ZiFDB version 1.0

Department of Genetics, Development and Cell Biology

ZiFDB houses information on individual zinc fingers as well as zinc finger arrays. To retrieve information about a particular zinc finger, any combination of three search criteria can be used: target triplet, finger position and/or finger source (see definitions below). By providing partial information, a list of all fingers matching the input is returned. By clicking the link in the article or experiment column, detailed information about related citations or experiments is displayed.

To search for information about an array, the user must provide the nucleotide triplets (subsites) recognized by each finger in the array. The database returns not only the arrays recognizing the three inputted subsites, but also arrays matching any two of the three inputted subsites. This partial information may inform the design of novel ZFAs by providing the user with a two finger framework that can be modified and tested for function. For arrays that match only two of the inputted subsites, the matching subsites and their recognition helices are colored in red for easy identification. The output also provides the amino acid sequence of the array, IDs for each finger in the array, and IDs for related articles or experiments. By clicking the relevant ID, the user is directed to information on specific fingers, articles or experiments.

To enhance its utility, ZiFDB is linked to the output from ZiFiT - a web accessible software package that assists biologists in finding sites for engineering zinc finger proteins within target genes. In ZiFiT, a user pastes a DNA sequence into a window, and although there are several versions of the software and a number of user-selected parameters that make each search unique, all versions provide the user with a list of potential target sites in the input sequence for which Consortium-developed reagents are available for ZFA engineering. The output of ZiFiT is directly linked to ZiFDB; that is, by clicking on a target sequence provided as output, the user initiates a search of the arrays in ZiFDB to determine if any exist that completely or partially match the target sequence. Similarly, a ZiFiT user can get information about a finger that recognizes a specific subsite by clicking on the triplet; the finger information will be automatically returned from the database. Thus, the ZiFiT and ZiFDB work synergistically to aid in ZFA design.

Information in ZiFDB about zinc finger modules includes:

• Triplet target: The sequence is provided for the cognate 3 bp DNA target of each finger.
• Recognition helix: The sequence is provided for the seven amino acids that constitute the DNA recognition helix, namely positions -1 to +7 relative the start of the alpha helix in the finger.
• Position with a three-finger array:Some fingers were designed to function optimally at certain positions within a three finger array. The fingers described by Sangamo BioSciences, for example, were selected at different positions within a three finger protein, and the recognition helices for the same triplet target at different positions in a three finger protein usually differ. This is likely due to position and context effects. In addition, the fingers generated in the Joung lab by OPEN were selected to function at a specific position within a three finger protein. The database records position information for the fingers described by Sangamo BioSciences and generated by OPEN.
• Source: The name of the group that generated the zinc finger is provided. The groups at present include the Barbas and Joung laboratories, Sangamo BioSciences and ToolGen.
• Amino acid sequence: The amino acid sequence of the entire finger is provided.
• Article: If the finger is published, a link to the relevant citation is provided so the user can get more detailed information about a particular finger.
• Experiment: If the finger has not been published, a link to information is provided that describes the method used to generate the finger, relevant functional data and other observations made by the experimenter.

Information in ZiFDB about zinc finger arrays includes:

• Identification numbers(IDs) of the component fingers: The IDs allow a user to look up detailed information about individual zinc fingers in an array.
• Binding subsites: These sequences correspond to the 3 bp nucleotide target of the corresponding component finger.
• Recognition helices: For each finger in an array, the sequence is provided of the seven amino acids that make up the recognition helix.
• Articles: If the array is published, a link to the relevant citation is provided so the user can get more detailed information about that array.
• Experiment: If the array has not been published, a link to information is provided that describes the method used to generate the arrays and relevant functional data or other observations made by the experimenter.

Voytas Laboratory
University of Minnesota
Phone:(612) 626-4509
Email: voytas@umn.edu