2015/05/05 by Yonatan Savir Jacob Kagan, Tsvi Tlusty, Kagan, Yonatan Savir Jacob +1
Biochemistry, Genetics and Molecular Biology · #Advanced biosensing and bioanalysis techniques #Biological Physics (physics.bio-ph) #DNA and Nucleic Acid Chemistry #FOS: Biological sciences #FOS: Physical sciences #Fractal and DNA sequence analysis #Genomics (q-bio.GN) #Genomics and Chromatin Dynamics #Molecular Networks (q-bio.MN) #RNA and protein synthesis mechanisms
paper · pdf · doi:10.48550/arxiv.1505.01215
openalex publication_date 2015/05/05 · openalex created_date 2022/09/30 · openalex updated_date 2026/07/28
We examine the binding of transcription factors to DNA in terms of an\ninformation transfer problem. The input of the noisy channel is the biophysical\nsignal of a factor bound to a DNA site, and the output is a distribution of\nprobable DNA sequences at this site. This task involves an inherent tradeoff\nbetween the information gain and the energetics of the binding interaction -\nhigh binding energies provide higher information gain but hinder the dynamics\nof the system as factors are bound too tightly. We show that adaptation of the\nbinding interaction towards increasing information transfer under a general\nenergy constraint implies that the information gain per specific binding energy\nat each base-pair is maximized. We analyze hundreds of prokaryote and eukaryote\ntranscription factors from various organisms to evaluate the discrimination\nenergies. We find that, in accordance with our theoretical argument, binding\nenergies nearly maximize the information gain per energy. This work suggests\nthe adaptation of information gain as a generic design principle of molecular\nrecognition systems.\n