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Abstract
Semisynthetic DNA-protein conjugates, generated by either covalent or non-covalent coupling chemistry, are versatile molecular tools applicable in bioanalytical and synthetic chemical procedures. This article reviews the synthesis and characterization of artificial nucleic acid-protein conjugates, in addition to applications arising in the life sciences and nanobiotechnology, such as the self-assembly of high-affinity reagents for immunological detection assays and biosensors, the fabrication of laterally microstructured biochips, and the biomimetic 'bottom-up' synthesis of nanostructured supramolecular devices.
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Affiliation(s)
- Christof M Niemeyer
- Universität Dortmund, Fachbereich Chemie, Biologisch-Chemische Mikrostrukturtechnik, Otto-Hahn Str. 6, D-44227 Dortmund, Germany.
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53
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Abstract
Covalent modification methods allow an almost unlimited range of functionality to be introduced into proteins. In concert with genetic techniques, chemical strategies have had significant impact in the field of enzyme design. Major recent developments include introducing catalytic activity into inactive proteins, modifying the selectivity and/or reactivity of existing enzymes and designing novel enzyme-based biosensors. New chemical methods promise to further increase the range of functionality that can be incorporated into proteins. These results suggest that semi-synthetic methods will play a key role in the development of future biocatalysts.
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Affiliation(s)
- C M Tann
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
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54
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Niemeyer CM. Semi-synthetic nucleic acid-protein conjugates: applications in life sciences and nanobiotechnology. J Biotechnol 2001; 82:47-66. [PMID: 11999713 DOI: 10.1016/s1389-0352(01)00027-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Semi-synthetic conjugates of nucleic acids and proteins can be generated by either covalent coupling chemistry, or else by non-covalent biomolecular recognition systems, such as receptor-ligands of complementary nucleic acids. These nucleic acid-protein conjugates are versatile molecular tools which can be applied, for instance, in the self-assembly of high-affinity reagents for immunological detection assays, the fabrication of laterally microstructured biochips containing functional biological groups, and the biomimetic 'bottom-up' synthesis of nanostructured supramolecular devices. This review summarizes the current state-of-the-art synthesis and characterization methods of artificial nucleic acid-protein conjugates, as well as applications and perspectives for future developments of such hybrid biomolecular components in life sciences and nanobiotechnology.
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Affiliation(s)
- C M Niemeyer
- Universität Bremen, FB2-UFT, Biotechnologie und Molekulare Genetik, Germany.
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55
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Qi D, Tann CM, Haring D, Distefano MD. Generation of new enzymes via covalent modification of existing proteins. Chem Rev 2001; 101:3081-111. [PMID: 11710063 DOI: 10.1021/cr000059o] [Citation(s) in RCA: 232] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- D Qi
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA
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56
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Abstract
Semisynthetic DNA-protein conjugates are versatile molecular tools useful, for instance, in the self-assembly of high-affinity reagents for immunological detection assays, the fabrication of highly functionalized laterally microstructured biochips, and the biomimetic "bottom-up" synthesis of nanostructured supramolecular devices. This concept paper summarizes the current state-of-the-art concerning the synthesis, characterization, and applications of such hybrid molecules, and also draws perspectives on future developments.
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Affiliation(s)
- C M Niemeyer
- Universität Bremen, Biotechnologie und Molekulare Genetik, Germany.
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57
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Shinozuka K, Nakashima Y, Shimizu K, Sawai H. Synthesis and characterization of polyamine-based biomimetic catalysts as artificial ribonuclease. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2001; 20:117-30. [PMID: 11303558 DOI: 10.1081/ncn-100001441] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Several polyamine derivatives (I-V) conjugated with or without an intercalative moiety were prepared as ribonuclease mimics. Although no DNA-cleaving activity was observed for all compounds tested, mimics I, III, and V bearing an intercalative moiety along with the primary amine and/or imidazole moieties exhibited potent RNA-cleaving activity at near physiological pH. The RNA-cleaving reactions of the compounds show characteristic bell-shaped pH dependency, and the optimal pH values for III and V were well correlated to the pKa values of their active sites, primary amine, and imidazole moieties.
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Affiliation(s)
- K Shinozuka
- Department of Chemistry, Faculty of Engineering, Gunma University, Kiryu City, Japan.
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58
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Affiliation(s)
- Hagan Bayley
- Department of Medical Biochemistry and Genetics, Texas A&M University System Health Science Center, 440 Reynolds Medical Building, College Station, Texas 77843-1114, Department of Chemistry, Texas A&M University, College Station, Texas 77843-3255, and Department of Chemistry and Center for Research at the Bio/Nano Interface, University of Florida, Gainesville, Florida 32605-1200
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59
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Suh J. Designing active sites of synthetic artificial enzymes. ACTA ACUST UNITED AC 2000. [DOI: 10.1016/s1068-7459(00)80008-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2023]
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60
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Catalytic hydrogenation of itaconic acid in a biotinylated Pyrphos–rhodium(I) system in a protein cavity. ACTA ACUST UNITED AC 1999. [DOI: 10.1016/s0957-4166(99)00193-7] [Citation(s) in RCA: 110] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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61
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Hamachi I, Shinkai S. Chemical Modification of the Structures and Functions of Proteins by the Cofactor Reconstitution Method. European J Org Chem 1999. [DOI: 10.1002/(sici)1099-0690(199903)1999:3<539::aid-ejoc539>3.0.co;2-f] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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62
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Yu M, Souaya J, Julin DA. Identification of the nuclease active site in the multifunctional RecBCD enzyme by creation of a chimeric enzyme. J Mol Biol 1998; 283:797-808. [PMID: 9790841 DOI: 10.1006/jmbi.1998.2127] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The recombinational hot spot chi modulates the nuclease and helicase activities of the RecBCD enzyme, leading to generation of an early DNA intermediate for homologous recombination. Here we identify the subunit location of the nuclease active site in RecBCD. The isolated RecB protein cleaves circular single-stranded M13 phage DNA, but RecB1-929, comprising only the 100 kDa N-terminal domain of RecB, does not. We reported previously that the reconstituted RecB1-929CD enzyme also is not a nuclease, suggesting that the C-terminal 30 kDa domain of RecB is a non-specific ssDNA endonuclease. However, we were unable to detect nuclease activity with the subtilisin-generated C-terminal 30 kDa fragment of RecB. Since the subtilisin-generated fragment did not bind to a ssDNA-agarose column, we designed a chimeric enzyme by attaching the C-terminal 30 kDa domain of RecB to the gene 32 protein of T4 phage, a ssDNA binding protein that does not have strand scission ability. In addition, Asp427 in the chimeric enzyme (Asp1080 in RecB), a residue that is conserved among several RecB homologs, was substituted to alanine (the D427A mutant). The wild-type chimeric enzyme cleaves the M13 DNA and the D427A mutation abolishes the endonuclease activity of the chimeric enzyme but does not affect its DNA binding ability. This finding indicates an unusual bipartite nature in the structural organization of RecB, in which the DNA-binding function is located in the N-terminal 100 kDa domain and the nuclease catalytic domain is located in the C-terminal 30 kDa domain. The purified RecBD1080ACD mutant is a processive helicase but not a nuclease, demonstrating that RecBCD has a single nuclease active site in the C-terminal 30 kDa domain of RecB.
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Affiliation(s)
- M Yu
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
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63
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Jang BB, Lee KP, Min DH, Suh J. Immobile Artificial Metalloproteinase Containing Both Catalytic and Binding Groups. J Am Chem Soc 1998. [DOI: 10.1021/ja981723+] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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64
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Chassignol M, Thuong NT. Phosphodisulfide bond: A new linker for the oligonucleotide conjugation. Tetrahedron Lett 1998. [DOI: 10.1016/s0040-4039(98)01854-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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65
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Distefano MD, Kuang H, Qi D, Mazhary A. The design of protein-based catalysts using semisynthetic methods. Curr Opin Struct Biol 1998; 8:459-65. [PMID: 9729737 DOI: 10.1016/s0959-440x(98)80123-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The combination of site-directed mutagenesis and chemical modification has resulted in the preparation of protein conjugates with new and useful properties. Proteins modified with metal-chelating groups are proving useful for mapping tertiary and quaternary interactions using the technique of affinity cleavage. The attachment of cofactors, including pyridoxal and pyridoxamine, has resulted in the preparation of semisynthetic transaminases that display enzyme-like properties, including enantioselectivity, substrate specificity and reaction-rate acceleration.
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Affiliation(s)
- M D Distefano
- Department of Chemistry, University of Minnesota, Minneapolis 55455, USA.
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66
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Qi D, Kuang H, Distefano MD. Effects of metal ions on the rates and enantioselectivities of reactions catalyzed by a series of semisynthetic transaminases created by site directed mutagenesis. Bioorg Med Chem Lett 1998; 8:875-80. [PMID: 9871558 DOI: 10.1016/s0960-894x(98)00129-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fatty acid binding proteins are a class of small 15 kDa proteins with a simple architecture that forms a large solvent sequestered cavity. In previous work, we demonstrated that reductive amination reactions could be performed in this cavity by covalent attachment of a pyridoxamine cofactor and that the rate, enantioselectivity and substrate specificity of these reactions could be altered by site directed mutagenesis. Herein, we show that the chemistry performed by these conjugates can be extended to include catalytic transamination and describe the effects of added metal ions on reaction rate and enantioselectivity. We conclude that metal ions can be used to increase the rate of reactions catalyzed by semisynthetic transaminases; however, the addition of metal ions can also retard the reaction rate. Furthermore, it appears that the presence of metal ions almost always results in an erosion of reaction enantioselectivity. This limits their utility as a practical means of increasing reaction rate. The results reported here, for four independent systems, should be considered in future designs of artificial transaminases.
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Affiliation(s)
- D Qi
- Department of Chemistry, University of Minnesota, Minneapolis 55455, USA
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67
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Kuang H, Distefano MD. Catalytic Enantioselective Reductive Amination in a Host−Guest System Based on a Protein Cavity. J Am Chem Soc 1998. [DOI: 10.1021/ja972771h] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hao Kuang
- Department of Chemistry, University of Minnesota Minneapolis, Minnesota 55455
| | - Mark D. Distefano
- Department of Chemistry, University of Minnesota Minneapolis, Minnesota 55455
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68
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Coombs GS, Corey DR. Site-Directed Mutagenesis and Protein Engineering. Proteins 1998. [DOI: 10.1016/b978-012058785-8/50006-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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69
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Davies RR, Distefano MD. A Semisynthetic Metalloenzyme Based on a Protein Cavity That Catalyzes the Enantioselective Hydrolysis of Ester and Amide Substrates. J Am Chem Soc 1997. [DOI: 10.1021/ja970820k] [Citation(s) in RCA: 114] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Ronald R. Davies
- Contribution from the Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Mark D. Distefano
- Contribution from the Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
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70
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Kuang H, Davies RR, Distefano MD. Modulation of the rate, enantioselectivity, and substrate specificity of semisynthetic transaminases based on lipid binding proteins using site directed mutagenesis. Bioorg Med Chem Lett 1997. [DOI: 10.1016/s0960-894x(97)00358-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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71
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Lanthanide metal complexes for the hydrolysis of ribonucleoside 3′,5′-cyclic phosphate and deoxyribonucleoside 3′,5′-cyclic phosphate. ACTA ACUST UNITED AC 1997. [DOI: 10.1016/s1381-1169(96)00354-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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72
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Kuang H, Brown ML, Davies RR, Young EC, Distefano MD. Enantioselective Reductive Amination of α-Keto Acids to α-Amino Acids by a Pyridoxamine Cofactor in a Protein Cavity. J Am Chem Soc 1996. [DOI: 10.1021/ja954271z] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hao Kuang
- Contribution from the Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Matthew L. Brown
- Contribution from the Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Ronald R. Davies
- Contribution from the Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Eva C. Young
- Contribution from the Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
| | - Mark D. Distefano
- Contribution from the Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455
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73
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Sigurdson ST, Eckstein F. Site specific labelling of sugar residues in oligoribonucleotides: reactions of aliphatic isocyanates with 2' amino groups. Nucleic Acids Res 1996; 24:3129-33. [PMID: 8774891 PMCID: PMC146078 DOI: 10.1093/nar/24.16.3129] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Considerable effort has been directed towards studying the structure and function of nucleic acids and several approaches rely on the attachment of reporter groups or reactive functional groups to nucleic acids. We report here the selective modification of 2-amino groups in oligoribonucleotides, through their reaction with aliphatic isocyanates, to give the corresponding 2'-urea derivatives in >95% yield. Furthermore, such modification with (2-isocyanato)ethyl 2-pyridyl disulfide enables subsequent coupling to other thiols (such as those contained in peptides and proteins) or to thiol-reactive electrophiles. A modified decamer was not significantly destabilized by the 2'-urea group, compared with a 2'-amino group, as demonstrated by a mere 1.3 degrees C drop in the melting temperature of the duplex.
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Affiliation(s)
- S T Sigurdson
- Max-Plank-Institut für Experimenal Medizin, Göttingen, Germany
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74
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Truffert JC, Asseline U, Brack A, Thuong NT. Synthesis, purification and characterization of two peptide-oligonucleotide conjugates as potential artificial nucleases. Tetrahedron 1996. [DOI: 10.1016/0040-4020(96)00018-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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75
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Abstract
We report two strategies for accelerating the hybridization of oligonucleotides to DNA. We demonstrate that oligodeoxyribonucleotides and peptide nucleic acid oligomers hybridize to inverted repeats within duplex DNA by D-loop formation. Oligonucleotides and duplex template form an active complex, which can be recognized by T7 DNA polymerase to prime polymerization. Quantitation of polymerization products allowed the rate of hybridization to be estimated, and peptide nucleic acid oligomers and oligonucleotide-protein adducts anneal with association constants 500- and 12,000-fold greater, respectively, than the analogous unmodified oligonucleotides. Together, these results indicate that sequences within duplex DNA can be targeted by Watson-Crick base pairing and that chemical modifications can dramatically enhance the rate of strand association. These findings should facilitate targeting of oligomers for priming DNA polymerization, the detection of diagnostic sequences, and the disruption of gene expression. The observed acceleration of hybridization may offer a new perspective on the ability of RecA or other proteins to accelerate strand invasion.
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Affiliation(s)
- M Iyer
- Howard Hughes Medical Institute, Department of Pharmacology, University of Texas Southwestern Medical Center at Dallas 75235, USA
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76
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Cornish VW, Mendel D, Schultz PG. Untersuchungen von Struktur und Funktion von Proteinen mit einem erweiterten genetischen Code. Angew Chem Int Ed Engl 1995. [DOI: 10.1002/ange.19951070604] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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77
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Kanaya E, Uchiyama Y, Ohtsuka E, Ueno Y, Ikehara M, Kanaya S. Kinetic analyses of DNA-linked ribonucleases H with different sizes of DNA. FEBS Lett 1994; 354:227-31. [PMID: 7525355 DOI: 10.1016/0014-5793(94)01131-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A series of DNA-linked ribonucleases H with DNA adducts varying in size and sequence, ranging from heptamer to nonamer, were constructed and examined for their ability to cleave the 12-base RNA (5'-CGGAGAUGACGG-3') site-specifically. The DNA-linked RNase H with the 9-base DNA (5'-GTCATCTCC-3') cleaved the 12-base RNA specifically at A6-U7. Kinetic studies revealed that the DNA-linked RNase H with the 8-base DNA (5'-TCATCTCC-3') cleaved it slightly more effectively than that with the 9-base DNA. Factors that may affect the specificity and catalytic efficiency of a DNA-linked RNase H are described.
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Affiliation(s)
- E Kanaya
- Protein Engineering Research Institute, Osaka, Japan
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78
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Synthesis and RNA cleaving activities of polyamine derived novel artificial ribonuclease. Bioorg Med Chem Lett 1994. [DOI: 10.1016/s0960-894x(01)80547-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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79
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80
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Park C, Campbell JL, Goddard WA. Design superiority of palindromic DNA sites for site-specific recognition of proteins: tests using protein stitchery. Proc Natl Acad Sci U S A 1993; 90:4892-6. [PMID: 8506333 PMCID: PMC46619 DOI: 10.1073/pnas.90.11.4892] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Using protein stitchery with appropriate attachment of cysteines linking to either C or N termini of the basic region of the v-Jun leucine zipper gene-regulatory protein, we constructed three dimers--pCC, pCN, and pNN. All three bind specifically to the appropriately rearranged DNA recognition sites for v-Jun: ATGAcgTCAT, ATGAcgATGA, and TCATcgTCAT, respectively (Kd, approximately 4 nM at 4 degrees C). Results of DNase I footprinting provide strong support for bent recognition helices in leucine zipper protein-DNA complexes. Comparison of the results for pCC and pNN with those for pCN shows the design superiority of palindromic sequences for protein recognition.
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Affiliation(s)
- C Park
- Materials and Molecular Simulation Center, Beckman Institute, Pasadena, CA
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81
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Sena EP, Zarling DA. Targeting in linear DNA duplexes with two complementary probe strands for hybrid stability. Nat Genet 1993; 3:365-72. [PMID: 7981759 DOI: 10.1038/ng0493-365] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A new in vitro hybridization reaction targets two short complementary RecA protein-coated DNA probes to homologous sequences at any position in a linear duplex DNA molecule. Stable hybrids are obtained after RecA protein removal when both complementary probe strands are present in a four-stranded hybrid, but not when one probe strand is present in a three-stranded hybrid. In four-stranded hybrids with one probe strand biotinylated and the other radiolabelled, the deproteinized hybrids can be isolated and detected by affinity capture on streptavidin-coated magnetic beads. RecA-mediated targeting of complementary biotinylated DNA probe strands allows the affinity capture of 48.5-kilobase duplex lambda genomic DNA. These reactions provide a means of isolating any desired duplex gene or chromosomal DNA fragment.
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Affiliation(s)
- E P Sena
- Cell and Molecular Biology Laboratory, SRI International, Menlo Park, California 94025
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82
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Abstract
The EcoRI adenine DNA methyltransferase forms part of a bacterial restriction/modification system; the methyltransferase modifies the second adenine within the canonical site GAATTC, thereby preventing the EcoRI endonuclease from cleaving this site. We show that five noncanonical EcoRI sites (TAATTC, CAATTC, GTATTC, GGATTC and GAGTTC) are not methylated in vivo under conditions when the canonical site is methylated. Only when the methyltransferase is overexpressed is partial in vivo methylation of the five sites detected. Our results suggest that the methyltransferase does not protect host DNA against potential endonuclease-mediated cleavage at noncanonical sites. Our related in vitro analysis of the methyltransferase reveals a low level of sequence-discrimination. We propose that the high in vivo specificity may be due to the active removal of methylated sequences by DNA repair enzymes (J. Bacteriology (1987), 169 3243-3250).
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Affiliation(s)
- D W Smith
- Department of Chemistry, University of California, Santa Barbara 93106
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83
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Jayasena SD, Johnston BH. Site-specific cleavage of the transactivation response site of human immunodeficiency virus RNA with a tat-based chemical nuclease. Proc Natl Acad Sci U S A 1992; 89:3526-30. [PMID: 1565648 PMCID: PMC48901 DOI: 10.1073/pnas.89.8.3526] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
tat, an essential transactivator of gene transcription in the human immunodeficiency virus (HIV), is believed to activate viral gene expression by binding to the transactivation response (TAR) site located at the 5' end of all viral mRNAs. The TAR element forms a stem-loop structure containing a 3-nucleotide bulge that is the site for tat binding and is required for transactivation. Here we report the synthesis of a site-specific chemical ribonuclease based on the TAR binding domain of the HIV type 1 (HIV-1) tat. A peptide consisting of this 24-amino acid domain plus an additional C-terminal cysteine residue was chemically synthesized and covalently linked to 1,10-phenanthroline at the cysteine residue. The modified peptide binds to TAR sequences of both HIV-1 and HIV-2 and, in the presence of cupric ions and a reducing agent, cleaves these RNAs at specific sites. Cleavage sites on TAR sequences are consistent with peptide binding to the 3-nucleotide bulge, and the relative displacement of cleavage sites on the two strands suggests peptide binding to the major groove of the RNA. These results and existing evidence of the rapid cellular uptake of tat-derived peptides suggest that chemical nucleases based on tat may be useful for inactivating HIV mRNA in vivo.
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Affiliation(s)
- S D Jayasena
- Cell and Molecular Biology Laboratory, SRI International, Menlo Park, CA 94025
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84
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85
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Waye MM, Mui F, Hodge K, Li VK. A phagemid vector library for cloning DNA with four-nucleotide 5' or 3' overhangs. Plasmid 1991; 26:74-7. [PMID: 1946750 DOI: 10.1016/0147-619x(91)90038-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A phagemid vector library for cloning DNA with four nucleotide 5' or 3' overhangs has been constructed. This library is based on the pT7T3 vector (Pharmacia) which is a modification of the phagemid pTZ18U vector. We have chosen pT7T3 as the parent vector because it can be used for Sanger's dideoxy sequencing and for the generation of RNA probes with either the T7 or T3 promoter. Each member of the cloning vector series pBM has recognition sites for both of the restriction enzymes BspM1 and BstX1 in addition to the basic multiple cloning sites. BspM1 recognizes the sequence 5'...ACCTGC NNNN/NNNN...3' whereas BstX1 recognizes the sequence 5'...CCAN NNNN/NTGG...3'. Thus these two sites can be overlapped, so that only 256 vectors (instead of 512 vectors) need be constructed to cover all the theoretical possible combinations of sites which give complementary cohesive ends for cloning DNA with four nucleotide 5' or 3' overhangs. This vector library can be used for amplification cloning of DNA in a tandem array by choosing appropriate vectors which have nonpalindromic sequences. We have obtained approximately 200 members of the 256 possible clones and have organized the vectors using a MacIntosh HyperCard program for easy retrieval.
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Affiliation(s)
- M M Waye
- Department of Dentistry, University of Toronto, Ontario, Canada
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86
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Cuenoud B, Schepartz A. A general scheme for incorporating nonnatural functionality into peptides. Tetrahedron Lett 1991. [DOI: 10.1016/s0040-4039(00)92697-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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87
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88
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89
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Pei D, Corey DR, Schultz PG. Site-specific cleavage of duplex DNA by a semisynthetic nuclease via triple-helix formation. Proc Natl Acad Sci U S A 1990; 87:9858-62. [PMID: 2124705 PMCID: PMC55273 DOI: 10.1073/pnas.87.24.9858] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
A Lys-84----Cys mutant staphylococcal nuclease was selectively linked to the 5' and/or 3' terminus of a thiol-containing polypyrimidine oligonucleotide via a disulfide bond. The oligonucleotide-staphylococcal nuclease adduct is capable of binding to a homopurine-homopyrimidine region of Watson-Crick duplex DNA by the formation of a triple-helical structure. Upon the addition of Ca2+, the nuclease cleaves DNA at sites adjacent to the homopurine tract. Specific double-strand cleavage occurred predominantly at A + T-rich sites to the 5' side of the homopurine tract for both the 5'-derivatized and the 5',3'-diderivatized nucleases; the 3'-derivatized nuclease gave no cleavage. The cleavage pattern is asymmetric and consists of multiple cleavage sites shifted to the 5' side on each strand, centered at the terminal base pair of the binding site. Microgram amounts of plasmid pDP20 DNA (4433 base pairs) containing a homopurine-homopyrimidine tract were selectively cleaved by a semisynthetic nuclease with greater than 75% efficiency at room temperature within 1 hr. Cleavage reaction conditions were optimized with respect to pH, temperature, reaction times, and reaction components. Semisynthetic nucleases of this type should provide a powerful tool in chromosomal DNA manipulations.
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Affiliation(s)
- D Pei
- Department of Chemistry, University of California-Berkeley 94720
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90
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Chollet A. Selective Attachment of Oligonucleotides to Interleukin-1β and Targeted Delivery to Cells. ACTA ACUST UNITED AC 1990. [DOI: 10.1080/07328319008045211] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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91
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Chu BC, Orgel LE. Optimization of the efficiency of cross-linking PtII oligonucleotide phosphorothioate complexes to complementary oligonucleotides. Nucleic Acids Res 1990; 18:5163-71. [PMID: 2402442 PMCID: PMC332138 DOI: 10.1093/nar/18.17.5163] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
We have investigated the efficiency with which PtII complexes cross-link phosphorothioates of oligonucleotides to complementary DNA targets. The A and G residues 2-5 bases downstream from the 5'-phosphorothioate group are preferred sites for cross-linking. Replacement of residues in this part of the target by T residues results in greatly decreased cross-linking when cis platinum diammine dichloride (cisPtII) or potassium platinous chloride (K2PtCl4) are used. Trans platinum diammine dichloride (transPtII) forms cross-links with T residues if A and G residues are absent from the susceptible region of the target. Oligomers containing an internal phosphorothioate group can also be linked to their templates with transPtII, but not with cisPtII or K2PtCl4. Cross-linking via an internal phosphorothioate group tends to be less efficient than cross-linking via a 5'-terminal phosphorothioate. The Sp isomers of internal phosphorothioates are cross-linked more efficiently than the Rp isomers. Preliminary experiments suggest that the efficiency of cross-linking to RNA targets will prove similar to that found for DNA targets.
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Affiliation(s)
- B C Chu
- Salk Institute for Biological Studies, San Diego, CA 92138
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92
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Hélène C, Toulmé JJ. Specific regulation of gene expression by antisense, sense and antigene nucleic acids. BIOCHIMICA ET BIOPHYSICA ACTA 1990; 1049:99-125. [PMID: 1694695 DOI: 10.1016/0167-4781(90)90031-v] [Citation(s) in RCA: 624] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- C Hélène
- Muséum National d'Histoire Naturelle, INSERM U201-CNRS UA.481, Paris, France
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93
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Synthesis and characterization of a reactive binuclear co(III) complex. Cooperative promotion of phosphodiester hydrolysis. Tetrahedron Lett 1990. [DOI: 10.1016/s0040-4039(00)97860-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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94
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Hélène C, Thuong NT, Saison-Behmoaras T, François JC. Sequence-specific artificial endonucleases. Trends Biotechnol 1989. [DOI: 10.1016/0167-7799(89)90113-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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95
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Abstract
Hybrid nucleases consisting of an oligonucleotide fused to a unique site on the relatively nonspecific phosphodiesterase staphylococcal nuclease have been shown to sequence specifically cleave DNA. We have introduced mutations into the binding pocket of the nuclease which lower the kcat/Km of the enzyme. Hybrid nucleases generated from these mutants sequence selectively hydrolyze single-stranded DNA in a catalytic fashion, and under a much wider range of conditions than was previously possible. One such hybrid nuclease (Y113A, K116C) was able to site selectively cleave single-stranded M13mp7 DNA (7214 nt), primarily at one phosphodiester bond. Another hybrid nuclease (Y113A, L37A, K116C) catalyzed the hydrolysis of a 78-nt DNA substrate with a kcat of 1.2 min-1 and a Km of 120 nM. The effects of variations in the length and sequence of the oligonucleotide binding region were examined, as were changes in the length of the tether between the oligonucleotide and the enzyme. Cleavage specificity was also assayed as a function of substrate DNA primary and secondary structure and added poly(dA).
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Affiliation(s)
- D R Corey
- Department of Chemistry, University of California, Berkeley 94720
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96
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Anthony-Cahill SJ, Griffith MC, Noren CJ, Suich DJ, Schultz PG. Site-specific mutagenesis with unnatural amino acids. Trends Biochem Sci 1989; 14:400-3. [PMID: 2683258 DOI: 10.1016/0968-0004(89)90287-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The incorporation of unnatural amino acids into proteins by site-specific mutagenesis provides a valuable new methodology for the generation of novel proteins that possess unique structural and functional features.
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97
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Zuckermann RN, Schultz PG. Site-selective cleavage of structured RNA by a staphylococcal nuclease-DNA hybrid. Proc Natl Acad Sci U S A 1989; 86:1766-70. [PMID: 2467291 PMCID: PMC286785 DOI: 10.1073/pnas.86.6.1766] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
A hybrid enzyme consisting of an oligodeoxyribonucleotide fused to a unique site on staphylococcal nuclease site-selectively cleaves a number of natural RNAs including Escherichia coli M1 RNA (377 bases), 16S rRNA (1542 bases), and yeast tRNA(Phe). The oligonucleotide directs the nuclease activity of the enzyme to the nucleotides directly adjacent to the complementary target sequence on the substrate RNA. In the case of M1 RNA, hydrolysis occurs primarily at one phosphodiester bond, converting 50% of the starting material to product. Furthermore, the reaction products can be enzymatically manipulated: tRNA(Phe) was cleaved in the anticodon region and was religated to form the full-length tRNA in high yield. Because the specificity of these hybrid enzymes can be easily altered, they should prove to be useful tools for probing RNA structure and function.
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Affiliation(s)
- R N Zuckermann
- Department of Chemistry, University of California, Berkeley 94720
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98
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99
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100
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Koob M, Grimes E, Szybalski W. Conferring new specificity upon restriction endonucleases by combining repressor-operator interaction and methylation. Gene 1988; 74:165-7. [PMID: 2854805 DOI: 10.1016/0378-1119(88)90277-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- M Koob
- McArdle Laboratory for Cancer Research, University of Wisconsin, Madison 53706
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