DNA-binding proteins of the zinc-finger class

Details DNA-binding proteins of the zinc-finger class DNA-binding proteins of the zinc-finger class

1999-02-19

2001-03-20

Brusca, John S. (Department: 1631)

Data processing: measuring, calibrating, or testing

Measurement system in a specific environment

Chemical analysis

C712S200000

Reexamination Certificate

active

06205404

ABSTRACT:

BACKGROUND OF THE INVENTION
A superfamily of eukaryotic genes encoding potential nucleic-acid-binding proteins contains zinc-finger (ZF) domains of the Cys
2
-His
2
(C
2
H
2
) class. Proteins that have these characteristic structural features play a key role in the regulation of gene expression[1-4]. Sequence comparisons, mutational analyses, and a recent crystallographic investigation have revealed that each finger domain, as a rule, interacts with the major groove of B-form DNA through contacts with some or all three base pairs within a DNA triplet. These base-specific interactions are mediated through amino acid (AA) side chains at specific positions in the a-helical region [5-10] of the protein domain.
Although the AA sequences of more than 1,300 ZF motifs have been identified, the exact DNA-binding sites are known only for a few proteins. The available information on DNA contact regions concerns mainly guanine-cytosine-rich strands [5-9] and fewer adenine-thymine-rich sites [11,12]. On the basis of experimental data, the first proposals for rules relating ZF sequences to preferred DNA-binding sites have been made [13,14]. However, no general rules for ZF protein-DNA recognition have been proposed. This is likely due to the fact that neither computer modeling [2,3,5] nor crystallographic analysis [7] have provided enough information on the overall structural variety in the ZF-DNA contact region.
Using physical atomic-molecular models to characterize the steric conditions in the specific contact positions for different ZF-DNA interactions, an objective of the work leading to the present invention was to determine a set of general rules for ZF-DNA recognition for the C
2
H
2
class of ZF domains. Once this objective had been reached, the work of the invention plan was to develop an algorithm, and a computer system using the algorithm, to design effective zinc-finger DNA-binding polypeptides. The achievement of these goals represents a major advance of knowledge in the field, knowledge characterized by the disclosures of Rebar, et. al. and Beerli, et. al. [15,16]. These two disclosures are concerned with the selection, using the phage display system, of specific zinc fingers with new DNA-binding specificities. On the other hand, the present disclosure is concerned with the design of DNA-binding proteins for any given DNA sequence.
SUMMARY OF THE INVENTION
The invention is directed to the design and specification of DNA-binding proteins binding via C
2
H
2
zinc-finger motifs (DBP's or, individually, a DBP). On the basis of the studies described herein, general rules for optimizing such binding have been determined, and a formula describing the class of DBP's having optimal DNA-binding properties has been constructed. Furthermore, a program has been developed, based on the rules, which affords the design of DBP's with such high binding affinity for any given DNA sequence. Lastly, rules have been determined for the design of DBP's which, while not having optimal binding, do have significant and useful DNA-binding properties.


REFERENCES:
patent: 5579250 (1996-11-01), Balaji et al.
Choo et al., “In vivo repression by a site-specific DNA-binding protein designed against an oncogenic sequence,” Nature, (1994), vol. 372, pp. 642-645.*
Pomerantz et al., “Structure-Based Design of Transcription Factors,” Science, (1995), vol. 267, pp. 93-96.*
Choo et al., “Selection of DNA binding sites for zinc fingers using rationally randomized DNA revels coded interactions,” Proc. Natl. Acad. Sci. USA, (1994), vol. 91, pp. 11168-11172.

Affiliated with

Also associated with

Rating

DNA-binding proteins of the zinc-finger class does not yet have a rating. At this time, there are no reviews or comments for this patent.

If you have personal experience with DNA-binding proteins of the zinc-finger class, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and DNA-binding proteins of the zinc-finger class will most certainly appreciate the feedback.

Rate now

Comments { 0 }

Profile ID: LFUS-PAI-O-2456450