Multi-alphabet consensus algorithm for identification of low specificity protein-DNA interactions

Multi-alphabet consensus algorithm for identification of low specificity protein-DNA interactions.

A method for the identification and characterization of protein-DNA interactions is presented. We have developed an approach for finding unknown multiple patterns that occur imperfectly in a set of several sequences. The pattern may contain letters from the nucleotide alphabet (A, C, G and T) including ambiguous characters (A/C, A/G, A/T; A/C/G, etc.). This method reveals weak DNA signals on an...

On the specificity of DNA-protein interactions.

In this paper we summarize the various factors that must be considered in establishing the operational specificity of the binding of a protein regulator of gene expression to a DNA target site. We consider informational (combinatorial) aspects of binding-site specification, actual recognition mechanisms, and the thermodynamics of target-site selection against a background of competing pseudospe...

The Specificity of Protein-DNA Interactions

Protein-DNA interactions are vital for living organisms. From viruses to humans, the interactions of these two different classes of biopolymers control processes as important and diverse as the expression of genes and the replication, rearrangement, and repair of DNA itself. These processes occur with exquisite specificity. It is still not well understood, however, how this specificity occurs. ...

Nonspecific DNA bending and the specificity of protein-DNA interactions.

Specificity, free energy and information content in protein-DNA interactions.

Site-specific DNA-protein interactions can be studied using experimental and computational methods. Experimental approaches typically analyze a protein-DNA interaction by measuring the free energy of binding under a variety of conditions. Computational methods focus on alignments of known binding sites for a protein, and, from these alignments, make estimates of the binding energy. Understandin...