The Experts below are selected from a list of 92016 Experts worldwide ranked by ideXlab platform
Yukio Sugiura - One of the best experts on this subject based on the ideXlab platform.
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Zinc Finger Zinc Finger interaction between the transcription factors gata 1 and sp1
Biochemical and Biophysical Research Communications, 2010Co-Authors: Miki Imanishi, Shigeru Negi, Chika Imamura, Chika Higashi, Wei Yan, Shiroh Futaki, Yukio SugiuraAbstract:In contrast to the extensive understanding of the Zinc Finger-DNA interactions, less is known about Zinc Finger-Zinc Finger interactions. GATA-1 and Sp1 are transcription factors with Zinc Finger domains for DNA binding. The interaction between the GATA-1 and Sp1 Zinc Finger domains is important for synergistic transcriptional effects in erythroid genes. Despite the biological importance of the GATA-1 and Sp1 interaction, the molecular mechanism of the interaction remains unclear. We constructed a series of deletion mutants of the Zinc Finger domains of GATA-1 and Sp1 to identify the regions within the GATA-1 and Sp1 Zinc Finger domains that interact. The Zinc Finger-Zinc Finger interaction modes were also estimated from calorimetric measurements. This revealed that the interaction between the Sp1 and GATA-1 Zinc Finger domains was primarily electrostatic, and that the linker region of the Sp1 Zinc Fingers is important for the association with the GATA-1 Zinc Finger domains. We propose a new molecular mechanism for Zinc Finger-Zinc Finger interactions that should contribute to our understanding of the bio-functional role of the interaction between GATA-1 and Sp1.
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Zinc Finger–Zinc Finger interaction between the transcription factors, GATA-1 and Sp1
Biochemical and biophysical research communications, 2010Co-Authors: Miki Imanishi, Shigeru Negi, Chika Imamura, Chika Higashi, Wei Yan, Shiroh Futaki, Yukio SugiuraAbstract:In contrast to the extensive understanding of the Zinc Finger-DNA interactions, less is known about Zinc Finger-Zinc Finger interactions. GATA-1 and Sp1 are transcription factors with Zinc Finger domains for DNA binding. The interaction between the GATA-1 and Sp1 Zinc Finger domains is important for synergistic transcriptional effects in erythroid genes. Despite the biological importance of the GATA-1 and Sp1 interaction, the molecular mechanism of the interaction remains unclear. We constructed a series of deletion mutants of the Zinc Finger domains of GATA-1 and Sp1 to identify the regions within the GATA-1 and Sp1 Zinc Finger domains that interact. The Zinc Finger-Zinc Finger interaction modes were also estimated from calorimetric measurements. This revealed that the interaction between the Sp1 and GATA-1 Zinc Finger domains was primarily electrostatic, and that the linker region of the Sp1 Zinc Fingers is important for the association with the GATA-1 Zinc Finger domains. We propose a new molecular mechanism for Zinc Finger-Zinc Finger interactions that should contribute to our understanding of the bio-functional role of the interaction between GATA-1 and Sp1.
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Non- Fok I-Based Zinc Finger Nucleases
Methods in molecular biology (Clifton N.J.), 2010Co-Authors: Miki Imanishi, Shigeru Negi, Yukio SugiuraAbstract:The design of functional proteins is one of the most challenging areas of protein research. We have constructed Zinc Finger peptides with metal-dependent hydrolytic abilities by mutating the Zinc ligands in classical Zinc Fingers, without the need to add a FokI or other DNA cleavage domain. The designed peptides acquired DNA cleavage ability successfully, retaining the proper Zinc Finger folding and DNA targeting ability. We have also succeeded in site-specific DNA cleavage in the presence of cerium ions by introducing a lanthanide ion-binding loop as a linker of Zinc Finger motifs.
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Novel Zinc Finger nuclease created by combining the Cys2His2- and His4-type Zinc Finger domains
Bioorganic & medicinal chemistry letters, 2009Co-Authors: Shigeru Negi, Yoshiyuki Umeda, Saeko Masuyama, Koji Kano, Yukio SugiuraAbstract:Abstract To improve the DNA hydrolytic activity of the Zinc Finger nuclease, we have created a new artificial Zinc Finger nuclease (ZWH4) by connecting two distinct Zinc Finger domains possessing different types of Zn(II) binding sites (Cys 2 His 2 - and His 4 -types). The overall fold of ZWH4 is similar to that of the wild-type Sp1 Zinc Finger (Sp1(zf123)) as revealed by circular dichroism spectroscopy. The gel mobility shift assay demonstrated that ZWH4 binds to the GC box DNA, although the DNA-binding affinity is lower than that of Sp1(zf123). Evidently, ZWH4 hydrolyzes the covalently closed circular plasmid DNA (form I) containing the GC box (pBSGC) to the linear duplex DNA (form III) in the presence of a higher concentration (50 times) of the protein than DNA for a 24-h reaction. Of special interest is the fact that the novel mixed Zinc Finger protein containing the Cys 2 His 2 - and His 4 -type domains was first created. The present results provide the useful information for the redesign strategy of an artificial nuclease based on the Zinc Finger motif.
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Design and synthesis of artificial Zinc Finger proteins.
Methods in molecular biology (Clifton N.J.), 2007Co-Authors: Wataru Nomura, Yukio SugiuraAbstract:Of the DNA-binding motifs, the (Cys)2(His)2-type Zinc Finger motif has great potential for manipulation. The Zinc Finger motif offers an attractive framework for the design of novel DNA-binding proteins. Specially, a structure-based design strategy is valuable for the creation of new artificial Zinc Finger proteins that have novel DNA-binding properties, namely, long-DNA recognition, DNA bending, and AT-rich sequence recognition. Herein, new strategies for the design of multi-Zinc Finger proteins for the recognition of a target DNA sequence, a DNA-bending Zinc Finger protein, a (His)4-type Zinc Finger protein, and an AT-recognizing Zinc Finger protein are described based on recent experimental results.
Miki Imanishi - One of the best experts on this subject based on the ideXlab platform.
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Zinc Finger Zinc Finger interaction between the transcription factors gata 1 and sp1
Biochemical and Biophysical Research Communications, 2010Co-Authors: Miki Imanishi, Shigeru Negi, Chika Imamura, Chika Higashi, Wei Yan, Shiroh Futaki, Yukio SugiuraAbstract:In contrast to the extensive understanding of the Zinc Finger-DNA interactions, less is known about Zinc Finger-Zinc Finger interactions. GATA-1 and Sp1 are transcription factors with Zinc Finger domains for DNA binding. The interaction between the GATA-1 and Sp1 Zinc Finger domains is important for synergistic transcriptional effects in erythroid genes. Despite the biological importance of the GATA-1 and Sp1 interaction, the molecular mechanism of the interaction remains unclear. We constructed a series of deletion mutants of the Zinc Finger domains of GATA-1 and Sp1 to identify the regions within the GATA-1 and Sp1 Zinc Finger domains that interact. The Zinc Finger-Zinc Finger interaction modes were also estimated from calorimetric measurements. This revealed that the interaction between the Sp1 and GATA-1 Zinc Finger domains was primarily electrostatic, and that the linker region of the Sp1 Zinc Fingers is important for the association with the GATA-1 Zinc Finger domains. We propose a new molecular mechanism for Zinc Finger-Zinc Finger interactions that should contribute to our understanding of the bio-functional role of the interaction between GATA-1 and Sp1.
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Zinc Finger–Zinc Finger interaction between the transcription factors, GATA-1 and Sp1
Biochemical and biophysical research communications, 2010Co-Authors: Miki Imanishi, Shigeru Negi, Chika Imamura, Chika Higashi, Wei Yan, Shiroh Futaki, Yukio SugiuraAbstract:In contrast to the extensive understanding of the Zinc Finger-DNA interactions, less is known about Zinc Finger-Zinc Finger interactions. GATA-1 and Sp1 are transcription factors with Zinc Finger domains for DNA binding. The interaction between the GATA-1 and Sp1 Zinc Finger domains is important for synergistic transcriptional effects in erythroid genes. Despite the biological importance of the GATA-1 and Sp1 interaction, the molecular mechanism of the interaction remains unclear. We constructed a series of deletion mutants of the Zinc Finger domains of GATA-1 and Sp1 to identify the regions within the GATA-1 and Sp1 Zinc Finger domains that interact. The Zinc Finger-Zinc Finger interaction modes were also estimated from calorimetric measurements. This revealed that the interaction between the Sp1 and GATA-1 Zinc Finger domains was primarily electrostatic, and that the linker region of the Sp1 Zinc Fingers is important for the association with the GATA-1 Zinc Finger domains. We propose a new molecular mechanism for Zinc Finger-Zinc Finger interactions that should contribute to our understanding of the bio-functional role of the interaction between GATA-1 and Sp1.
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Non- Fok I-Based Zinc Finger Nucleases
Methods in molecular biology (Clifton N.J.), 2010Co-Authors: Miki Imanishi, Shigeru Negi, Yukio SugiuraAbstract:The design of functional proteins is one of the most challenging areas of protein research. We have constructed Zinc Finger peptides with metal-dependent hydrolytic abilities by mutating the Zinc ligands in classical Zinc Fingers, without the need to add a FokI or other DNA cleavage domain. The designed peptides acquired DNA cleavage ability successfully, retaining the proper Zinc Finger folding and DNA targeting ability. We have also succeeded in site-specific DNA cleavage in the presence of cerium ions by introducing a lanthanide ion-binding loop as a linker of Zinc Finger motifs.
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Creation and characteristics of unnatural CysHis3-type Zinc Finger protein
Biochemical and Biophysical Research Communications, 2004Co-Authors: Shigeru Negi, Masako Itazu, Akiko Nomura, Miki Imanishi, Yukio SugiuraAbstract:Abstract To investigate the properties of unnatural Zinc Finger peptides with CysHis 3 -type ligand combinations, the HCHH- and CHHH-type Zinc Finger proteins (zf(HCHH) and zf(CHHH), respectively) were created by mutating Cys to His in the Cys 2 His 2 -type Zinc Finger of the transcription factor Sp1 (zf(CCHH)). The CD measurements clearly show that the single-Finger CysHis 3 -type Zinc Finger peptides (zf(HCHH)f2 and zf(CHHH)f2) are folded by complexation with Zn(II). From the gel mobility shift assays, the CysHis 3 -type Zinc Finger proteins (zf(HCHH) and zf(CHHH)) evidently bind to the GC-box DNA, though the DNA binding affinity is lower than that of the wild CCHH-type Zinc Finger protein. Furthermore, the zf(HCHH)f2 and zf(CHHH)f2 peptides catalyze the hydrolysis of the 4-nitrophenyl acetate in contrast to the catalytically inactive zf(CCHH) peptide. This is the first study of the CysHis 3 -type Zinc Finger proteins and also provides useful information for redesigning artificial metalloproteins.
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Design of novel Zinc Finger proteins: towards artificial control of specific gene expression.
European Journal of Pharmaceutical Sciences, 2001Co-Authors: Miki Imanishi, Makoto Nagaoka, Yuichiro Hori, Yukio SugiuraAbstract:Abstract In this review, we summarize design strategies for generating proteins with desired sequences such as long contiguous base pairs and diverse sequence specificities based on the nature of Cys2-His2 Zinc Finger proteins. Recent progress towards artificial DNA binding proteins has been achieved by structure-based design processes and by selection strategies. Indeed, a multi-Zinc Finger protein with an 18 (or 27)-base pair address, and new Zinc Finger proteins for diverse DNA target sites (TATA-box and p53 binding site) have been created successfully. Such novel Zinc Finger proteins will probably be useful tools in molecular biology and potentially in human medicine.
Shigeru Negi - One of the best experts on this subject based on the ideXlab platform.
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Zinc Finger Zinc Finger interaction between the transcription factors gata 1 and sp1
Biochemical and Biophysical Research Communications, 2010Co-Authors: Miki Imanishi, Shigeru Negi, Chika Imamura, Chika Higashi, Wei Yan, Shiroh Futaki, Yukio SugiuraAbstract:In contrast to the extensive understanding of the Zinc Finger-DNA interactions, less is known about Zinc Finger-Zinc Finger interactions. GATA-1 and Sp1 are transcription factors with Zinc Finger domains for DNA binding. The interaction between the GATA-1 and Sp1 Zinc Finger domains is important for synergistic transcriptional effects in erythroid genes. Despite the biological importance of the GATA-1 and Sp1 interaction, the molecular mechanism of the interaction remains unclear. We constructed a series of deletion mutants of the Zinc Finger domains of GATA-1 and Sp1 to identify the regions within the GATA-1 and Sp1 Zinc Finger domains that interact. The Zinc Finger-Zinc Finger interaction modes were also estimated from calorimetric measurements. This revealed that the interaction between the Sp1 and GATA-1 Zinc Finger domains was primarily electrostatic, and that the linker region of the Sp1 Zinc Fingers is important for the association with the GATA-1 Zinc Finger domains. We propose a new molecular mechanism for Zinc Finger-Zinc Finger interactions that should contribute to our understanding of the bio-functional role of the interaction between GATA-1 and Sp1.
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Zinc Finger–Zinc Finger interaction between the transcription factors, GATA-1 and Sp1
Biochemical and biophysical research communications, 2010Co-Authors: Miki Imanishi, Shigeru Negi, Chika Imamura, Chika Higashi, Wei Yan, Shiroh Futaki, Yukio SugiuraAbstract:In contrast to the extensive understanding of the Zinc Finger-DNA interactions, less is known about Zinc Finger-Zinc Finger interactions. GATA-1 and Sp1 are transcription factors with Zinc Finger domains for DNA binding. The interaction between the GATA-1 and Sp1 Zinc Finger domains is important for synergistic transcriptional effects in erythroid genes. Despite the biological importance of the GATA-1 and Sp1 interaction, the molecular mechanism of the interaction remains unclear. We constructed a series of deletion mutants of the Zinc Finger domains of GATA-1 and Sp1 to identify the regions within the GATA-1 and Sp1 Zinc Finger domains that interact. The Zinc Finger-Zinc Finger interaction modes were also estimated from calorimetric measurements. This revealed that the interaction between the Sp1 and GATA-1 Zinc Finger domains was primarily electrostatic, and that the linker region of the Sp1 Zinc Fingers is important for the association with the GATA-1 Zinc Finger domains. We propose a new molecular mechanism for Zinc Finger-Zinc Finger interactions that should contribute to our understanding of the bio-functional role of the interaction between GATA-1 and Sp1.
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Non- Fok I-Based Zinc Finger Nucleases
Methods in molecular biology (Clifton N.J.), 2010Co-Authors: Miki Imanishi, Shigeru Negi, Yukio SugiuraAbstract:The design of functional proteins is one of the most challenging areas of protein research. We have constructed Zinc Finger peptides with metal-dependent hydrolytic abilities by mutating the Zinc ligands in classical Zinc Fingers, without the need to add a FokI or other DNA cleavage domain. The designed peptides acquired DNA cleavage ability successfully, retaining the proper Zinc Finger folding and DNA targeting ability. We have also succeeded in site-specific DNA cleavage in the presence of cerium ions by introducing a lanthanide ion-binding loop as a linker of Zinc Finger motifs.
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Novel Zinc Finger nuclease created by combining the Cys2His2- and His4-type Zinc Finger domains
Bioorganic & medicinal chemistry letters, 2009Co-Authors: Shigeru Negi, Yoshiyuki Umeda, Saeko Masuyama, Koji Kano, Yukio SugiuraAbstract:Abstract To improve the DNA hydrolytic activity of the Zinc Finger nuclease, we have created a new artificial Zinc Finger nuclease (ZWH4) by connecting two distinct Zinc Finger domains possessing different types of Zn(II) binding sites (Cys 2 His 2 - and His 4 -types). The overall fold of ZWH4 is similar to that of the wild-type Sp1 Zinc Finger (Sp1(zf123)) as revealed by circular dichroism spectroscopy. The gel mobility shift assay demonstrated that ZWH4 binds to the GC box DNA, although the DNA-binding affinity is lower than that of Sp1(zf123). Evidently, ZWH4 hydrolyzes the covalently closed circular plasmid DNA (form I) containing the GC box (pBSGC) to the linear duplex DNA (form III) in the presence of a higher concentration (50 times) of the protein than DNA for a 24-h reaction. Of special interest is the fact that the novel mixed Zinc Finger protein containing the Cys 2 His 2 - and His 4 -type domains was first created. The present results provide the useful information for the redesign strategy of an artificial nuclease based on the Zinc Finger motif.
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Creation and characteristics of unnatural CysHis3-type Zinc Finger protein
Biochemical and Biophysical Research Communications, 2004Co-Authors: Shigeru Negi, Masako Itazu, Akiko Nomura, Miki Imanishi, Yukio SugiuraAbstract:Abstract To investigate the properties of unnatural Zinc Finger peptides with CysHis 3 -type ligand combinations, the HCHH- and CHHH-type Zinc Finger proteins (zf(HCHH) and zf(CHHH), respectively) were created by mutating Cys to His in the Cys 2 His 2 -type Zinc Finger of the transcription factor Sp1 (zf(CCHH)). The CD measurements clearly show that the single-Finger CysHis 3 -type Zinc Finger peptides (zf(HCHH)f2 and zf(CHHH)f2) are folded by complexation with Zn(II). From the gel mobility shift assays, the CysHis 3 -type Zinc Finger proteins (zf(HCHH) and zf(CHHH)) evidently bind to the GC-box DNA, though the DNA binding affinity is lower than that of the wild CCHH-type Zinc Finger protein. Furthermore, the zf(HCHH)f2 and zf(CHHH)f2 peptides catalyze the hydrolysis of the 4-nitrophenyl acetate in contrast to the catalytically inactive zf(CCHH) peptide. This is the first study of the CysHis 3 -type Zinc Finger proteins and also provides useful information for redesigning artificial metalloproteins.
Jeremy M Berg - One of the best experts on this subject based on the ideXlab platform.
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DNA UNWINDING INDUCED BY Zinc Finger PROTEIN BINDING
Biochemistry, 1996Co-Authors: Jeremy M BergAbstract:Zinc Finger domains of the Cys2His2 type are found in a large number of eukaryotic proteins. Various proteins containing these domains have been shown to bind specifically to DNA, RNA, and DNA-RNA hybrids. Structural studies of Zinc Finger protein-DNA complexes have revealed that the DNA molecules are underwound relative to canonical B-form. It has not been clear if Zinc Finger proteins recognize preexisting underwound conformations of DNA or if they induce such conformations upon binding. We report that the DNA binding domains of Sp1 and several designed Zinc Finger proteins unwind DNA upon binding. The extent of unwinding is consistent with that observed in Zinc Finger protein-DNA cocrystal structures. These DNA deformations may be important in determining overall binding affinities as well as influencing binding site preferences. Furthermore, changes in DNA conformation upon Zinc Finger protein binding may affect protein-protein interactions important for transcriptional regulation and other activities of Zinc Finger proteins.
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Specific DNA-RNA hybrid binding by Zinc Finger proteins
Science, 1995Co-Authors: Jeremy M BergAbstract:Zinc Finger proteins of the Cys2His2 type represent a large class of proteins that have been assumed to function by means of specific interactions with DNA. Experiments motivated by structural characteristics of Zinc Finger protein-DNA complexes revealed that certain Zinc Finger proteins bound DNA-RNA hybrids with affinities comparable to or greater than those for DNA duplexes. The interactions between the Zinc Finger proteins and the DNA-RNA hybrids were dependent on which strand was RNA and were sequence-specific. Thus, interactions with DNA-RNA hybrids should be considered with regard to the biological roles of Zinc Finger proteins.
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Zinc-Finger proteins
Current Opinion in Structural Biology, 1993Co-Authors: Jeremy M BergAbstract:Abstract Considerable progress has been made over the past year concerning the structures of various classes of Zinc-Finger proteins and the mechanisms by which they recognize particular nucleic acid targets. Both NMR and X-ray structures have become available for the DNA-binding domain of the yeast protein GAL4. These have revealed the detailed architecture of the Zn2(Cys)6 binuclear cluster and the accompanying structure that binds DNA. Indirect studies have yielded models for the structure of the TFIIA-5S RNA gene complex. In addition, more detailed data has become available concerning the roles of the invariant metal-binding and hydrophobic residues in stabilizing the Zinc-Finger structure. Structural information concerning the TFIIA-like Zinc Fingers has guided experiments that are leading to potentially useful rules relating to DNA binding site preference. The role of Zinc in the biological function of retroviral nucleocapsid proteins has also become clearer.
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toward rules relating Zinc Finger protein sequences and dna binding site preferences
Proceedings of the National Academy of Sciences of the United States of America, 1992Co-Authors: John R. Desjarlais, Jeremy M BergAbstract:Abstract Zinc Finger proteins of the Cys2-His2 type consist of tandem arrays of domains, where each domain appears to contact three adjacent base pairs of DNA through three key residues. We have designed and prepared a series of variants of the central Zinc Finger within the DNA binding domain of Sp1 by using information from an analysis of a large data base of Zinc Finger protein sequences. Through systematic variations at two of the three contact positions (underlined), relatively specific recognition of sequences of the form 5'-GGGGN(G or T)GGG-3' has been achieved. These results provide the basis for rules that may develop into a code that will allow the design of Zinc Finger proteins with preselected DNA site specificity.
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Identification and characterization of "Zinc-Finger" domains by the polymerase chain reaction.
Proceedings of the National Academy of Sciences of the United States of America, 1991Co-Authors: Gerald R. Pellegrino, Jeremy M BergAbstract:We have developed a method for amplifying DNA fragments containing tandem arrays of "Zinc-Finger" sequences of the transcription factor IIIA (Cys2-His2) type by using the polymerase chain reaction. Because these sequences occur as tandem arrays, a ladder of bands is produced upon amplification using primers derived from the amino- and carboxyl-terminal sequences of a Zinc-Finger domain. The "rungs" of this ladder correspond to DNA fragments encoding one Zinc-Finger domain, two adjacent Zinc-Finger domains, and so on. This is demonstrated by isolating individual bands corresponding to n Zinc-Finger domains and reamplifying them with the same primers. This yields a band of the original size as well as bands corresponding to 1 through (n - 1) Zinc-Finger domains. Direct evidence that these bands encode Zinc-Finger domains was obtained by cloning and sequencing a collection of the amplification products. Due to the lack of redundancy in the sequences obtained, we conclude that each band corresponds to a large number of unique Zinc-Finger-encoding sequences. The results from amplification reaction mixtures using genomic DNA from a variety of sources as template provide further evidence that Zinc-Finger domains occur widely and frequently in eukaryotic genomes. We believe that this method is a powerful technique for the isolation and characterization of Zinc-Finger-encoding genes.
Jong Seok Kang - One of the best experts on this subject based on the ideXlab platform.
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Correlation between functional and binding activities of designer Zinc-Finger proteins.
Biochemical Journal, 2007Co-Authors: Jong Seok KangAbstract:Rapid progress in the ability to develop and utilize Zinc-Finger proteins with customized sequence specificity have led to their increasing use as tools for modulation of target gene transcription in the post-genomic era. In the present paper, a series of in vitro binding assays and in vivo reporter analyses were used to demonstrate that a Zinc-Finger protein can effectively specify a base at each position of the target site in vivo and that functional activity of the Zinc-Finger protein as either a transcriptional repressor or activator is positively correlated with its binding affinity. In addition, this correlation can be extended to artificial engineered Zinc-Finger proteins. These data suggest that the binding affinity of designer Zinc-Finger proteins with novel specificity might be a determinant for their ability to regulate transcription of a gene of interest.
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Zinc Finger Proteins as Designer Transcription Factors
Journal of Biological Chemistry, 2000Co-Authors: Jong Seok KangAbstract:Abstract Recent progress in the design and selection of novel Zinc Finger proteins with desired DNA binding specificities now allows construction of tailor-made DNA-binding proteins that specifically recognize almost any predetermined DNA sequence. Such novel or “designer” Zinc Finger proteins with desired DNA binding specificities can serve as efficient transcription factors in various mammalian cell lines. In addition, they may be broadly useful in the regulation of endogenous genes in transgenic organisms and eventually in gene therapy applications. In this report, we use a series of transient and stable transfection experiments to demonstrate that the expression of a target gene can be controlled by changing the in vivo concentration of designer Zinc Finger proteins in a dose-dependent manner. We also report that designer Zinc Finger proteins can access their binding sites integrated into the genome and function as potent transcription factors. Our results suggest that designer Zinc Finger transcription factors that specifically recognize appropriate sites in the promoter of a target gene may have broad applications in the post-genomic era.
