Quantitative assessment of the interplay between DNA elasticity and cooperative binding of ligands.
Binding of ligands to DNA can be studied by measuring the change of the persistence length of the complex formed, in single-molecule assays. We propose a methodology for persistence length data analysis based on a quenched disorder statistical model and describing the binding isotherm by a Hill-type equation. We obtain an expression for the effective persistence length as a function of the total ligand concentration, which we apply to our data of the DNA-cationic β-cyclodextrin and to the DNA-HU protein data available in the literature, determining the values of the local persistence lengths, the dissociation constant, and the degree of cooperativity for each set of data. In both cases the persistence length behaves nonmonotonically as a function of ligand concentration and based on the results obtained we discuss some physical aspects of the interplay between DNA elasticity and cooperative binding of ligands.
Departamento de Física, ICEx, Universidade Federal de Minas Gerais, Caixa Postal 702, CEP 31270-901 Belo Horizonte, Minas Gerais, Brazil.
L
L
Siman
I S S
IS
Carrasco
J K L
JK
da Silva
M C
MC
de Oliveira
M S
MS
Rocha
O N
ON
Mesquita
D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism; D004548:Elasticity; D008024:Ligands; D008956:Models, Chemical; D015233:Models, Statistical; D013329:Structure-Activity Relationship; D047392:beta-Cyclodextrins / Q000737:chemistry / Q000378:metabolism
D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; D008024:Ligands; D047392:beta-Cyclodextrins; C040330:histone-like protein HU, bacteria; D004247:DNA; C031215:betadex