Sequence-directed DNA-binding molecules compositions and methods
First Claim
1. A method for altering the binding characteristics of a DNA-binding protein to a duplex DNA, comprisingcontacting the duplex DNA with a small molecule characterized by sequence-preferential binding to a target region where, when the small molecule is bound to the target region, the small molecule is adjacent to a binding site for the DNA-binding protein and not overlapping the binding site for the DNA-binding protein by more than four basepairs, at a concentration of small molecule effective to alter the binding of the DNA-binding protein to its binding site of the duplex DNA.
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Abstract
The present invention defines a DNA:protein-binding assay useful for screening libraries of synthetic or biological compounds for their ability to bind DNA test sequences. The assay is versatile in that any number of test sequences can be tested by placing the test sequence adjacent to a defined protein binding screening sequence. Binding of molecules to these test sequence changes the binding characteristics of the protein molecule to its cognate binding sequence. When such a molecule binds the test sequence the equilibrium of the DNA:protein complexes is disturbed, generating changes in the concentration of free DNA probe. Numerous exemplary target test sequences (SEQ ID NO:1 to SEQ ID NO:600) are set forth. The assay of the present invention is also useful to characterize the preferred binding sequences of any selected DNA-binding molecule.
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Citations
15 Claims
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1. A method for altering the binding characteristics of a DNA-binding protein to a duplex DNA, comprising
contacting the duplex DNA with a small molecule characterized by sequence-preferential binding to a target region where, when the small molecule is bound to the target region, the small molecule is adjacent to a binding site for the DNA-binding protein and not overlapping the binding site for the DNA-binding protein by more than four basepairs, at a concentration of small molecule effective to alter the binding of the DNA-binding protein to its binding site of the duplex DNA.
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10. A method for inhibiting the binding of a DNA-binding protein to duplex DNA, comprising
contacting a compound with a duplex DNA which contains a test sequence adjacent to and not overlapping by more than four basepairs a screening sequence, where the DNA-binding protein binds to the screening sequence in the absence of the compound, where the compound binds to the test sequence without binding to more than four basepairs of said screening sequence, and further where the binding of said compound to the test sequence inhibits the binding of the DNA-binding protein to the screening sequence.
Specification