PT  - JOURNAL ARTICLE
AU  - F Gago
AU  - W G Richards
TI  - Netropsin binding to poly[d(IC)].poly[IC)] and poly[d(GC].poly[d(GC)]: a computer simulation.
DP  - 1990 Mar 01
TA  - Molecular Pharmacology
PG  - 341--346
VI  - 37
IP  - 3
4099  - http://molpharm.aspetjournals.org/content/37/3/341.short
4100  - http://molpharm.aspetjournals.org/content/37/3/341.full
SO  - Mol Pharmacol1990 Mar 01; 37
AB  - The thermodynamic cycle perturbation approach has been used to calculate the difference in the free energy of binding of netropsin to two different DNA molecules. In the computer simulations, all the inosine residues have been gradually 'mutated' into guanosine in a DNA dodecamer and in a complex of the same dodecamer with netropsin. The difference in binding free energy of about 4.3 kcal mol-1 agrees well with the experimentally determined value of 4.0 kcal mol-1. One structural determinant of the specificity seems to be the width of the minor groove in the two complexes.