1
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Choudhury K, Leibowitz MJ. Pentamidine-induced alteration in restriction endonuclease cleavage of plasmid DNA. J Biomol Struct Dyn 2003; 21:127-34. [PMID: 12854964 DOI: 10.1080/07391102.2003.10506910] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
We have used restriction enzymes and DNaseI as probes to determine the specificity of pentamidine binding to plasmid DNA. Cleavage of plasmid pAZ130 by EcoRI, EcoRV and ApaI is inhibited by pentamidine, cleavage by XbaI, NotI and AvaI is unaffected, while cleavage by XhoI, which recognizes the same sequence as AvaI, is stimulated. DNaseI footprinting of DNA containing these restriction sites revealed that pentamidine protection is not strictly limited to AT-rich regions. We suggest that perturbation of the DNA micro- environment by pentamidine binding is responsible for its effect on nucleases.
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Affiliation(s)
- Kanakendu Choudhury
- Department of Molecular Genetics, Microbiology and Immunology, Robert Wood Johnson Medical School-UMDNJ, Piscataway, NJ 08854, USA
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2
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Meyer CR, Bork JA, Nadler S, Yirsa J, Preiss J. Site-directed mutagenesis of a regulatory site of Escherichia coli ADP-glucose pyrophosphorylase: the role of residue 336 in allosteric behavior. Arch Biochem Biophys 1998; 353:152-9. [PMID: 9578610 DOI: 10.1006/abbi.1998.0648] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Site-directed mutagenesis was used to probe the role of glycine residue 336 in the regulatory properties of Escherichia coli ADP-glucose pyrophosphorylase. This residue was previously found to be changed from glycine to aspartate in the gene of an Escherichia coli mutant strain. The mutant enzyme had altered kinetic properties, including higher activity in the absence of the activator fructose 1,6-bisphosphate (FBP), higher apparent affinity for FBP and substrates, and lower apparent affinity for the inhibitor AMP. The observed changes in activity were caused by this single mutation, because the aspartate mutant was prepared from the wild-type gene. The kinetic properties of the site-directed mutant are identical to those of the enzyme from the mutant strain. A series of mutants was prepared to explore the effects of charge, size, shape, and hydrophobicity of the amino acid at residue 336 on the enzyme regulatory properties. All of the mutants, except for the lysine and arginine enzymes, were expressed and purified for kinetic analysis. The glycine-336 residue is able to tolerate diverse substitutions without compromise of catalytic activity. A range of allosteric changes was observed, with the most dramatic effects seen with the highly active aspartate enzyme and the low-activity G336Q mutant, which exhibited lower apparent affinities for activator and substrates and higher apparent affinity for inhibitor. The altered allosteric properties of the G336D mutant enzyme were almost completely abolished by substitution of asparagine. Thus, the aspartate negative charge is essential for the altered binding of effectors.
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Affiliation(s)
- C R Meyer
- Department of Biochemistry, Michigan State University, East Lansing, Michigan 48824, USA
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3
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Meyer CR, Yirsa J, Gott B, Preiss J. A kinetic study of site-directed mutants of Escherichia coli ADP-glucose pyrophosphorylase: the role of residue 295 in allosteric regulation. Arch Biochem Biophys 1998; 352:247-54. [PMID: 9587413 DOI: 10.1006/abbi.1998.0593] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The effects of amino acid substitutions at residue 295 on the regulatory properties of Escherichia coli ADP-glucose pyrophosphorylase were studied. In previous studies, this residue, altered from proline to serine (P295S) in the gene of a mutant strain of E. coli, resulted in a high-activity form of enzyme [higher activity in absence of activator fructose 1,6-bisphosphate (FBP), higher apparent affinity for FBP and substrates, and lower apparent affinity for the inhibitor, AMP]. The effects of size and charge on this site were explored by replacing Pro with Gly, Asp, Asn, Gln, or Glu. All mutant enzymes were expressed and purified for kinetic analysis. All mutant enzymes, to varying extents, were in more active form than the wild-type enzyme. Enzymes with a substituted negative charge (P295D, P295E) had the highest activity in the absence of FBP, while the P295G enzyme was most similar to the wild type. The P295D and P295E enzymes had the lowest apparent affinities for AMP; this effect was partially abolished by the neutral substitutions P295N and P295Q. Another mutation, G336D, had previously been found to produce an even higher activity enzyme form. In order to examine interactions between substitutions at the 295 and 336 positions, the double mutant P295D-G336D was constructed and characterized. The double mutant enzyme was more active in the absence of FBP, with a higher affinity for FBP and a lower apparent affinity for AMP than either single mutated enzyme. The significance of residue 295 in regulation is discussed.
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Affiliation(s)
- C R Meyer
- Department of Biochemistry, Michigan State University, East Lansing 48824, USA
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4
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Pfannschmidt C, Langowski J. Superhelix organization by DNA curvature as measured through site-specific labeling. J Mol Biol 1998; 275:601-11. [PMID: 9466934 DOI: 10.1006/jmbi.1997.1476] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
For determining the position of a defined site in a superhelical DNA we have developed a method for introducing a covalent biotin label at a specific sequence while preserving the superhelicity. This is done by first introducing a specific nick, labeling the DNA by limited nick translation and sealing the nick with ligase. The superhelicity is controlled by including ethidium in the ligation reaction. Using scanning force of microscopy on DNAs labeled by this method, we have then compared the position of streptavidin markers at a specific site relative to the end loop of the superhelix. We found that in DNAs with permanently curved inserts the label is located preferentially at a defined distance from the end loop, while in controls without curved inserts the label position was random. This indicates that curves are located in or near the end loops in a superhelix.
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Affiliation(s)
- C Pfannschmidt
- Division Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, Germany
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5
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Song B, Sigel RKO, Sigel H. Acid-Base Properties of Adenosine 5′-O-Thiomonophosphate in Aqueous Solution. Chemistry 1997. [DOI: 10.1002/chem.19970030106] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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6
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Budd ME, Campbell JL. A yeast gene required for DNA replication encodes a protein with homology to DNA helicases. Proc Natl Acad Sci U S A 1995; 92:7642-6. [PMID: 7644470 PMCID: PMC41201 DOI: 10.1073/pnas.92.17.7642] [Citation(s) in RCA: 141] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
A yeast gene has been identified by screening for DNA replication mutants using a permeabilized cell replication assay. The mutant is temperature sensitive for growth and shows a cell cycle phenotype typical of DNA replication mutants. RNA synthesis is normal in the mutant but DNA synthesis ceases upon shift to the nonpermissive temperature. The DNA2 gene was cloned by complementation of the dna2ts gene phenotype. The gene is essential for viability. The gene encodes a 172-kDa protein with characteristic DNA helicase motifs. A hemagglutinin epitope-Dna2 fusion protein was prepared and purified by conventional and immunoaffinity chromatography. The purified protein is a DNA-dependent ATPase and has 3' to 5' DNA helicase activity specific for forked substrates. A nuclease activity that endonucleolytically cleaves DNA molecules having a single-stranded 5' tail adjacent to a duplex region copurifies through all steps with the fusion protein.
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Affiliation(s)
- M E Budd
- Braun Laboratories, California Institute of Technology, Pasadena 91125, USA
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7
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Yaskowiak ES, March PE. Small clusters of divergent amino acids surrounding the effector domain mediate the varied phenotypes of EF-G and LepA expression. Mol Microbiol 1995; 15:943-53. [PMID: 7596295 DOI: 10.1111/j.1365-2958.1995.tb02363.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Elongation factors G, Tu, and related proteins (including LepA) form a distinct subgroup within the GTPase superfamily. This observation is based primarily upon amino acid comparisons of the effector region (G2) of the GTP-binding domain. To examine the functional importance of the highly conserved elongation factor G2 domain a series of chimeric proteins were constructed between Escherichia coli EF-G and Micrococcus luteus EF-G, and between E. coli EF-G and LepA (a protein of unknown function). The M. luteus EF-G/E. coli EF-G hybrid, M. luteus EF-G, and E. coli EF-G efficiently complemented EF-G function in an E. coli strain (PEM101) harbouring a temperature-sensitive mutation in fusA (the gene encoding EF-G). A comparison of the amino acid sequences of the M. luteus EF-G and E. coli EF-G indicated that groups of divergent amino acid residues (amino acids 1-9 and 72-80) were not important for function. LepA and LepA/EF-G chimeric proteins were tested for the ability to complement EF-G function in vivo, for cross-linking to 8-azido-[gamma-32P]-GTP in vitro and for fusidic acid-dependent co-sedimentation with 70S ribosomes. With one exception, all chimeras could be readily cross-linked to azido-GTP in an EF-G-like manner, indicating that hybrid protein construction did not generally result in improperly folded GTP-binding domains. However, the inability of such chimeras to complement EF-G function in vivo indicates that the effector domains are not functionally interchangeable. All LepA/EF-G chimeric proteins were severely defective in fusidic acid-dependent complex formation with 70S ribosomes. A comparison of the amino acid sequences of all three proteins suggests that residues 30-33, 43-48, and 63-66 of E. coli EF-G are important for EF-G specific ribosome-associated function.
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Affiliation(s)
- E S Yaskowiak
- School of Microbiology and Immunology, University of New South Wales, Sydney, Australia
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8
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Zühlke RD, Zhang HJ, Joho RH. [4] Xenopus oocytes: A system for expression cloning and structure-function studies of ion channels and receptors. METHODS IN NEUROSCIENCES 1995. [DOI: 10.1016/s1043-9471(05)80034-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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9
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Walter NG, Strunk G. Strand displacement amplification as an in vitro model for rolling-circle replication: deletion formation and evolution during serial transfer. Proc Natl Acad Sci U S A 1994; 91:7937-41. [PMID: 8058737 PMCID: PMC44519 DOI: 10.1073/pnas.91.17.7937] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Strand displacement amplification is an isothermal DNA amplification reaction based on a restriction endonuclease nicking its recognition site and a polymerase extending the nick at its 3' end, displacing the downstream strand. The reaction resembles rolling-circle replication of single-stranded phages and small plasmids. The displaced sense strand serves as target for an antisense reaction and vice versa, resulting in exponential growth and the autocatalytic nature of this in vitro reaction as long as the template is the limiting agent. We describe the optimization of strand displacement amplification for in vitro evolution experiments under serial transfer conditions. The reaction was followed and controlled by use of the fluorescent dye thiazole orange binding to the amplified DNA. We were able to maintain exponential growth conditions with a doubling time of 3.0 min throughout 100 transfers or approximately 350 molecular generations by using an automatic handling device. Homology of in vitro amplification with rolling-circle replication was mirrored by the occurring evolutionary processes. Deletion events most likely caused by a slipped mispairing mechanism as postulated for in vivo replication took place. Under our conditions, the mutation rate was high and a molecular quasi-species formed with a mutant lacking internal hairpin formation ability and thus outgrowing all other species under dGTP/dCTP deficiency.
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Affiliation(s)
- N G Walter
- Department of Biochemical Kinetics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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10
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Crisell P, Thompson S, James W. Inhibition of HIV-1 replication by ribozymes that show poor activity in vitro. Nucleic Acids Res 1993; 21:5251-5. [PMID: 8255782 PMCID: PMC310644 DOI: 10.1093/nar/21.22.5251] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Self-cleaving RNAs (ribozymes) can be engineered to cleave target RNAs of choice in a sequence-specific manner (1). Consequently, they could be used to inhibit virus replication or to analyse host gene function in vivo. However, ribozymes that are catalytic in vitro are generally disappointing when analysed in cells unless expressed at high levels relative to their target RNAs (2, 3). Here we provide evidence that this can be overcome by optimizing ribozyme structure using cellular rather than cell-free assays. We show that ribozymes of relatively long flanking complementary regions (FCRs), while poor catalysts in vitro, can produce profound inhibition of HIV replication in cells. By examining a series of ribozymes in which the FCRs vary from 9 to 564 nucleotides, we establish that the optimum length for activity in the cell is > or = 33 nucleotides.
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Affiliation(s)
- P Crisell
- Sir William Dunn School of Pathology, University of Oxford, UK
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11
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Oertel-Buchheit P, Porte D, Schnarr M, Granger-Schnarr M. Isolation and characterization of LexA mutant repressors with enhanced DNA binding affinity. J Mol Biol 1992; 225:609-20. [PMID: 1602473 DOI: 10.1016/0022-2836(92)90389-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The LexA repressor from Escherichia coli is a sequence-specific DNA binding protein that shows no pronounced sequence homology with any of the known structural motifs involved in DNA binding. Since little is known about how this protein interacts with DNA, we have selected and characterized a great number of intragenic, second-site mutations which restored at least partially the activity of LexA mutant repressors deficient in DNA binding. In 47 cases, the suppressor effect of these mutations was due to an Ind- phenotype leading presumably to a stabilization of the mutant protein. With one exception, these second-site mutations are all found in a small cluster (amino acid residues 80 to 85) including the LexA cleavage site between amino acid residues 84 and 85 and include both already known Ind- mutations as well as new variants like GN80, GS80, VL82 and AV84. The remaining 26 independently isolated second-site suppressor mutations all mapped within the amino-terminal DNA binding domain of LexA, at positions 22 (situated in the turn between helix 1 and helix 2) and positions 57, 59, 62, 71 and 73. These latter amino acid residues are all found beyond helix 3, in a region where we have previously identified a cluster of LexA (Def) mutant repressors. In several cases the parental LexA (Def) mutation has been removed by subcloning or site-directed mutagenesis. With one exception, these LexA variants show tighter in vivo repression than the LexA wild-type repressor. The most strongly improved variant (LexA EK71, i.e. Glu71----Lys) that shows an about threefold increased repression rate in vivo, was purified and its binding to a short consensus operator DNA fragment studied using a modified nitrocellulose filter binding assay. As expected from the in vivo data, LexA EK71 interacts more tightly with both operator and (more dramatically) with non-operator DNA. A determination of the equilibrium association constants of LexA EK71 and LexA wild-type as a function of monovalent salt concentration suggests that LexA EK71 might form an additional ionic interaction with operator DNA as compared to the LexA wild-type repressor. A comparison of the binding of LexA to a non-operator DNA fragment further shows that LexA interacts with the consensus operator very selectively with a specificity factor of Ks/Kns of 1.4 x 10(6) under near-physiological salt conditions.
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Affiliation(s)
- P Oertel-Buchheit
- Institut de Biologie Moléculaire et Cellulaire, CNRS UPR 6201 affiliated to INSERM, Strasbourg, France
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12
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Zhu JD, Sun XP, Wang F. The DNA intercalator, ethidium bromide, alters the pattern of DNAse I hypersensitive sites of the beta A-globin gene in chicken erythrocytes. BIOCHIMICA ET BIOPHYSICA ACTA 1991; 1089:158-66. [PMID: 2054379 DOI: 10.1016/0167-4781(91)90003-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We have analysed the effects of a DNA intercalator, ethidium bromide (EB), on chromatin structure in nuclei from both chicken mature erythrocytes (RBC) and reticulocytes (Ret). A differential release of nuclear proteins was obtained from both types of nuclei exposed to EB. Among these proteins, a species of 45 kDa is the major component. Furthermore, in the 10 mM EB-treated nuclei, the pattern of DNAse I hypersensitive sites (DHS) around the chicken beta A-globin gene were significantly altered, i.e., the original set was replaced by a new set of DHS. We have discussed the implications of our observations, in the light of current concepts of functional aspects of the conformational heterogeneity of DNA in both protein-DNA interactions and chromatin structure, as well as the effects of DNA intercalators on DNA conformation.
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Affiliation(s)
- J D Zhu
- Shanghai Institute of Cell Biology, Academia Sinica, China
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13
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14
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Kern D, Mejdoub H, Vincendon P, Boulanger Y, Reinbolt J. The three cysteine residues of cytoplasmic aspartyl-tRNA synthetase from Saccharomyces cerevisiae are not essential for its activity. EUROPEAN JOURNAL OF BIOCHEMISTRY 1990; 193:97-103. [PMID: 2226452 DOI: 10.1111/j.1432-1033.1990.tb19309.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Cytoplasmic aspartyl-tRNA synthetase from Saccharomyces cerevisiae is a dimer made up of identical subunits (Mr 63,000) each of these containing three cysteines (residues 255, 512 and 519 in the amino acid sequence). Thiol-specific probes were used to label these cysteines and study the resulting effect of the modification on the kinetic parameters of both the ATP/PPi exchange and tRNA aminoacylation reactions. Using the classical techniques of protein chemistry it was shown that none of the three cysteines was labelled with iodoacetic acid, whilst N-ethylmaleimide and 5,5'-dithiobis(2-nitrobenzoate) reacted with Cys512 and Cys255, respectively. Only the latter modification was accompanied by a decrease in the rates of both enzyme activities whilst the Km values for the various substrates remained unaffected. Site-directed mutagenesis was also used to replace each of the three cysteines by other residues, either individually or simultaneously. For these experiments the enzyme was expressed in Escherichia coli using an expression vector bearing the structural gene in which the first 13 codons were replaced by the first 14 of the CII lambda gene. The resulting substitution in the amino-terminal part of the expressed enzyme had no effect on the kinetic parameters, compared to those of the enzyme purified from S. cerevisiae. Taking into account the consequences of such substitutions, as well as those of chemical modifications on the two reactions catalysed by the enzyme. ATP/PPi exchange and tRNA aminoacylation, it could be concluded that none of these three cysteines plays any essential role in either substrate binding or catalysis.
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Affiliation(s)
- D Kern
- Laboratoire de Biochmie, Centre National de la Recherche Scientifique, Strasbourg, France
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15
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Olsen D, Kotzorek G, Sayers J, Eckstein F. Inhibition of the restriction endonuclease BanII using modified DNA substrates. Determination of phosphate residues critical for the formation of an active enzyme-DNA complex. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(18)77314-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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16
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Hatzfeld M, Weber K. The coiled coil of in vitro assembled keratin filaments is a heterodimer of type I and II keratins: use of site-specific mutagenesis and recombinant protein expression. J Biophys Biochem Cytol 1990; 110:1199-210. [PMID: 1691189 PMCID: PMC2116092 DOI: 10.1083/jcb.110.4.1199] [Citation(s) in RCA: 213] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Recombinant DNA technology has been used to analyze the first step in keratin intermediate filament (IF) assembly; i.e., the formation of the double stranded coiled coil. Keratins 8 and 18, lacking cysteine, were subjected to site specific in vitro mutagenesis to change one amino acid in the same relative position of the alpha-helical rod domain of both keratins to a cysteine. The mutations lie at position -36 of the rod in a "d" position of the heptad repeat pattern, and thus air oxidation can introduce a zero-length cystine cross-link. Mutant keratins 8 and 18 purified separately from Escherichia coli readily formed cystine homodimers in 2 M guanidine-HCl, and could be separated from the monomers by gel filtration. Heterodimers with a cystine cross-link were obtained when filaments formed by the two reduced monomers were allowed to oxidize. Subsequent ion exchange chromatography in 8.5 M urea showed that only a single dimer species had formed. Diagonal electrophoresis and reverse phase HPLC identified the dimer as the cystine containing heterodimer. This heterodimer readily assembled again into IF indistinguishable from those obtained from the nonmutant counterparts or from authentic keratins. In contrast, the mixture of cystine-stabilized homodimers formed only large aberrant aggregates. However, when a reducing agent was added, filaments formed again and yielded the heterodimer after oxidation. Thus, the obligatory heteropolymer step in keratin IF assembly seems to occur preferentially at the dimer level and not during tetramer formation. Our results also suggest that keratin I and II homodimers, once formed, are at least in 2 M guanidine-HCl a metastable species as their mixtures convert spontaneously into heterodimers unless the homodimers are stabilized by the cystine cross-link. This previously unexpected property of homodimers explains major discrepancies in the literature on the keratin dimer.
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Affiliation(s)
- M Hatzfeld
- Max Planck Institute for Biophysical Chemistry, Goettingen, Federal Republic of Germany
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17
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Olsen DB, Eckstein F. High-efficiency oligonucleotide-directed plasmid mutagenesis. Proc Natl Acad Sci U S A 1990; 87:1451-5. [PMID: 2154748 PMCID: PMC53493 DOI: 10.1073/pnas.87.4.1451] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
A number of single- and double-base substitutions have been introduced into either the polylinker region or the lacZ gene in the plasmid vector pUC19. The efficiencies of these changes upon transfection of TG-1 bacterial cells were generally 70-80%. A strategy has been devised by which the wild-type DNA can be selectively destroyed. It is primarily based on the resistance of phosphorothioate internucleotide linkages to some restriction enzymes. A mismatch oligonucleotide is introduced into a gapped region and the gap is filled using three deoxynucleoside 5'-triphosphates and one deoxynucleoside 5'-[alpha-thio]triphosphate. Reaction with a restriction enzyme that is unable to hydrolyze phosphorothioates ensures that the DNA containing the mismatch oligonucleotide is only nicked. Concomitantly, the DNA that does not contain the desired mutation is linearized. Subsequent reactions with an exonuclease and DNA polymerase I yield mutant homoduplex DNA for transfection.
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Affiliation(s)
- D B Olsen
- Max-Planck Institut für Experimentelle Medizin, Abteilung Chemie, Göttingen, Federal Republic of Germany
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18
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Abstract
The observation that phosphorothioate analogues of the nucleoside triphosphates are substrates for DNA- and RNA-polymerases has proven a boon for the molecular biologist. As these phosphorothioate-containing polymers are stable to degradation by nucleases and the sulfur atom confers many favourable chemical properties, several applications in molecular biology have been developed, including new methods for site-directed mutagenesis and DNA sequencing.
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19
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Spitzer S, Eckstein F. Inhibition of deoxyribonucleases by phosphorothioate groups in oligodeoxyribonucleotides. Nucleic Acids Res 1988; 16:11691-704. [PMID: 2850541 PMCID: PMC339104 DOI: 10.1093/nar/16.24.11691] [Citation(s) in RCA: 109] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The Rp- and Sp-diastereomers of the phosphorothioate-containing oligonucleotide d[ApAp(S)ApA] have been synthesized. They and the tetramer d[ApApApA] were tested as substrates for staphylococcal nuclease, DNase II and spleen phosphodiesterase. For digestions with DNase I these oligonucleotides were converted to the 5'-phosphorylated derivates. The reactions with the nucleases were analysed by HPLC. The phosphorothioate groups of both diastereomers were resistant to the action of staphylococcal nuclease, DNase I and DNase II. While the phosphorothioate group of the Rp-diastereomer was resistant to the action of spleen phosphodiesterase, the Sp-diastereomer was hydrolysed at an estimated rate 1/100 the rate of cleavage of the unmodified tetramer. The presence of the phosphorothioate group in the center of the molecule affected the rate of hydrolysis of neighbouring phosphate groups for some enzymes. In particular, very slow release of 3'-dAMP from the Rp-diastereomer occurred on incubation with staphylococcal nuclease but the Sp-diastereomer was completely resistant. DNase II produced 3'-dAMP quite rapidly from both diastereomers of d[ApAp(S)ApA] and DNase I released 5'-dAMP from both diastereomers of d[pApAp(S)ApA] only slowly.
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Affiliation(s)
- S Spitzer
- Max-Planck-Institut für Experimentelle Medizin, Abteilung Chemie, Göttingen, FRG
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