Molecular Mechanisms and Kinetics between DNA and DNA Binding Ligands

Sischka, Andy; Tœnsing, Katja; Eckel, Rainer; Wilking, Sven David; Sewald, Norbert; Ros, Robert; Anselmetti, Dario

doi:10.1529/biophysj.103.036293

Cited by 168 publications

(234 citation statements)

References 46 publications

(79 reference statements)

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“…31 An explanation for this discrepancy is that at such low base-pair to dye ratio not all dye molecules can be accommodated in the regular way of one YOYO-1 molecule bis-intercalated between three adjacent base-pairs. A fraction of the YOYO-1 molecules might be intercalated in an irregular way (such as multiple intercalated dye molecules per stretch of four base-pairs) or bound sideways to the duplex.…”

Section: Effects Of Intercalationmentioning

confidence: 99%

Effects of electrostatic screening on the conformation of single DNA molecules confined in a nanochannel

Zhang

Kan

et al. 2008

The Journal of Chemical Physics

154

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Single T4-DNA molecules were confined in rectangular-shaped channels with a depth of 300 nm and a width in the range 150-300 nm casted in a poly(dimethylsiloxane) nanofluidic chip. The extensions of the DNA molecules were measured with fluorescence microscopy as a function of the ionic strength and composition of the buffer as well as the DNA intercalation level by the YOYO-1 dye. The data were interpreted with scaling theory for a wormlike polymer in good solvent, including the effects of confinement, charge, and self-avoidance. It was found that the elongation of the DNA molecules with decreasing ionic strength can be interpreted in terms of an increase of the persistence length. Self-avoidance effects on the extension are moderate, due to the small correlation length imposed by the channel cross-sectional diameter.Intercalation of the dye results in an increase of the DNA contour length and a partial neutralization of the DNA charge, but besides effects of electrostatic origin it has no significant effect on the bare bending rigidity. In the presence of divalent cations, the DNA molecules were observed to contract, but they do not collapse into a condensed structure. It is proposed that this contraction results from a divalent counterion mediated attractive force between the segments of the DNA molecule.

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Section: Effects Of Intercalationmentioning

confidence: 99%

Effects of electrostatic screening on the conformation of single DNA molecules confined in a nanochannel

Zhang

Kan

et al. 2008

The Journal of Chemical Physics

154

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“…In this binding mode, a molecule is inserted between adjacent stacked bases, increasing the length of the DNA. Single molecule spectroscopy has been used to analyze DNA intercalation 8,30,70,71 as a method of understanding drug binding for cancer therapy. Perhaps the best known intercalative binding drug is ethidium, the solution form of ethidium bromide.…”

Section: Drug Intercalation and Force-induced Meltingmentioning

confidence: 99%

Mechanisms of DNA binding determined in optical tweezers experiments

McCauley¹,

Williams²

2006

Biopolymers

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The last decade has seen rapid development in single molecule manipulation of RNA and DNA. Measuring the response force for a particular manipulation has allowed the free energies of various nucleic acid structures and configurations to be determined. Optical tweezers represent a class of single molecule experiments that allows the energies and structural dynamics of DNA to be probed up to and beyond the transition from the double helix to its melted single strands. These experiments are capable of high force resolution over a wide dynamic range. Additionally, these investigations may be compared with results obtained when the nucleic acids are in the presence of proteins or other binding ligands. These ligands may bind into the major or minor groove of the double helix, intercalate between bases or associate with an already melted single strand of DNA. By varying solution conditions and the pulling dynamics, energetic and dynamic information may be deduced about the mechanisms of binding to nucleic acids, providing insight into the function of proteins and the utility of drug treatments. © 2006 Wiley Periodicals, Inc. Biopolymers 85:154–168, 2007.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com

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“…In some cases, the prefactors for the scaling laws are known exactly [41][42][43]. These thermodynamic quantities depend on the contour length L of the polymer, its persistence length l p , the effective width w of the polymer backbone, and the channel size D. The persistence length and effective width of DNA, which are affected by the relative amount of screening of electrostatics by the ionic environment, can be obtained from polyelectrolyte theory [44][45][46][47], albeit with some uncertainty arising from the effect of the intercalating dye [48][49][50][51][52][53][54]. Intercalation also increases the DNA contour length relative to the rise of naked DNA [55].…”

Section: Introductionmentioning

confidence: 99%

Wall depletion length of a channel-confined polymer

Cheong

Dorfman

2017

Phys. Rev. E

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Numerous experiments have taken advantage of DNA as a model system to test theories for a channel-confined polymer. A tacit assumption in analyzing these data is the existence of a well defined depletion length characterizing DNA-wall interactions such that the experimental system (a polyelectrolyte in a channel with charged walls) can be mapped to the theoretical model (a neutral polymer with hard walls). We test this assumption using pruned-enriched Rosenbluth method (PERM) simulations of a DNA-like semiflexible polymer confined in a tube. The polymer-wall interactions are modeled by augmenting a hard wall interaction with an exponentially decaying, repulsive soft potential. The free energy, mean span, and variance in the mean span obtained in the presence of a soft wall potential are compared to equivalent simulations in the absence of the soft wall potential to determine the depletion length. We find that the mean span and variance about the mean span have the same depletion length for all soft potentials we tested. In contrast, the depletion length for the confinement free energy approaches that for the mean span only when depletion length no longer depends on channel size. The results have implications for the interpretation of DNA confinement experiments under low ionic strengths. * dorfman@umn.edu

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Molecular Mechanisms and Kinetics between DNA and DNA Binding Ligands

Cited by 168 publications

References 46 publications

Effects of electrostatic screening on the conformation of single DNA molecules confined in a nanochannel

Effects of electrostatic screening on the conformation of single DNA molecules confined in a nanochannel

Mechanisms of DNA binding determined in optical tweezers experiments

Wall depletion length of a channel-confined polymer

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