Modeling the entropic structural transition of DNA complexes formed with intercalating drugs

2014

Eur Biophys J

We have performed single molecule stretching experiments and dynamic light scattering (DLS) in order to characterize the interaction between the DNA molecule and the fluorescent stain GelRed. The results from single molecule stretching show that the persistence length of the DNA-GelRed complexes increases as the ligand concentration increases up to some critical concentration, then decreasing for higher concentrations. The contour length of the complexes, on the other hand, increases monotonically as a function of GelRed concentration, suggesting that intercalation is the main binding mechanism. In order to characterize the physical chemistry of the interaction, we use the McGhee-von Hippel binding isotherm to extract the physicochemical parameters of the interaction from the contour length data. Such analysis has allowed us to conclude that the GelRed stain is in fact a bis-intercalator. In addition, DLS experiments were performed to study the changes of the effective size of the DNA-GelRed complexes, measured by the hydrodynamic radius, as a function of ligand concentration. We found a qualitative agreement between the results obtained from the two techniques by comparing the behaviors of the hydrodynamics radius and the radius of gyration, since this last quantity can be expressed as a function of mechanical parameters determined from the stretching experiments.

Section: Stretching Experimentssupporting

confidence: 65%

Section: Stretching Experimentsmentioning

confidence: 64%

Characterizing the interaction between DNA and GelRed fluorescent stain

Crisafuli

2014

Eur Biophys J

“…Recently our group has studied in detail the changes in the persistence and contour lengths of DNA complexes formed with various intercalating molecules [75][76][77]94,133 , by using optical tweezers in a very low force regime (F < 2 pN). We reported an abrupt structural transition in the persistence length due to drug intercalation, which is probably related to a partial denaturation of the DNA molecule due to the pulling force used to stretch the complexes 76,77,133,147 . The contour length, otherwise, does not present such a transition, increasing monotonically with drug concentration until saturation.…”

Section: B Intercalatorsmentioning

confidence: 96%

Extracting physical chemistry from mechanics: a new approach to investigate DNA interactions with drugs and proteins in single molecule experiments

2015

Integr. Biol.

115

In this review we focus on the idea of establishing connections between the mechanical properties of DNAligand complexes and the physical chemistry of DNA-ligand interactions. This type of connection is interesting because it opens the possibility of performing a robust characterization of such interactions by using only one experimental technique: single molecule stretching. Furthermore, it also opens new possibilities in comparing results obtained by very different approaches, in special when comparing single molecule techniques to ensemble-averaging techniques. We start the manuscript reviewing important concepts of the DNA mechanics, from the basic mechanical properties to the Worm-Like Chain model. Next we review the basic concepts of the physical chemistry of DNA-ligand interactions, revisiting the most important models used to analyze the binding data and discussing their binding isotherms. Then, we discuss the basic features of the single molecule techniques most used to stretch the DNA-ligand complexes and to obtain force × extension data, from which the mechanical properties of the complexes can be determined. We also discuss the characteristics of the main types of interactions that can occur between DNA and ligands, from covalent binding to simple electrostatic driven interactions. Finally, we present a historical survey on the attempts to connect mechanics to physical chemistry for DNA-ligand systems, emphasizing a recently developed fitting approach useful to connect the persistence length of the DNA-ligand complexes to the physicochemical properties of the interaction. Such approach in principle can be used for any type of ligand, from drugs to proteins, even if multiple binding modes are present.

“…This abrupt transition may be caused by local formation of denaturing bubbles, as proposed in Refs. [12] and [13], which softens the structure of the Psol-DNA complex. In Ref.…”

Section: Figmentioning

confidence: 99%

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

Applied Physics Letters

Lúcio

Alexandre

et al. 2009

The authors measure the persistence and contour lengths of DNA-psoralen complexes, as a function of psoralen concentration, for intercalated and crosslinked complexes. In both cases, the persistence length monotonically increases until a certain critical concentration is reached, above which it abruptly decreases and remains approximately constant. The contour length of the complexes exhibits no such discontinuous behavior. By fitting the relative increase of the contour length to the neighbor exclusion model, we obtain the exclusion number and the intrinsic intercalating constant of the interaction. Ab initio calculations are employed in order to provide an atomistic picture of these experimental findings.