Interactive Chromatin Folding

Sequence Input Options:

Default Sequennce

Type Sequennce

Upload Sequennce

The default sequence selection will use the MMTVV011 sequence in the sample sequence menu below.

If you would like to type your sequence, please insert your sequence here

Fast Directions: 
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Click GO (this will use a default sequence (MMTV under samples) and the default parameters listed on the left).

Detailed Information:

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The sequence must be greater than 147 characters to accommodate a nucleosome. Shorter sequences produce only an ideal B-form dsDNA structure.  The energy landscape and other data are returned quickly for 1000-2000bp but Jmol takes awhile to display.
  
On 'go' a  separate window opens with a nucleosome energy level diagram and two Jmol panels. The red bars on the energy level diagram indicate nucleosome positions.

One panel will contain a molecular model of the ideal shape of nucleosome free dsDNA and the other will contain the folded conformation.

By default 50% of the possible positions are occupied using the lowest energy positions inthe energy level diagram. Change the linker length and the percent occupancy using the options below.

Setting the 'Percent Occupancy'  to '0' results in a regular packing of nucleomes separated by the specified linker length. The energy landscape is ignored in this case.

Try one of our samples here:

Sample Sequences

Discuss how sequence affects comformation.

Sample Sequence References

A. Scipioni, S. Pisano, C. Anselmi, M. Savino, P. De Santis, 2004, Biophys. Chem. v.107, p.7

Nucleosome Placement Options

Use Energy Calculations

Specify Nucleosome Placement

Energy Options E_nuc = ½ &sum(K(X - X₀)²)

K =

FORCE CONSTANT

TEXT

;

X =

Nucleosome Geometry

Brief discussion of what X does

Nucleosome Geometry

KO, KI => Bishop 2008
pdbid => See RCSB.org

;

X₀ =

;