# Biomod/2011/TUM/TNT/LabbookA/Calculation of intercalator concentrations

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< Biomod | 2011 | TUM/TNT/LabbookA

## Contents |

# Calculation of DNA binder concentrations

## Intention

- First approach was to determine the appropriate concentrations of DNA binders with a simple approximation:

with *K*_{D} the dissociation constant of the DNA binder, *c*_{B} the concentration of DNA binder, *c*_{bp} the concentration of base pairs and *c*_{Bbp} the concentration of the occupied basepairs

However, this formula is not suited for such small concentrations, therefore we derived a more exact one.

## Derivation

- Take the dissociation constant K
_{D}and replace the concentrations with the total concentrations of the DNA binders and base pairs:

→

and

→

- Now assume that every n-th base a DNA binder should have bound in equilibrium

- With this, we get to a K
_{D}which is only dependent on the total concentrations of base pairs (c.f. structure) and DNA binders

## Result

- Now we are able to calculate the right concentration of the DNA binders in the sample to get an occupancy of n (i.e. one DNA binder each n-th base pair)