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

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Current revision (22:24, 2 November 2011) (view source) (→Intention) |
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<math>K_{D} = \frac{c_{B}c_{bp}}{c_{B bp}}</math> | <math>K_{D} = \frac{c_{B}c_{bp}}{c_{B bp}}</math> | ||

- | with <math>K_{D}</math> the dissociation constant of the DNA binder, <math>c_{B}</math> the concentration of DNA binder, <math>c_{bp}</math> the concentration of base pairs and <math>c_{B bp}</math> the concentration of the occupied basepairs | + | with <math>K_{D}</math> the dissociation constant of the DNA binder, <math>c_{B}</math> the concentration of DNA binder, <math>c_{bp}</math> the concentration of base pairs and <math>c_{B bp}</math> the concentration of the occupied basepairs<br> |

+ | <br> | ||

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

==Derivation== | ==Derivation== |

## Current revision

## 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)