Lecture 8: Genome Packing and Lecture 8: Genome Packing and AccessibilityAccessibility

Rob PhillipsCalifornia Institute of Technology

(Beautiful work of David Goodsell)

(Bustamante et al.)

Experiments on Nucleosome AccessibilityExperiments on Nucleosome Accessibility

Accessibility vs Burial DepthAccessibility vs Burial Depth

Donor Cy3

81 27

LexA Binding site

147

Acceptor Cy5

Dynamics of Nucleosomal Dynamics of Nucleosomal AccessibilityAccessibility

(Widom et al.)

The Life Cycle of a BacteriophageThe 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 Experiments Reveal Crystalline

Order for Viral DNAOrder 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 Forces and Packing Rates: As a Function of Fraction PackedFunction of Fraction Packed

(Bustamante et al.)

Force resisting further packaging

Rate of packing

Viral Packing: Relevant Scales Viral Packing: Relevant Scales

Capsid size = 40nm(Hendrix)

Persistence length of DNA, length over which DNA canbe 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 Viral Packing: Free Energy of Confinement 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 DNA-DNA Interaction: Osmotic Stress MeasurementsMeasurements

d

where F0=55000pN/nm2 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(n

m)

Percent packed

asymptote

Comparison With Experiments: Comparison With Experiments:

Geometry of PackingGeometry of Packing

Spacing of packaged DNA in capsids has been measured by cryoEM and x-rays.

(Cerritelli et al.)

HK97 Wikoff Percent packed

Fo

rce

(p

N)

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 Predictions for Packing Forces in Other

PhagePhage

(Jardine et al.)