Zinc Finger Tools
Zinc Finger Tools designs amino acid sequences for zinc finger proteins and identifies DNA target sites to enable targeted gene regulation and zinc finger nuclease (ZFN) design.
Key Features:
- Target Site Identification: Identifies potential DNA target sites from user-supplied sequences suitable for zinc finger binding for gene regulation or nuclease targeting.
- Design of Zinc Finger Proteins: Generates amino acid sequences for zinc finger proteins (ZFPs) predicted to bind specified DNA target sites, supporting design of artificial transcription factors or ZFNs.
- Reverse Engineering Utility: Predicts DNA binding sites from known ZFP amino acid sequences to infer target loci.
- Database of Zinc Finger Domains: Utilizes a database of experimentally characterized zinc finger domains annotated for specificity and affinity to assemble polydactyl proteins recognizing extended DNA sequences.
Scientific Applications:
- Gene Regulation Studies: Enables design of artificial transcription factors to upregulate or downregulate specific genes for functional studies.
- Phenotype Selection: Facilitates selection of transcription factor–DNA interactions to modulate gene expression for phenotype selection in cell lines.
- Nuclease Targeting: Supports design of zinc finger nucleases (ZFNs) for targeted genome editing, including creation of targeted mutations or insertions.
Methodology:
Integration of specificity data with computer modeling to refine zinc finger domain design and predict binding affinities.
Topics
Details
- Tool Type:
- web application
- Operating Systems:
- Linux, Windows, Mac
- Added:
- 2/10/2017
- Last Updated:
- 11/25/2024
Operations
Publications
Blancafort P, Magnenat L, Barbas CF. Scanning the human genome with combinatorial transcription factor libraries. Nature Biotechnology. 2003;21(3):269-274. doi:10.1038/nbt794. PMID:12592412.
Dreier B, Segal DJ, Barbas CF. Insights into the molecular recognition of the 5′-GNN-3′ family of DNA sequences by zinc finger domains 1 1Edited by M. Yaniv. Journal of Molecular Biology. 2000;303(4):489-502. doi:10.1006/jmbi.2000.4133. PMID:11054286.
Dreier B, Fuller RP, Segal DJ, Lund CV, Blancafort P, Huber A, Koksch B, Barbas CF. Development of Zinc Finger Domains for Recognition of the 5′-CNN-3′ Family DNA Sequences and Their Use in the Construction of Artificial Transcription Factors. Journal of Biological Chemistry. 2005;280(42):35588-35597. doi:10.1074/jbc.m506654200. PMID:16107335.
Mandell JG, Barbas CF. Zinc Finger Tools: custom DNA-binding domains for transcription factors and nucleases. Nucleic Acids Research. 2006;34(Web Server):W516-W523. doi:10.1093/nar/gkl209. PMID:16845061. PMCID:PMC1538883.
Dreier B, Beerli RR, Segal DJ, Flippin JD, Barbas CF. Development of Zinc Finger Domains for Recognition of the 5′-ANN-3′ Family of DNA Sequences and Their Use in the Construction of Artificial Transcription Factors. Journal of Biological Chemistry. 2001;276(31):29466-29478. doi:10.1074/jbc.m102604200. PMID:11340073.
Segal DJ, Dreier B, Beerli RR, Barbas CF. Toward controlling gene expression at will: Selection and design of zinc finger domains recognizing each of the 5′-GNN-3′ DNA target sequences. Proceedings of the National Academy of Sciences. 1999;96(6):2758-2763. doi:10.1073/pnas.96.6.2758. PMID:10077584. PMCID:PMC15842.