Conformation Model of Back-Folding and Looping of a Single DNA Molecule Confined Inside a Nanochannel

Dai, Liang; Ng, Siow Yee; Doyle, Patrick S.; Maarel, Johan R. C. van der

doi:10.1021/mz300323a

Cited by 51 publications

(120 citation statements)

References 25 publications

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“…Even with these potential sources of systematic error, we posit that the skew-left distribution for P(X; L) is a robust result, as it is consistent with phenomenological models for channel confinement near the persistence length 20 as well as the physics underlying Odijk's theory. 16,22 However, this skew-left behavior poses challenges for any theory attempting to describe DNA confinement when backfolding is permitted but large scale folding is a rare event (i.e., ξ ≈ 1).…”

Section: Discussionsupporting

confidence: 58%

“…7(c)) interspersed with regions of ordered deflection segments. These bunches could be analogous to the S-loop model for DNA in nanochannels near the persistence length, 20 but they could be knots as well. 37,38 We do not have the optical resolution to examine the conformation of the chain at the scale required to demonstrate the presence of an S-loop or a knot, so we will use the more generic term "bunching" to refer to the stored length.…”

Section: A Physical Basis For a Skewed Probability Densitymentioning

confidence: 99%

“…However, the theory surrounding DNA confinement for channel sizes D ≈ l p is contentious. [16][17][18][19][20][21][22] It would be greatly beneficial to have a fundamental understanding of the thermodynamics of DNA confinement in circa 50 nm channel sizes to guide the development of the emerging genome barcoding technology.…”

Section: Introductionmentioning

confidence: 99%

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Distribution of distances between DNA barcode labels in nanochannels close to the persistence length

Reinhart

Reifenberger

Gupta

et al. 2015

The Journal of Chemical Physics

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We obtained experimental extension data for barcoded E. coli genomic DNA molecules confined in nanochannels from 40 nm to 51 nm in width. The resulting data set consists of 1 627 779 measurements of the distance between fluorescent probes on 25 407 individual molecules. The probability density for the extension between labels is negatively skewed, and the magnitude of the skewness is relatively insensitive to the distance between labels. The two Odijk theories for DNA confinement bracket the mean extension and its variance, consistent with the scaling arguments underlying the theories. We also find that a harmonic approximation to the free energy, obtained directly from the probability density for the distance between barcode labels, leads to substantial quantitative error in the variance of the extension data. These results suggest that a theory for DNA confinement in such channels must account for the anharmonic nature of the free energy as a function of chain extension. C 2015 AIP Publishing LLC. [http://dx

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Section: Discussionsupporting

confidence: 58%

Section: A Physical Basis For a Skewed Probability Densitymentioning

confidence: 99%

See 1 more Smart Citation

Distribution of distances between DNA barcode labels in nanochannels close to the persistence length

Reinhart

Reifenberger

Gupta

et al. 2015

The Journal of Chemical Physics

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“…Although the theory of DNA extension under 1-d confinement is still an active field of research, 28,59 a good experimental understanding exists. 33,60 Broadly, the extension of confined DNA molecules results from a balance between entropy and excluded volume interactions within the DNA.…”

Section: Discussionmentioning

confidence: 99%

Probing transient protein-mediated DNA linkages using nanoconfinement

et al. 2014

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We present an analytic technique for probing protein-catalyzed transient DNA loops that is based on nanofluidic channels. In these nanochannels, DNA is forced in a linear configuration that makes loops appear as folds whose size can easily be quantified. Using this technique, we study the interaction between T4 DNA ligase and DNA. We find that T4 DNA ligase binding changes the physical characteristics of the DNA polymer, in particular persistence length and effective width. We find that the rate of DNA fold unrolling is significantly reduced when T4 DNA ligase and ATP are applied to bare DNA. Together with evidence of T4 DNA ligase bridging two different segments of DNA based on AFM imaging, we thus conclude that ligase can transiently stabilize folded DNA configurations by coordinating genetically distant DNA stretches. V C 2014 AIP Publishing LLC.

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“…Researchers have proposed the existence of an extended de Gennes regime 13,15,18 and hairpin regime. 22 Recent work 21 proposed that the extended de Gennes regime does not exist and instead suggested a universal Gauss−de Gennes regime.…”

Section: Introductionmentioning

confidence: 99%

Extended de Gennes Regime of DNA Confined in a Nanochannel

2014

Self Cite

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Scaling regimes for polymers confined to tubular channels are well established when the channel cross-sectional dimension is either very small (Odjik regime) or large (classic de Gennes regime) relative to the polymer Kuhn length. However, experiments of confined polymers using DNA as a model system are usually located in the intermediate region between these two regimes. In the literature, controversy exists regarding the existence of the extended de Gennes regime in this intermediate region. Here we use simulations and theory to reconcile conflicting theories and confirm the existence of extended de Gennes regime. We show that prior work did not support the notion of this regime because of the use of a wrong confinement free energy. In a broad sense, the extended de Gennes regime corresponds to the situation when excluded volume interaction is weaker than thermal energy. Such a situation also occurs in many other cases, such as semidilute polymer solutions and polymers under tension. This work should benefit the practical applications of nanochannels to stretch DNA, such as deepening the understanding of the relationship between the chain extension and channel size and providing the scaling behaviors of recoiling force for DNA at the entrance of nanochannels.

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Conformation Model of Back-Folding and Looping of a Single DNA Molecule Confined Inside a Nanochannel

Cited by 51 publications

References 25 publications

Distribution of distances between DNA barcode labels in nanochannels close to the persistence length

Distribution of distances between DNA barcode labels in nanochannels close to the persistence length

Probing transient protein-mediated DNA linkages using nanoconfinement

Extended de Gennes Regime of DNA Confined in a Nanochannel

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