Modular dna-binding domains and methods of use

a module and dna technology, applied in the field of modules dna-binding domains and methods of use, can solve the problems of time-consuming, potentially quite costly, and technical demands of methods, and achieve the effect of enabling targeted dna modifications

Inactive Publication Date: 2011-09-29
BONAS ULLA +2
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Benefits of technology

[0012]The invention also provides a method for directed modification of a target DNA sequence by the construction of a polypeptide including at least a repeat domain of the present invention that recognizes said target DNA sequence and that said polypeptide also contains a functional domain capable of modifying the target DNA (such as via site specific recombination, restriction or integration of donor target sequences) thereby enabling targeted DNA modifications in complex genomes.

Problems solved by technology

Such methods are time intensive, technically demanding and potentially quite costly.

Method used

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  • Modular dna-binding domains and methods of use
  • Modular dna-binding domains and methods of use
  • Modular dna-binding domains and methods of use

Examples

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example 1

Identification of the Basis for DNA Specificity of TAL Effectors

[0267]The fact that AvrBs3 directly binds the UPA-box, a promoter element in induced target genes (Kay et al. (2007) Science 318, 648-651; Römer et al. (2007) Science 318:645-648), prompted us to investigate the basis for DNA-sequence specificity. Each repeat region generally consists of 34 amino acid, and the repeat units are nearly identical; however, amino acids 12 and 13 are hypervariable (Schornack et al. (2006) J. Plant Physiol. 163:256-272; FIG. 1A). The most C-terminal repeat of AvrBs3 shows sequence similarity to other repeat units only in its first 20 amino acids and is therefore referred to as half repeat. The repeat units can be classified into different repeat types based on their hypervariable 12th and 13th amino acids (FIG. 1B). Because the size of the UPA-box (18 (20) / 19 (21) bp) almost corresponds to the number of repeat units (17.5) in AvrBs3, we considered the possibility that one repeat unit of AvrBs...

example 2

Identification of a TAL Repeat Unit That Binds to G Nucleotides

[0304]The DNA binding domain of TAL effectors is composed of tandem-arranged 34-amino acid repeat units. The amino acid sequences of the repeat units are mostly conserved, except for two adjacent highly variable residues (HVRs) at positions 12 and 13 that define DNA target specificity (Boch et al. (2009) Science 326:1509-1512; Moscou & Bogdanove (2009) Science 326:1501). Functional analysis identified HVR motifs that bind preferentially to A (NI), C(HD), T (NG, IG) or equally well to G and A (NN) (Boch et al. (2009) Science 326:1509-1512). Bioinformatic analysis revealed HVRs that in the given promoter-TAL effector interactions match specifically to G (Moscou & Bogdanove (2009) Science 326:1501). However this, analysis was based on a single (HN & NA) or two (NK) interaction sites. In our view the number of interaction sites is too low to make reliable conclusions on the HVR specificity. Yet, these HVRs can be considered ...

example 3

Method for Generation of Designer Effectors via Golden Gate Cloning

[0307]The DNA binding domain of TAL effectors is composed of tandem-arranged 34-amino acid repeat units. The amino acid sequences of the repeat units are mostly conserved, except for two adjacent highly variable residues (HVRs) at positions 12 and 13 that define DNA target specificity (Boch et al. (2009) Science 326:1509-1512; Moscou & Bogdanove (2009) Science 326:1501). Different HVR motifs bind with different levels of specificity to individual A, C, G or T nucleotides. Importantly, statistical analysis suggests that tandem arranged repeat units do not to interfere with the specificity of adjacent units (Moscou & Bogdanove (2009) Science 326:1501). Thus modular assembly of repeat units with pre-characterized specificities is likely to provide an efficient way for generation of DNA-recognition modules with desired DNA specificity.

[0308]However, the generation of DNA constructs that encode desired repeat domains is c...

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Abstract

The present invention refers to methods for selectively recognizing a base pair in a DNA sequence by a polypeptide, to modified polypeptides which specifically recognize one or more base pairs in a DNA sequence and, to DNA which is modified so that it can be specifically recognized by a polypeptide and to uses of the polypeptide and DNA in specific DNA targeting as well as to methods of modulating expression of target genes in a cell.

Description

CROSS-REFERENCE TO RELATED APPLICATIONS[0001]This application is a continuation-in-part of U.S. Ser. No. 13 / 016,297, filed Jan. 28, 2011 which is a continuation of International Application PCT / IB2010 / 000154, filed Jan. 12, 2010, which designates the U.S and was published by the International Bureau in English on Jul. 15, 2010, and which claims the benefit of U.S. Provisional Patent Application No. 61 / 225,043, filed Jul. 12, 2009, European (EP) Patent Applicaiton No. 09165328.7, filed Jul. 13, 2009, German (DE) Patent Application No. 102009004659.3, filed Jan. 12, 2009; all of which are hereby incorporated herein in their entirety by reference.TECHNICAL FIELD OF THE INVENTION[0002]The present invention refers to methods for selectively recognizing a base pair in a target DNA sequence by a polypeptide, to modified polypeptides which specifically recognize one or more base pairs in a target DNA sequence and, to DNA which is modified so that it can be specifically recognized by a polyp...

Claims

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Application Information

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Patent Type & Authority Applications(United States)
IPC IPC(8): A01K67/00C12N9/96C12N5/10C12N1/15C12N1/21C12N15/63C07K1/00C07H21/04A01H15/00A01H5/00
CPCC12N15/1034C12N2501/998C12N15/8217C12N15/8238C12N15/8239C12N15/825C12N15/8279C12Q1/6816G01N33/5308C12N15/8216C07K14/195C12N5/0602C12N5/04C12N1/20C12Q2563/119C12Q2565/113C07H21/04C07K14/001C07K2319/09C07K2319/60C07K2319/80
Inventor BONAS, ULLABOCH, JENSSTREUBEL, JANA
Owner BONAS ULLA
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