Sequence-specificity and energy landscapes of DNA-binding molecules

Abstract

A central goal of biology is to understand how transcription factors target and regulate specific genes and networks to control cell fate and function. An equally important goal of synthetic biology, chemical biology, and personalized medicine is to devise molecules that can regulate genes and networks in a programmable manner. To achieve these goals, it is necessary to chart the sequence specificity of natural and engineered DNA-binding molecules. Cognate site identification (CSI) is now achieved via unbiased, high-throughput platforms that interrogate an entire sequence space bound by typical DNA-binding molecules. Analysis of these comprehensive specificity profiles is facilitated through the use of sequence-specificity landscapes (SSLs). SSLs reveal new modes of sequence cognition and overcome the limitations of current approaches that yield amalgamated "consensus" motifs. The landscapes also reveal the impact of nonconserved flanking sequences on binding to cognate sites. SSLs also serve as comprehensive binding energy landscapes that provide insights into the energetic thresholds at which natural and engineered molecules function within cells. Furthermore, applying the CSI binding data to genomic sequence (genomescapes) provides a powerful tool for identification of potential in vivo binding sites of a given DNA ligand, and can provide insight into differential regulation of gene networks. These tools can be directly applied to the design and development of synthetic therapeutic molecules and to expand our knowledge of the basic principles of molecular recognition.