Mechanical and structural properties of YOYO-1 complexed DNA

Günther, Katrin; Mertig, Michael; Seidel, Ralf

doi:10.1093/nar/gkq434

Cited by 204 publications

(268 citation statements)

References 23 publications

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“…In the presence of DNA intercalators, however, it is known that elongation of double DNA requires less force. For example, recent experiments showed that the presence of a YOYO-1 force of a few picoNewtons could elongate DNA contour by approximately 1.5-fold (36). Although the structure of the nonhysteretic overstretched DNA remains unknown, we imagine that DNA bound with YOYO-1 may resemble the DNA structure because it is only 10% shorter.…”

Section: Discussionmentioning

confidence: 95%

Two distinct overstretched DNA structures revealed by single-molecule thermodynamics measurements

Zhang

Chen

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

116

128

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Double-stranded DNA is a dynamic molecule whose structure can change depending on conditions. While there is consensus in the literature about many structures DNA can have, the state of highlystretched DNA is still not clear. Several groups have shown that DNA in the torsion-unconstrained B-form undergoes an "overstretching" transition at a stretching force of around 65 pN, which leads to approximately 1.7-fold elongation of the DNA contour length. Recent experiments have revealed that two distinct structural transitions are involved in the overstretching process: (i) a hysteretic "peeling" off one strand from its complementary strand, and (ii) a nonhysteretic transition that leads to an undetermined DNA structure. We report the first simultaneous determination of the entropy (ΔS) and enthalpy changes (ΔH) pertaining to these respective transitions. For the hysteretic peeling transition, we determined ΔS ∼ 20 cal∕ðK:molÞ and ΔH ∼ 7 kcal∕mol. In the case of the nonhysteretic transition, ΔS ∼ −3 cal∕ðK:molÞ and ΔH ∼ 1 kcal∕mol. Furthermore, the response of the transition force to salt concentration implies that the two DNA strands are spatially separated after the hysteretic peeling transition. In contrast, the corresponding response after the nonhysteretic transition indicated that the strands remained in close proximity. The selection between the two transitions depends on DNA base-pair stability, and it can be illustrated by a multidimensional phase diagram. Our results provide important insights into the thermodynamics of DNA overstretching and conformational structures of overstretched DNA that may play an important role in vivo.entropy and enthalpy | S-DNA | ssDNA | B-to-S transition

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Section: Discussionmentioning

confidence: 95%

Two distinct overstretched DNA structures revealed by single-molecule thermodynamics measurements

Zhang

Chen

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

116

128

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“…Previous studies of DNA extension under dynamic conditions, such as in flow 49 or electrokinetic stretching around solid obstacles, 50,51 suggest that the backbone length should increase by 25% to 30% at full dye loading, corresponding to an increase from the naked contour length of 16.5 μm, based on a rise of 0.34 nm per base pair, to a stained contour length around 22 μm. 37 At the dye to base pair ratio used here of 1:10, others 4,43 suggested that the increased contour length due to dye intercalation is approximately 19.8 μm. Alternatively, if we assume that the increase in the backbone length is linear in dye loading up to the maximum loading, then the 40% loading we used here should lead to a dyed contour length of L = 18.3 μm.…”

Section: B Comparing Simulation and Experimentsmentioning

confidence: 90%

“…The intercalating dyes in these experiments introduce an additional unknown parameter, the contour length in the presence of the dye. Although many studies have investigated the physical properties of DNA in the presence of these dyes, 34,43,44 there exists a lack of consensus on how l p and w vary as a function of dye concentration. Therefore, we chose the simplest approach and estimated the parameters, l p and w using established theories [29][30][31] for undyed DNA.…”

Section: B Parameter Estimationmentioning

confidence: 99%

Mixed confinement regimes during equilibrium confinement spectroscopy of DNA

Gupta

Sheats²,

Muralidhar

et al. 2014

The Journal of Chemical Physics

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We have used a combination of fluorescence microscopy experiments and Pruned Enriched Rosenbluth Method simulations of a discrete wormlike chain model to measure the mean extension and the variance in the mean extension of λ-DNA in 100 nm deep nanochannels with widths ranging from 100 nm to 1000 nm in discrete 100 nm steps. The mean extension is only weakly affected by the channel aspect ratio. In contrast, the fluctuations of the chain extension qualitatively differ between rectangular channels and square channels with the same cross-sectional area, owing to the "mixing" of different confinement regimes in the rectangular channels. The agreement between experiment and simulation is very good, using the extension due to intercalation as the only adjustable parameter.

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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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Mechanical and structural properties of YOYO-1 complexed DNA

Cited by 204 publications

References 23 publications

Two distinct overstretched DNA structures revealed by single-molecule thermodynamics measurements

Two distinct overstretched DNA structures revealed by single-molecule thermodynamics measurements

Mixed confinement regimes during equilibrium confinement spectroscopy of DNA

Wall depletion length of a channel-confined polymer

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