Sequence-Dependent DNA Dynamics by Scanning Force Microscopy Time-Resolved Imaging

Scipioni, Anita; Zuccheri, Giampaolo; Anselmi, Claudio; Bergia, Anna; Samorı̀, Bruno; Santis, P. De

doi:10.1016/s1074-5521(02)00282-x

Cited by 15 publications

(22 citation statements)

References 24 publications

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“…We found that even though WLL behave on large scales as BRW, as expected, the effective step size of this BRW is larger than that calculated from the local persistence length of the loop. This new prediction can in principle be directly tested by experiments on double stranded DNA loops that can monitor both local (persistence length) and global (e.g., radius of gyration) properties of the polymers (see, e.g., [14][15][16]). It would be interesting to test these results and predictions against Monte Carlo simulations along the lines of [17] (where worm-like chain is modelled as the set of short straight segments with torsional and bending angles properly chosen to approach the smooth limit).…”

mentioning

confidence: 99%

Worm-like polymer loops and Fourier knots

Rappaport¹,

Rabin²,

Grosberg³

2006

J. Phys. A: Math. Gen.

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Every smooth closed curve can be represented by a suitable Fourier sum as a function of an arbitrary parameter τ . We show that the ensemble of curves generated by randomly chosen Fourier coefficients with amplitudes inversely proportional to spatial frequency (with a smooth exponential cutoff) can be accurately mapped on the physical ensemble of inextensible worm-like polymer loops. The τ → s mapping of the curve parameter τ on the arc length s of the inextensible polymer is achieved at the expense of coupling all Fourier harmonics in a non-trivial fashion. We characterize the obtained ensemble of conformations by looking at tangent-tangent and position-position correlations. Measures of correlation on the scale of the entire loop yield a larger persistence length than that calculated from the tangent-tangent correlation function at small length scales. The topological properties of the ensemble, randomly generated worm-like loops, are shown to be similar to those of other polymer models. , use the analogy between conformation of a chain molecule and a Brownian random walk (BRW). In mathematically idealized form, such a random walk is thought of as a Wiener trajectory r(τ ) generated by the measure P {r(τ )} ∝ exp −const (∂r/∂τ ) 2 dτ , where τ is a parameter running along the trajectory. Despite its successes, the BRW model cannot reproduce the finite extensibility of polymer chains stretched by a strong force [2] and fails miserably in the study of polymers with knots. Indeed, simulations of discrete polymer models, or random polygons with N steps, show [3][4][5] that the probability of trivial knot configuration decays exponentially with N as P 0 (N) ∼ exp(−N/N * ), where N * defines the crossover from an unknotted to a knotted regime. It was argued that Wiener trajectory polymer models cannot be used to calculate

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mentioning

confidence: 99%

Worm-like polymer loops and Fourier knots

Rappaport¹,

Rabin²,

Grosberg³

2006

J. Phys. A: Math. Gen.

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“…In our experience (Nagami et al, 2002;Scipioni et al, 2002;Zuccheri et al, 1998), AFM imaging in liquid is feasible and useful, but not simple. The huge amount of good-quality images that are necessary to attempt a quantitative characterization of the RNA secondary structures would require an almost prohibitive effort if the imaging was performed under liquid.…”

Section: Possible Experimental Improvementsmentioning

confidence: 98%

Single molecule studies of RNA secondary structure: AFM of TYMV viral RNA

Giro

Bergia

Zuccheri

et al. 2004

Microscopy Res & Technique

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Nowadays, the development of experimental procedures for the determination of the secondary structure of RNA molecules is taking advantage of the novel single-molecule probing and imaging techniques. We report a method for the mapping of the secondary structure of RNA molecules spread on a flat surface by means of the atomic force microscope. Globular domains comprising groups of RNA secondary and tertiary structure elements separated by unstructured domains can be discerned in the micrographs and their position along the molecule contour can be measured directly on unstained specimens. We have analyzed the morphology of a population of single molecules of 3' fragments of the Turnip Yellow Mosaic Virus RNA shorter than 1 kb in different temperature and electrolytic conditions. We found a satisfying agreement of the shape of the imaged structures with previously available evidence. The method we have developed can be used to map also different types of RNA molecules and has the advantage of showing the distribution of the single molecule conformations within the population.

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“…17 This scale of rigidity was supported by the analysis of DNA sequences we carried out on AFM images. [42][43][44][45] Assuming first-order elasticity, we evaluated the elastic contributions to the partition functions, related to the sum of the bending, DE b (k), and twisting, DE t (k), energies necessary to distort the kth free DNA tract assumed as the standard state in the nucleosomal form.…”

Section: Cn Amentioning

confidence: 99%

“…41 Finally, the curvature and flexibility functions calculated adopting the dinucleotide step orientational parameters proposed in previous papers were successfully compared with experimental average curvature and related dispersion of DNA tracts we directly obtained from the statistical analysis of Atomic Force Microscopy images of DNA tracts. [42][43][44][45] Because of the little variance of the orientational angles, it is convenient to adopt a representation of the curvature as a vector in the complex plane, corresponding to the first-order Taylor expansion of the pertinent rotation matrix product 38 …”

Section: Introductionmentioning

confidence: 99%

A statistical thermodynamic approach for predicting the sequence‐dependent nucleosome positioning along genomes

2009

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Nucleosomes are the fundamental repeating unit of chromatin and constitute the structural building blocks of the eukaryotic genome. The distribution of nucleosomes along the genome is a significant aspect of chromatin structure and influences gene regulation through modulation of DNA accessibility. For this reason, an increasing interest is arising in models capable of predicting the nucleosome positioning along genomes. Toward this goal, we propose a theoretical model for predicting nucleosome thermodynamic stability in terms of DNA sequence. The model, based on a statistical mechanical approach allows the calculation of the canonical ensemble free energy involved in nucleosome formation. The theoretical free energies were evaluated for about one hundred nucleosome DNA tracts and successfully compared with those obtained in different laboratories with nucleosome competitive reconstitution (correlation coefficient equal to 0.92). We extended these results to the nucleosome positioning along genomes. To test our model, the theoretical nucleosome distribution was compared with that of yeast genome experimentally determined. The results are comparable with those obtained by different authors adopting models based on identifying some recurrent sequence features obtained from the statistical analysis of a very large pool of nucleosomal DNA sequences provided by the positioning maps of genomes.

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Sequence-Dependent DNA Dynamics by Scanning Force Microscopy Time-Resolved Imaging

Cited by 15 publications

References 24 publications

Worm-like polymer loops and Fourier knots

Worm-like polymer loops and Fourier knots

Single molecule studies of RNA secondary structure: AFM of TYMV viral RNA

A statistical thermodynamic approach for predicting the sequence‐dependent nucleosome positioning along genomes

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