation of fibrinogen to fibrin.
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Affiliation(s)
- Yu Ouyang
- The Institute of Chemistry,
Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Jiantong Dong
- The Institute of Chemistry,
Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Itamar Willner
- The Institute of Chemistry,
Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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Wang F, Lu CH, Willner I. From cascaded catalytic nucleic acids to enzyme-DNA nanostructures: controlling reactivity, sensing, logic operations, and assembly of complex structures. Chem Rev 2014; 114:2881-941. [PMID: 24576227 DOI: 10.1021/cr400354z] [Citation(s) in RCA: 486] [Impact Index Per Article: 48.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Fuan Wang
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
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3
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Kumar SA. The structure and mechanism of action of bacterial DNA-dependent RNA polymerase. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1981; 38:165-210. [PMID: 6170089 DOI: 10.1016/0079-6107(81)90013-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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4
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Hazen MW, Kuo MT, Arrighi FE. Genome analysis of Peromyscus (Rodentia, Cricetidae) VII. Localization of satellite DNA sequences and cytoplasmic poly(A) RNA sequences of P. eremicus on metaphase chromosomes. Chromosoma 1977; 64:133-42. [PMID: 562738 DOI: 10.1007/bf00327053] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A satellite DNA fraction from P. eremicus, having a buoyant density of 1.705 g/ml in neutral CsCl density gradients, was isolated. In situ hybridization experiments, using 3H-RNA complementary to this DNA fraction indicated that the short (heterochromatic) arms of most of the autosomes contained this sequence. Conversely, in situ hybridization using 3H-complementary DNA (cDNA) synthesized from the cytoplasmic poly (A) RNA of P. eremicus (comprising a substantial fraction of total messenger RNA) showed that the number of silver grains in the long arms (euchromatin) was significantly higher than that in the short arms. The X chromosomes showed a distinct localization pattern of both sequences.
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Sethi VS, Okano P. Interaction of rifamycins with mammalian nucleic acid polymerizing enzymes. BIOCHIMICA ET BIOPHYSICA ACTA 1976; 454:230-47. [PMID: 63293 DOI: 10.1016/0005-2787(76)90227-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Procedures were established for the isolation and partial purification of DNA polymerase, RNA polymerase and poly(A) polymerase activities from the cytoplasm and nuclei of NIH-Swiss mouse embryos. Based on the elution pattern of these enzyme activities from DEAE-cellulose and phosphocellulose columns in Tris-HCl buffer, pH 8.0, the apparent basicities of the enzymes can be arranged as follows: cytoplasmic(C) poly(A) polymerase greater than (C)DNA polymerase beta greater than (C)DNA polymerase alpha and nuclear(N) poly(A) polymerase greater than (N)DNA polymerase greater than (N)RNA polymerase I greater than (N)RNA polymerase II. Twenty rifamycins, including rifamycin B, rifamycin S, rifamycin SV, and rifamycin SV derivatives, were examined for their ability to inhibit the above mentioned nucleic acid polymerizing enzymes and Simian sarcoma virus type I (SSV-1) reverse transcriptase. Rifamycin SV 3'-formyldiphenylhydrazone, rifamycin SV 3'-formyl-n-octyloxime (AF/013) and rifamycin SV 3'-formyldiphenylmethyloxime (AF/05) inhibited all the tested enzyme activities. Rifamycin SV 3'-formylpropylphenyloxime (AF/015) inhibited cellular nucleic acid polymerase activities but not SSV-1 DNA polymerase activity. Rifamycin SV 3'-formyldinitrophenylhydrazone (AF/DNFL) strongly inhibited reverse transcriptase activity but did not inhibit cellular DNA polymerase activities. AF/DNFI slightly inhibited RNA and poly(A) polymerase activities. Rifamycin SV 3'-formyldipropylhydrazone (AF/DPI) and 2,6-dimethyl-4-N-benzyldemethyl-rifampicin (AF/ABDMP) slightly inhibited reverse transcriptase activity but did not inhibit cellular nucleic acid polymerase activities. Active rifamycin derivatives inhibited enzyme reactions by interacting with the enzyme proteins. Nascent polynucleotide chain elongation continued although at a reduced rate in the presence of inhibitor. The addition of increasing concentrations of nonionic detergent (Triton X-100) to rifamycin-inhibited enzyme reactions fully restored enzyme activities. The presence of highly lipophilic 3'-side chains on active rifamycins and the reversibility of enzyme inhibition by Triton X-100 suggest that the tested nucleic acid polymerizing enzymes may have hydrophobic regions with which inhibitory rifamycins interact.
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Kawai M, Ishihama A, Yura T. RNA polymerase mutants of Escherichia coli. III. A temperature-sensitive rifampicin-resistant mutant. MOLECULAR & GENERAL GENETICS : MGG 1976; 143:233-41. [PMID: 765757 DOI: 10.1007/bf00269399] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Temperature-sensitive mutants of Escherichia coli that are unable to grow at high temperature can be obtained among those selected for resistance to streptovaricin or rifampicin at low temperature (Yura et al., 1973). One of these mutants (KY5323) that was supposed to carry a single mutation affecting both rifampicin resistance and temperature sensitivity was further investigated. Using purified RNA polymerase preparations obtained from the mutant and the wild type, it was found that the activity for RNA chain elongation is more sensitive to heat treatment than that for RNA chain initiation or DNA binding, and that the mutant enzyme is significantly more labile than the wild-type enzyme with respect to RNA chain elongation, when heat treatment is carried out at high salt concentration. These results, taken together with those of the enzyme reconstitution experiments, strongly suggest that the beta subunit of the polymerase is directly involved in both RNA chain initiation and elongation reactions. Enzyme reconstitution experiments using isolated subunits derived from the mutant and the wild-type polymerases demonstrate that the alteration of beta subunit is primarily responsible for both rifampicin resistance and thermolability of the mutant enzyme. In addition, the results suggested the apparent alteration of both beta and alpha subunits in this mutant. Extensive transduction experiments provided genetic evidence that are consistent with the view that the strain KY5323 carries a second mutation affecting the beta subunit, beside the primary mutation affecting the beta subunit. The hypothetical beta subunit mutation seems to modify quantitatively the rifampicin resistance caused by the beta subunit mutation.
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Morishita T, Yura T. Altered nutritional requirements associated with mutations affecting the structures of ribonucleic acid polymerase in Lactobacillus casei. J Bacteriol 1976; 125:416-22. [PMID: 1379 PMCID: PMC236098 DOI: 10.1128/jb.125.2.416-422.1976] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Rifampin-resistant mutants were isolated from Lactobacillus casei S1 and examined for possible simultaneous alteration in nutritional properties. Among the 36 mutants obtained either spontaneously or after mutagenesis with 2-aminopurine, 22 were found to be altered with respect to the specific growth requirements. The majority (20 of 22) of the latter mutants were shown to require L-glutamine in addition to the nutrients required by the parental strain for maximal growth, whereas the remaining mutants had apparently lost the requirement for L-aspartate. Further studies with one of the glutamine-requiring mutants revealed that the rifampin resistance of this strain is due to the resistance of ribonucleic acid polymerase itself and that a single mutation is responsible for both rifampin resistance and the glutamine requirement. These results strongly indicate that a structural alteration of the ribonucleic acid polymerase caused by the rifampin resistance mutation somehow affected glutamine metabolism, possibly through change in selective transcription of the genes involved.
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Faerber P, Vizethum W. Fluorescence measurements on the formation of RNA polymerase--DNA complexes. FEBS Lett 1976; 61:267-71. [PMID: 765155 DOI: 10.1016/0014-5793(76)81054-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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9
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Sethi VS. Mechanism of polyadenylate polymerase: formation of enzyme-substrate and enzyme--primer complexes. FEBS Lett 1975; 59:3-7. [PMID: 1225616 DOI: 10.1016/0014-5793(75)80327-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Nakamura Y, Yura T. Evidence for a positive regulation of RNA polymerase synthesis in Escherichia coli. J Mol Biol 1975; 97:621-42. [PMID: 1102717 DOI: 10.1016/s0022-2836(75)80063-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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11
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Sethi VS, Gallo RC. Deoxyribonucleic acid-dependent ribonucleic acid polymerases from spleen of uninfected and Rauscher murine leukemia virus-infected NIH Swiss mice.? BIOCHIMICA ET BIOPHYSICA ACTA 1975; 378:269-81. [PMID: 1125231 DOI: 10.1016/0005-2787(75)90115-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The RNA polymerase activities from the nuclei of the spleen of uninfected and Rauscher murine leukemia virus-infected NIH Swiss mice were resolved by DEAE-cellulose column chromatography, and their properties were compared. The RNA polymerase activities from infected and uninfected spleens were the same with respect to column elution profiles, optimum requirements for various salts, ratios of activities with Mn2+ and Mg2+, sedimentation values, and response to most templates. With the exception of minor differences in activities with certain DNA templates, the significance of which is not clear, no qualitative differences in the enzymes from these two sources were found, but an increase in the specific activity of the alpha-amanitin sensitive enzyme, RNA polymerase II, was found in the leukemic spleen. These preliminary results suggest that there may be no novel RNA polymerase induced by Rauscher murine luekemia virus-infection, and they are in keeping with the interpretation that the viral DNA genome is transcribed by a host RNA polymerase.
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Biswas BB, Ganguly A, Das A. Eukaryotic RNA polymerases and the factors that control them. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1975; 15:145-84. [PMID: 166413 DOI: 10.1016/s0079-6603(08)60119-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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13
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14
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Dharmgrongartama B, Mahadik SP, Srinivasan PR. Modification of RNA polymerase after T3 phage infection of Escherichia coli B. Proc Natl Acad Sci U S A 1973; 70:2845-9. [PMID: 4126728 PMCID: PMC427122 DOI: 10.1073/pnas.70.10.2845] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
E. coli B cells infected with T3 phage contain a modified host RNA polymerase in addition to the normal RNA polymerase found in uninfected cells. The modified RNA polymerase behaves differently in its elution properties from the normal enzyme on DEAE-cellulose, phosphocellulose, and DNA-cellulose column chromatography. The modified enzyme also differs from the normal polymerase in some of its enzymatic parameters. The specific activity of the modified RNA polymerase is markedly lower (i.e., (1/4)) than that of the normal enzyme. The decrease in activity is probably due to an alteration in the beta' subunit of the polymerase. A similar modification is also observed in nonpermissive cells infected with a gene-l amber mutant incapable of producing active T3 specific polymerase. An analogous modification in host RNA polymerase does not seem to occur in E. coli cells infected with T7 phage.
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Nakamura Y, Yura T. Localization of the structural gene for the ' subunit of RNA polymerase in Escherichia coli. Biochem Biophys Res Commun 1973; 53:645-52. [PMID: 4577588 DOI: 10.1016/0006-291x(73)90710-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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16
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Iwakura Y, Ishihama A, Yura T. RNA polymerase mutants of Escherichia coli. Streptolydigin resistance and its relation to rifampicin resistance. MOLECULAR & GENERAL GENETICS : MGG 1973; 121:181-96. [PMID: 4571524 DOI: 10.1007/bf00277531] [Citation(s) in RCA: 60] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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17
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Higashinakagawa T, Mita T. Novel features of DNA-dependent RNA polymerase from protozoan Tetrahymena pyriformis. FEBS Lett 1972; 25:73-76. [PMID: 11946724 DOI: 10.1016/0014-5793(72)80457-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- T Higashinakagawa
- Mitsubishi-Kasei Institute of Life Sciences, c/o Central Research Laboratory, Mitsubishi Chemical Industries Limited, 290 Hisamoto, Takatsu-ku, Kawasaki, Japan
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Messing J, Staudenbauer WL, Hofschneider PH. Inhibition of minicircular DNA replication in Escherichia coli 15 by rifampicin. NATURE: NEW BIOLOGY 1972; 238:202-3. [PMID: 4559665 DOI: 10.1038/newbio238202a0] [Citation(s) in RCA: 30] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Pilz I, Kratky O, Rabussay D. Studies on the conformation of DNA-dependent RNA polymerase in solution by small-angle x-ray measurements. EUROPEAN JOURNAL OF BIOCHEMISTRY 1972; 28:205-20. [PMID: 4560735 DOI: 10.1111/j.1432-1033.1972.tb01904.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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