Download Structure of DNA in Nucleus

HIV Entry into the Nucleus and
Organization of the Genome
Over the Next 3 lectures we will analyze the mechanism of virus
entry into the nucleus and its propagation in the nucleus.
Principles to be covered
A. Directed Diffusion
B. Osmolarity
C. Motor and Topoisomerase Function
Structure of HIV Reverse Transcriptase
Nucleosome Structure
Nuclear Localization Signals
Cause Transport to Nucleus
Nuclear Transport is DiffusionDependent
In Smaller Cells Transport from the Cytoplasm to the Nucleus
is Dependent upon thermal energy through random diffusion.
One-dimensional random walk with a flip of a coin and a step
in + or - direction gives a Gaussian distribution with many
particles and long time.
Diffusive Processes Can be
Described by Diffusion Equation
Einstein-Smoluchowski equation relates the
friction coefficient of a particle moving through
a medium to the diffusion coefficient of the
particle in that medium.
Dsphere = kT/d = kT/6r
Frictional Coefficient d = 6r
Where  = viscosity and r = radius
Diffusive Movements Depend
Upon the Square of Distance
For one-dimensional diffusion 2D1t = <X2>
For two-dimensional diffusion 4 D2t = <X2+Y2>
Example: 1 mm sphere Dsphere = 4.4 x 10-9 cm2/sec
After 10s <X2> = 8.8 x 10-8 cm2
X = 3 x 10-4 cm = 3 mm
Large Particles (~26 nm) Can be
Transported (Diffusive Pores <9 nm)
Nuclear Pore Complex Structure
Princ of Virology. Flint et al.
Fig. 5.19
Model of Nuclear Import
Princ of Virology. Flint et al. Fig. 5.20
Ran-GTP-GDP Exchange
Catalyzes the Transport
Another Way to Enter the
Nucleus?
Some viruses don’t have a nuclear
localization signal. The other way to enter
the nucleus is to wait for nucleus breakdown
in mitosis. At that time the nuclear
membrane moves into the ER and
vesiculates.
Nucleus Moves into ER-like
Vesicles During Mitosis
Nuclear Lamins Provide a
Structural Support for Nucleus
DNA Packaging Problem
There are 2 physical problems that must be overcome in
packaging the 2 meters of double stranded DNA in a
nucleus of about 6 mm in diameter.
A. Packing Problem: How to fold the DNA to fit into the
nucleus.
B. Osmolarity: Each base has a negative charge and that
charge needs to be balanced by a plus charge, commonly
potassium is cytoplasm.
Osmolarity in the Nucleus
Osmolarity in cytoplasm: typically 310 milli osmolar,
which is the sum of the concentration of potassium,
sodium, chloride, phosphate, and other charged small
molecules. Neutrality is always preserved (concentration
of minus equals conc of minus ions)
Osmolarity in nucleus: cytoplasmic ions and small
molecules plus counterions for DNA? (2 X 6 x 109
Phosphate anions- or 2 x 10-14 moles of P- in 4/3r3 = 410 X 10-14 l or 0.2-0.5 M of negative charge that needs
counterions)
Structure of DNA
in Nucleus
Nucleosome Structure
DNA Superhelicity and Knots
Unwinding of DNA for replication or transcription introduces
superhelicity in the DNA.
Movement of DNA can create knots or tangles (as in fishing
line) that can only be straightened out by breaking the line.
Topoisomerase I
Topoisomerase II
Reading for Next Class
Alberts et al., MBOC (vol.4) Chapters 5 and 6 on DNA
replication and transcription.
Alternatively, read the equivalent chapters in one of the other
Cell Biology Texts.