Lecture 8: Genome Packing and Accessibility Rob Phillips California Institute of Technology (Beautiful work of David Goodsell) (Bustamante et al.)

Experiments on Nucleosome Accessibility

Accessibility vs Burial Depth

Donor Cy LexA Binding site 147 Acceptor Cy5 Dynamics of Nucleosomal Accessibility (Widom et al.)

The Life Cycle of a Bacteriophage The life cycle involves the infection of the host cell (i.e. injection of its DNA into that cell), exploitation of the machinery of the host cell to make the relevant proteins and DNA, self-assembly and destruction of the host cell. Each stage involves fascinating physical processes as evidenced by kinetic verbs – infection, replication, assembly, packing, etc. Model systems for quantitative analysis. Rate of packing: 100bp/sec Self-assembly

Experiments Reveal Crystalline Order for Viral DNA Experiments Reveal Crystalline Order for Viral DNA Cryo-electron microscopy reveals that the packaged DNA is highly ordered. Crystalline order characterized by concentric rings of DNA wrapped around a central axis. (Cerritelli et al.)

Forces and Packing Rates: As a Function of Fraction Packed (Bustamante et al.) Force resisting further packaging Rate of packing

Viral Packing: Relevant Scales Capsid size = 40nm (Hendrix) Persistence length of DNA, length over which DNA can be thought of as being stiff. There is a negative charge every.17nm of length along DNA – electrostatic energy crucial also. Note: kT = 4.1 pN nm – coexistence of thermal and deterministic forces Governing dimensionless parameter

Viral Packing: Free Energy of Confinement DNA has elasticity DNA is charged The idea: set up a free energy function that reflects the competition between these two effects (Riemer et al.,Odijk, Gelbart et al.) Hoop model of packed DNA

DNA-DNA Interaction: Osmotic Stress Measurements d where F 0 =55000pN/nm 2 and c=.27nm. The measured pressure can be turned into an interaction energy between pairs of DNA strands. This energy, per strand length is: Rau and Parsegian

(nm) T7 (nm) Percent packed asymptote Comparison With Experiments: Geometry of Packing Spacing of packaged DNA in capsids has been measured by cryoEM and x-rays. (Cerritelli et al.)

HK97Wikoff Percent packed Force (pN) T7 HK97 29 T4 Consider several other bacteriophage under same conditions as that of the Bustamante experiment. Maximum force in the case of T7 nearly a factor of two larger than that in phi29. (Significance for motors in these other phage?) Predictions for Packing Forces in Other Phage (Jardine et al.)

How Big is a Genome? Part 2

Polymers as Random Walks Bustamante et al.