Transition on the entropic elasticity of DNA induced by intercalating molecules

Abstract

We use optical tweezers to perform stretching experiments on DNA molecules when interacting with the drugs daunomycin and ethidium bromide, which intercalate the DNA molecule. Our results show that the persistence length of the DNA-drug complexes increases strongly as the drug concentration increases up to some critical value. Above this critical value, the persistence length decreases abruptly and remains approximately constant for larger drug concentrations, at least in the concentration range used in our experiments. Measured intercalators critical concentrations for the persistence length transition coincide with the reported values for the helix-coil transition of DNA-drug complexes obtained from sedimentation experiments. The contour length of the molecules increases monotonically and saturates as the drug concentration increases. The neighbor exclusion model fits to our results for the total drug concentration as a function of the relative increase of the contour length.

DNA-psoralen: Single-molecule experiments and first principles calculations

“…[6] for details). Considering that each intercalated psoralen molecule increases the length of DNA by the base-pair distance 0.34 nm [4], Θ is equal to the intercalated psoralen fraction r. In this case the NEM gives…”

“…and ethidium bromide (EtBr), exhibit intercalative binding [1,3,6]. Psoralen, by contrast, presents other forms of linkage to the DNA bases.…”

“…The details about our experimental setup, experimental procedure, and optical-tweezers calibration can be found in Refs. [5,6,11].…”

Structure of DNA Coils in Dilute and Semidilute Solutions

“…At EtBr concentrations in the 5 to 20 M range in phosphate buffered saline, dye intercalation extends DNA contour length by a factor of $1:4 but does not affect its persistence length [21,22]. We use 10 M EtBr concentrations at which the dye binds DNA in $1:5 dye=base pair ratio.…”

Marginal Nature of DNA Solutions

“…Data in [28] were used to calculate dye quantities in order to keep bound dye per bp ratio constant at 1:5 for each DNA concentration. In this dye: bp ratio range, DNA properties are rather insensitive to the exact values of the ratio; such labeling does not change DNA persistence length, although it extends DNA contour length by $1:4 factor to L % 22 m [28].…”