<i>J</i>-factors of short DNA molecules

Zoli, Marco

doi:10.1063/1.4952978

Cited by 26 publications

(33 citation statements)

References 83 publications

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“…As previously noted [49,50], the seemingly high J factor of Vafabakhsh and Ha below 100 bp is not surprising given that their J factor (J VH ) was extracted from J VH = R/k on , where R = k loop + k unloop is an apparent relaxation rate toward the equilibrium state. Hence, J VH by definition is larger than J = k loop /k on that is more closely related to the theoretical J factor.…”

Section: B the Role Of Base Stacking In The Stability Of Dna Loopmentioning

confidence: 58%

Determinants of cyclization–decyclization kinetics of short DNA with sticky ends

Jeong

Kim

2020

Nucleic Acids Research

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Cyclization of DNA with sticky ends is commonly used to construct DNA minicircles and to measure DNA bendability. The cyclization probability of short DNA (<150 bp) has a strong length dependence, but how it depends on the rotational positioning of the sticky ends around the helical axis is less clear. To shed light upon the determinants of the cyclization probability of short DNA, we measured cyclization and decyclization rates of ∼100-bp DNA with sticky ends over two helical periods using single-molecule Fluorescence Resonance Energy Transfer (FRET). The cyclization rate increases monotonically with length, indicating no excess twisting, while the decyclization rate oscillates with length, higher at half-integer helical turns and lower at integer helical turns. The oscillation profile is kinetically and thermodynamically consistent with a three-state cyclization model in which sticky-ended short DNA first bends into a torsionally-relaxed teardrop, and subsequently transitions to a more stable loop upon terminal base stacking. We also show that the looping probability density (the J factor) extracted from this study is in good agreement with the worm-like chain model near 100 bp. For shorter DNA, we discuss various experimental factors that prevent an accurate measurement of the J factor.

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Section: B the Role Of Base Stacking In The Stability Of Dna Loopmentioning

confidence: 58%

Determinants of cyclization–decyclization kinetics of short DNA with sticky ends

Jeong

Kim

2020

Nucleic Acids Research

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“…The method followed here is similar in spirit to the procedure reported in different earlier publications. [6,9,10,12,21,[47][48][49][50][51][52]].…”

Section: Calculation Of the Persistence Length (L P )mentioning

confidence: 99%

Ionic liquids make DNA rigid

Garai

Ghoshdastidar

Senapati

et al. 2018

The Journal of Chemical Physics

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Persistence length of double-stranded DNA (dsDNA) is known to decrease with an increase in ionic concentration of the solution. In contrast to this, here we show that the persistence length of dsDNA increases dramatically as a function of ionic liquid (IL) concentration. Using all atom explicit solvent molecular dynamics simulations and theoretical models, we present, for the first time, a systematic study to determine the mechanical properties of dsDNA in various hydrated ILs at different concentrations. We find that dsDNA in 50 wt % ILs have lower persistence length and stretch modulus in comparison to 80 wt % ILs. We further observe that both the persistence length and stretch modulus of dsDNA increase as we increase the concentration of ILs. The present trend of the stretch modulus and persistence length of dsDNA with IL concentration supports the predictions of the macroscopic elastic theory, in contrast to the behavior exhibited by dsDNA in monovalent salt. Our study further suggests the preferable ILs that can be used for maintaining DNA stability during long-term storage.

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“…As the method has been described in several papers, we skip here the details and refer e.g., to Refs. [26,42] for a broad analysis. For the current purposes it should be mentioned that, by virtue of the spacetime mapping technique, the partition function Z N for the system in Carrying out the integral over the Fourier coefficients, an increasing number of trajectories is added to Z N until the latter numerically converges.…”

Section: Methodsmentioning

confidence: 99%

“…Here we contribute to this field focusing on the interplay between crowding and DNA structure, namely analyzing how the real space confinement of a DNA molecule due to the presence of crowders may concur to shape the helical conformation and the overall size of the molecule itself. Our study is based on a statistical mechanical method which has been widely discussed in previous researches on some fundamental indicators of DNA flexibility at short length scale such as the cyclization probabilities, the persistence lengths [26,27] and also the single molecule response to stretching perturbations induced by external loads [28,29].…”

Section: Introductionmentioning

confidence: 99%

DNA size in confined environments

Zoli

2019

Phys. Chem. Chem. Phys.

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For short DNA molecules in crowded environments, we evaluate macroscopic parameters such as the average end-to-end distance and the twist conformation by tuning the strength of the site specific confinement driven by the crowders. The ds-DNA is modeled by a mesoscopic Hamiltonian which accounts for the three dimensional helical structure and incorporates fluctuational effects at the level of the base pair. The computational method assumes that the base pair fluctuations are temperature dependent trajectories whose amplitudes can be spatially modulated according to the crowders distribution. We show that the molecule elongation, as measured by the end-to-end distance varies non-monotonically with the strength of the confinement. Furthermore it is found that, if the crowders mostly confine the DNA mid-chain, the helix over-twists and its end-to-end distance grows in the strong confinement regime. Instead, if the crowders mostly pin one chain end, the helix untwists while the molecule stretches for large confinement strengths. Thus, our results put forward a peculiar relation between stretching and twisting which significantly depends on the crowders profile. The method could be applied to disegn specific DNA shapes by controlling the environment which constrains the molecule.

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J-factors of short DNA molecules

Cited by 26 publications

References 83 publications

Determinants of cyclization–decyclization kinetics of short DNA with sticky ends

Determinants of cyclization–decyclization kinetics of short DNA with sticky ends

Ionic liquids make DNA rigid

DNA size in confined environments

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