Short DNA persistence length in a mesoscopic helical model
arXiv:1810.00178 · doi:10.1209/0295-5075/123/68003
Abstract
The flexibility of short DNA chains is investigated via computation of the average correlation function between dimers which defines the persistence length. Path integration techniques have been applied to confine the phase space available to base pair fluctuations and derive the partition function. The apparent persistence lengths of a set of short chains have been computed as a function of the twist conformation both in the over-twisted and the untwisted regimes, whereby the equilibrium twist is selected by free energy minimization. The obtained values are significantly lower than those generally attributed to kilo-base long DNA. This points to an intrinsic helix flexibility at short length scales, arising from large fluctuational effects and local bending, in line with recent experimental indications. The interplay between helical untwisting and persistence length has been discussed for a heterogeneous fragment by weighing the effects of the sequence specificities through the non-linear stacking potential.
References in corpus (10)
- Flexibility of short DNA helices with finite-length effect: from base pairs to tens of base pairs
- Ionic liquids make DNA rigid
- The probability analysis of opening of DNA
- Stacking Interactions in Denaturation of DNA Fragments
- J-factors of short DNA molecules
- End-to-end distance and contour length distribution functions of DNA helices
- Twisting and Bending Stress in DNA Minicircles
- Twisting short dsDNA with applied tension
- Anharmonic stacking in supercoiled DNA
- Unwinding of circular helicoidal molecules versus size
Cited by in corpus (7)
- Mechanical properties of DNA and DNA nanostructures: comparison of atomistic, martini and oxDNA
- DNA size in confined environments
- First-passage probability: a test for DNA Hamiltonian parameters
- Stretching DNA in hard-wall potential channels
- Mesoscopic helical models for DNA
- Twist-stretch relations in nucleic acids
- Mesoscopic model for nano-channel confined DNA