Videos by Workshop 5: Mathematical and experimental approaches to dynamics of protein-DNA interactions
DNA Looping Probabilities and Semi-Classical Path Integrals
John Maddocks(Joint work with L. Cotta-Ramusino and R. Manning)
DNA interactions with proteins frequently involves looping in which the location and orientation of the two ends of a DNA segment are prescribed. I will show how path integral methods can be used to obtain a sequence-dependent formula for the probability of loop formation, including the case of minicircle cy...
DNA Architecture and Transcriptional Regulation: The Physics of Genome Management
Hernan GarciaDNA architecture plays a key role in determining spatial and temporal patterns of gene expression. This architecture encompasses both the nucleotide sequence (i.e., the information content) and the physical state of the DNA such as its spatial organization and mechanical properties. We study several regulatory motifs in E. coli using a three pronged approach: theoretical m...
Modeling and predicting DNA-binding specificity
Gary StormoMany different kinds of data are available for modeling the specificity of a DNA-binding protein, and the quality of the model depends on both the type of data used and the algorithms for estimating binding energies. We discuss our approaches for modeling from several different types of data, and assess the accuracy of each based on experimental measurements. Given specifi...
First-principles calculation of DNA looping in tethered particle experiments
Phil NelsonWe show how to calculate the probability of DNA loop formation mediated by regulatory proteins such as Lac repressor, using a mathematical model of DNA elasticity. Our approach has new features enabling us to compute quantities directly observable in Tethered Particle Motion (TPM) experiments; e.g. it accounts for all the entropic forces present in such experiments. Our mo...
A simple biophysical model of nucleosome positioning and energetics
Alexandre MorozovGenomic DNA is packaged into chromatin in eukaryotic cells. The fundamental building block of chromatin is the nucleosome, a 147 bp-long DNA segment wrapped around the surface of a histone octamer. Nucleosomes function to compact genomic DNA and to regulate access to it both by physical occlusion and by providing the substrate for numerous covalent epigenetic tags. We have...