Issue October 2008

category image Volume 26
No. 2 (p 163-272)
October 2008
ISSN 0739-110

Distribution of Unselectively Bound Ligands Along DNA (p. 187-196)

Unselective and reversible adsorption of ligands on DNA for a model of binding proposed by Zasedatelev, Gursky, and Volkenshtein is considered. In this model, the interaction between neighboring ligands located at the distance of i binding centers is characterized by the statistical weight ai. Each ligand covers L binding centers. For this model, expressions for binding averages are represented in a new simple form. This representation is convenient for the calculation of the fraction of inter-ligand distances of i binding centers fd(i) and the fraction of binding centers included in the distances of i binding centers fbc(i) for various types of interaction between bound ligands. It is shown that, for non-cooperative binding, contact cooperativity and long-range cooperativity, the fraction of the zero inter-ligand distance fd(0) is maximal at any relative concentration of bound ligands (r). Calculations demonstrate that, at low r, fd(0) approximately r · ao, and fd(i) approximately r at 1 ≤ i < 0.3 · r-1 for non-cooperative binding (ai = 1 for all i) and contact inter-ligand interaction (ao ≠ 1, ai = 1 for i ≠ 0). The function fd(i) decreases in this i interval, but the decrease is very slow. If i > 1/r-L, then fd(i) rapidly decreases with i at any r for all types of inter-ligand interaction. At high ligand concentration (r is close to rmax = L-1), fd(0) is close to unity and fd(i) rapidly decreases with i for any type of inter-ligand interaction. For strong contact cooperativity, fd(0) is close to unity in a much lager r interval ((0.5-1) · rmax), and fd(1) ? ao-1 at r ∼ 0.5 · rmax. In the case of long-range interaction between bound ligands, the dependence fd(i) is more complex and has a maximum at i ∼ (1/r-L)1/2 for anti-cooperative binding. fbc(i) is maximal at i approximately 1/r-L for all types of binding except the contact cooperativity. A strong asymmetry in the influence of contact cooperativity and anticooperativity on the ligand distribution along DNA is demonstrated.

Dmitri Y. Lando1,*
Yury D. Nechipurenko2

1Institute of Bioorganic Chemistry
Belarus National Academy of Sciences
5/2, Kuprevich Str.
220141, Minsk, Belarus
2Engelhardt Institute of Molecular Biology
Russia Academy of Sciences
32, Vavilov str.
119991 Moscow, Russia
*lando@iboch.bas-net.by

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